Typing tool
|
Complete norovirus genomes
MF140674 | GII.4 Sydney | ||
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GII.P31 |
ORF1: 1..5080 ORF2: 5061..6683 ORF3: 6683..7485LOCUS MF140674 7485 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.Pe-GII.4/Rotterdam/E1300308_p4_d0 ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene, partial cds. ACCESSION MF140674 VERSION MF140674.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7485) AUTHORS 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 7485) 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..7485 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.Pe- GII.4/Rotterdam/E1300308_p4_d0" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="12-Apr-2013" /note="genotype: GII.Pe-GII.4" CDS <1..5080 /codon_start=2 /product="ORF1" /protein_id="ATN23718.1" /translation="ASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKE IPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTAFS VPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELA PLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMI QRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIL NILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVP IVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANE LAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDFEEEKARKLSTKSASPDI VGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAAS LTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCD RIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPG QPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHER LDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQAL KNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQNATVQTNNELAGALHHLRCARIRYY VKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGCLKPKDDE EFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEY LQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRK RSPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITST HVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLI KRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIY KRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKL STKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRP NVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTG KLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIRCA RAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDV LAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIA HWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPT RPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFE TMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMR FSDLSTWEGDRNLAPSFVNEDGVE" CDS 5061..6683 /codon_start=1 /product="ORF2" /protein_id="ATN23719.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6683..>7485