Typing tool
|
Complete norovirus genomes
MF140658 | GII.4 Yerseke | ||
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GII.P4 Yerseke |
ORF1: 1..5083 ORF2: 5064..6686 ORF3: 6686..7487LOCUS MF140658 7487 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2009/GII.P4-GII.4/Rotterdam/E1300265_p15_d102 ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene, partial cds. ACCESSION MF140658 VERSION MF140658.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7487) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M.G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Whole genome next generation sequencing to study within-host evolution of chronic norovirus infection among immunocompromised patients JOURNAL J. Infect. Dis. (2017) In press PUBMED 29029115 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7487) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Direct Submission JOURNAL Submitted (19-MAY-2017) Centre for infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.9.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7487 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2009/GII.P4- GII.4/Rotterdam/E1300265_p15_d102" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="14-Sep-2009" /note="genotype: GII.P4-GII.4" CDS <1..5083 /codon_start=2 /product="ORF1" /protein_id="ATN23670.1" /translation="DASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPPPR EIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESNTAF SVPPLNQRENRDAKEPLPGTILEMWDGEIYHYGIYVERGLVLGVHKPPAAISLARIEL TPLSLYWRPVYTPQYLISPDALKKLHEETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM IQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNI LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFQLQGPEDLAVELV PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN ELAIVRSIEDAVLDLEAIENNHLTILLKDKDSLATYMRTLDLEEEKARKLSTKSASPD IVGTINALLARIAAARSLVHRAKEELSSRLRPVVLMISGRPGIGKTHLAREVAKKIAA SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE RLDDFEMQGPTITTFNFDRNKLLAFRQLAAENKYGLMDTMKVGRQLKDVRTMPELKQA LKNISIKKCQIVYGGCTYTLESDGKGNVKVDKVQSASVQTNNELTGALHHLRCARIRY YVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTSKDGCPKPRDD EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEE YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPSRKQRKEERASLGLVTGSEIR KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL IKRPTGELMPLAVRMGTHATMRIQGRAVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILGPGNAPK LSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT GKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYNKIKKRLLWGSDLATMIRC ARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYAYHYDADYSRWDSTQQRD VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKP TRPDKTEGPLVISDDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPA ETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5064..6686 /codon_start=1 /product="ORF2" /protein_id="ATN23671.1" /translation="MKMASSDAAPSDGPTANLVPAVNNEVMALEPVAGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGISPCQVTMFPHIITDVRQLEPVLIPLPD VRNNFYHYNQSNEPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTQIGSTQTYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIRGML TQTTKSDGSTRGHVATVSTGSAHFTPKLGRVQFSTDTSNDLEARQNTRFTPVGVIQDG STTHRNEPQQWVLPDYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD CLLPQEWVQHFYQESAPAQSDVALLRFVNPDTSRVLFECKLHKQGFLTVAHTGQHDLI IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6686..>7487 /codon_start=1 /product="ORF3" /protein_id="ATN23672.1" /translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAVN APMTKVLDWSGTRYWAPDARITTYNAGHFSTPQPSGAPPGRTNLRATTPARGSSSTLS NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIHKRGESR" ORIGIN 1 cgacgcttcc gctgccgctg ttgctaacag caacaacgac accgcaaaat cttcaagtga 61 cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaagca 121 gcctcccccg agggaaatac cacaaagacc cccacgacca cctaccccag aactggtcaa 181 aaatatcccc cctcccccgc ccaatggaga ggatgaaata gtggtttctt atagtgtcaa 241 agatggtatt tccggtttgc ctgatctttc caccgtcagg caaccggaag aatctaacac 301 ggccttcagt gtccctccac tcaatcagag ggagaataga gatgctaagg agccattacc 361 tggaacaatt ctggaaatgt gggatggaga aatctaccat tatggcatat atgtggagcg 421 aggtcttgta ctaggcgtgc acaaaccacc agccgccatc agcctcgcta ggatagagtt 481 aacaccactc tccttgtact ggaggcctgt gtatacccct caatacctca tctctccaga 541 cgctctcaag aaattacatg aagagacgtt cccctacaca gccttcgaca acaactgcta 601 tgccttttgt tgctgggtcc tggacctaaa cgactcgtgg ctgagtagga ggatgatcca 661 gagaacaact ggctttttca ggccctacca agaatggaac aggaaacccc tccccactat 721 ggatgactcc aagttaaaga aggtggctaa catattcctg tgtgctctgt cttcgctatt 781 caccagaccc ataaaagata taatagggaa actaaggcct cttaacatcc ttaacatctt 841 ggcctcatgt gattggactt ttgcaggcat agtggagtct ttgatactct tggcagaact 901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct tgctcggtga 961 ttttcagttg caaggaccgg aggaccttgc agtggaactc gtccctgtag tgatgggggg 1021 aattggtttg gtgctaggat tcaccaaaga gaagattggt aaaatgttgt catctgctgc 1081 gtccaccttg agagcttgta aagatcttgg tgcatatggg ttagagatcc taaagttggt 1141 tatgaagtgg ttcttcccga agaaagagga agcaaatgaa ctggctatag tgagatccat 1201 cgaggatgca gtcctggatc tcgaggcaat tgaaaacaat catttaacca tcttgctcaa 1261 agacaaagac agtctggcaa cctacatgag aacccttgat cttgaggagg agaaagccag 1321 aaaactctca accaagtctg cttcacctga cattgtgggc acaatcaacg cccttttggc 1381 gaggatcgct gctgcacgtt ctctggtgca tcgagcgaag gaggaacttt ccagcagact 1441 aagacctgta gtattgatga tatcaggcag accaggaata gggaagaccc accttgctag 1501 ggaagtggcc aagaaaatcg cagcctccct tacaggggac caacgtgtgg gcctcatccc 1561 acgcaatggt gttgaccatt gggatgcgta caagggtgag agggtcgtcc tatgggatga 1621 ctatggaatg agcaatccca tccacgatgc cctcaggttg caagaactcg ctgacacttg 1681 ccctcttacc ctaaactgtg acaggattga gaataaagga aaggtttttg acagcgatgt 1741 catcatcatc accactaatc tggctaatcc agcaccactg gactatgtca actttgaagc 1801 atgctcaagg cgcatcgact tcctcgtgta tgcagaagct cctgaagtcg agaaggcgaa 1861 gcgtgatttc ccaggccagc ccgacatgtg gaagaacgcc ttcagctctg atttctcaca 1921 cataaaacta gcattggctc cacagggtgg cttcgacaag aacgggaaca ccccacacgg 1981 gaagggcgtc atgaagactc tcaccactgg ctcccttatt gctcgggcat cagggctact 2041 ccatgagagg ttagatgatt ttgaaatgca gggcccaact atcaccacct tcaactttga 2101 tcgcaacaaa ttgcttgcct ttagacaact tgctgctgaa aacaaatatg ggttgatgga 2161 cacaatgaaa gttgggaggc agctcaagga tgtcagaaca atgccagaac ttaagcaagc 2221 actcaagaat atctcaatta agaagtgcca gatagtgtat ggtggttgca cctatacact 2281 tgagtctgat ggcaagggca atgtgaaagt tgacaaagtt caaagcgcct ccgtgcagac 2341 caataatgag ctgactggcg cactgcacca tctaaggtgc gccagaatca gatactacgt 2401 caagtgtgtc caggaggccc tgtattccat catccagatt gctggggctg catttgtcac 2461 cacgcgcatc gtcaagcgca tgaacataca agacctatgg tccaaaccac aagtggaaaa 2521 cacagaggag actaccagca aggacgggtg tccaaaaccc agagatgatg aggagttcgt 2581 catttcatcc gacgacatca aaactgaggg taagaaagga aagaacaaga ctggccgcgg 2641 caagaaacac acagccttct caagcaaagg tctcagtgat gaagagtacg atgagtacaa 2701 gaggattaga gaggaaagga atggcaggta ctccatagaa gagtaccttc aggacaggga 2761 caaatactac gaggaggtgg ccattgccag ggcaaccgag gaggacttct gtgaagagga 2821 agaggccaag atccggcaaa ggatcttcag gccatcaagg aaacaacgca aggaggaaag 2881 agcttctctc ggtttagtca caggttctga aattaggaaa agaaatccag atgatttcaa 2941 acccaaagga aaactgtggg ctgatgatga cagaagtgtg gactacaacg agaaactcag 3001 ttttgaagcc ccaccaagca tctggtcaag gatagtcaac tttggttcag gttggggatt 3061 ctgggtctcc cctagtttgt tcataacatc aacccacgtc ataccccagg gcgcaaagga 3121 gttctttgga gtccctatca aacaaattca ggtacacaaa tcaggcgagt tctgtcgctt 3181 gagattccca aagccaatca ggactgatgt gacaggcatg atcttagaag aaggtgcacc 3241 cgagggcact gtggtcacac tgctcatcaa aaggcccact ggagaactca tgcccctggc 3301 agttaggatg gggacccatg caaccatgag aattcaaggg cgcgctgttg gaggccaaat 3361 gggcatgctt ctgacagggt ccaacgccaa aagcatggat ctaggtacca caccaggtga 3421 ttgtggctgt ccctacatct acaagagagg aaatgactat gtggtcattg gagtccacac 3481 ggctgccgct cgtgggggaa acactgttat atgtgccacc caggggagtg agggagaggc 3541 tgtacttgaa ggtggtgaca ataaagggac atactgtggt gcaccaatcc taggaccagg 3601 aaatgctcca aaactcagca ccaaaaccaa gttctggaga tcgtccacag caccactccc 3661 acctggtacc tatgaaccag cctatcttgg tggcaaggac cccagagtca agggtggccc 3721 ttcactgcag caagtcatga gggatcaatt gaagccattc acagagccta ggggcaagcc 3781 accaaagcca agtgtgctag aagctgccaa gaaaaccatc atcaatgtcc ttgagcaaac 3841 aattgatcca cctgagaaat ggtcattcgc acaagcttgc gcgtcccttg acaagaccac 3901 atccagtggc catccgcacc acatgcggaa aaatgactgt tggaacgggg aatccttcac 3961 aggcaagctg gcagatcagg cttctaaggc caacctaatg tttgaagaag gaaagaacat 4021 gaccccagtc tacacagctg cacttaagga tgaattagtt aaaactgaca aaatttataa 4081 taagatcaag aagaggctcc tctggggttc ggatttggcg accatgatcc ggtgtgctcg 4141 agcattcgga ggcctgatgg atgaactcaa agcgcactgc gtctcacttc ccattagagt 4201 tggtatgaat atgaacgagg atggccccat catcttcgag aggcattcca ggtacgcata 4261 ccactatgat gctgattact cacgatggga ttcaacacaa cagagagacg tattggcagc 4321 agctctagaa attatggtta aattctcccc agaaccacat ttggctcagg tagtcgcaga 4381 agaccttctc tctcctagcg tggtggacgt gggtgacttc acaatatcaa tcaacgaggg 4441 tctcccctct ggggtgccct gcacctccca atggaattcc atcgcccact ggcttctcac 4501 tctctgtgcg ctctctgaag ttacaaactt gtcccctgac accatacagg ctaattccct 4561 cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg acccagaaaa 4621 gttaacagca aaactcaggg aatatgggtt aaaaccaacc cgccctgata aaactgaagg 4681 accccttgtc atctctgacg acttaaatgg cctgactttc ctgcggagaa ctgtgacccg 4741 cgacccagct ggttggtttg gaaaactgga acagagttca atactcaggc aaatgtactg 4801 gactaggggt cccaaccatg gagatccagc tgaaacaatg attccacact cccaaagacc 4861 catacaattg atgtccctac tgggggaggc cgcacttcac ggcccagcat tctacagcaa 4921 aatcagcaag ttggtcatcg cagagctaaa agagggtggc atggattttt acgtgcccag 4981 acaagagcca atgttcaggt ggatgagatt ctcagatctg agcacgtggg agggcgatcg 5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccgcc ccatctgatg 5101 ggcccacagc taacctcgtc ccagcggtca acaatgaggt tatggctttg gagcccgttg 5161 ccggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta 5221 gaaataattt tgtacaagcc cctggtggag aatttacagt atcccctaga aacgctccag 5281 gtgaaatatt atggagcgcg cccttgggtc ctgacttgaa tccctacctt tcccatttgg 5341 ccagaatgta taatggttat gcaggtggtt ttgaggtgca ggtaatcctc gcggggaacg 5401 cgttcaccgc tgggaaaatc atatttgcag cagttccacc aaattttcca accgaaggga 5461 taagcccctg ccaagtcact atgttccccc atataataac agatgttaga caactggaac 5521 ctgtgttaat ccccttgcct gatgttagga acaacttcta tcattataat caatcaaatg 5581 aacccaccat caaattgata gcaatgctgt acacaccact tagggctaat aatgctgggg 5641 acgatgtctt cacagtctct tgtcgagttc tcacgagacc atcccccgat tttgatttca 5701 tatttctggt gccacccaca gttgagtcaa gaaccaaacc attctctgtc ccagtcttaa 5761 ctgttgagga gatgaccaac tcaagattcc ccattccttt agaaaagttg ttcacgggtc 5821 ccagcagtgc ctttgttgtt caaccacaaa atggcagatg cacgactgat ggcgtgctct 5881 taggtactac tcaactgtct cctgtcaaca tctgcacctt cagaggggat gtcactcaaa 5941 ttggaagtac tcaaacttac acaatgaacc tggcctccca aaattggaat aattatgatc 6001 caacagaaga aatcccagcc cccctgggaa ccccagattt tgtaggaagg atccgaggca 6061 tgctcaccca aaccacaaag agtgatggct cgacccgtgg tcacgtagcc acagtgagca 6121 ctggaagtgc tcattttact ccaaagttgg gcagagttca attctccact gacacaagca 6181 atgaccttga agctcgccaa aacacgagat tcaccccagt cggcgtcatc caggatggta 6241 gtaccaccca ccgaaatgaa ccccaacaat gggtgctccc agattattca ggtagagata 6301 gtcacaatgt acacctagca cctgctgtgg cccccacttt tccgggcgag caacttcttt 6361 tctttaggtc cactataccc ggatgcagcg ggtaccccaa catggaattg gattgcctac 6421 tcccccagga gtgggtgcag cacttctacc aagaatcagc cccagcacaa tctgatgtgg 6481 cactgctgag atttgtgaat ccagacacaa gtagggtttt gtttgagtgc aagcttcaca 6541 agcaaggctt tttaacagtg gctcatactg gccaacatga tttgattatc cctcccaatg 6601 gctattttag atttgattcc tgggttaacc aattctacac acttgccccc atgggaaatg 6661 gaacggggcg aagacgtgca ttataatggc tggagctttc tttgctggat tagcatctga 6721 tgtccttggc tctgggctta gctctctaat caatgctggg gctgggacca ttaatcaaaa 6781 agttgatttt gacaataata gaaaattgca acaagcttcc ttccaatata gtagcaatct 6841 acaacaggct tcctttcaac atgataaaga gatgctccaa gcacaaattg aggccaccaa 6901 aaagttgcaa caagaaatga tgaaaattaa acagacaatg ctcctagagg gtgggttctc 6961 tgagacagat gcagcccgtg gggcagtcaa cgcccccatg acaaaggttt tggactggag 7021 cggaacaagg tactgggctc ccgatgctag gattacaaca tacaatgcag gccacttttc 7081 cacccctcaa ccctcgggag caccaccagg gagaaccaat ctcagggcta ccacccccgc 7141 tcgaggctcc tccagtacac tttcaaatgc ttctactgtc acttctgtgc actcaaatca 7201 aactgcttca acgagacttg gttctacagc tggttctggc accagtgtct cgagcctccc 7261 gtcaactgca aggactagga gctgggttga ggatcaaaac aggaacttgt cacctttcat 7321 gaggggggtc cacaacatat catttgtcac cccaccatct agcagatcct ctagccaagg 7381 cacagtctca accgtgccta aagaagtttt ggactcctgg actggcgctt tcaacacgcg 7441 caggcagcct ctcttcgccc acattcataa gcgaggggag tcacggg //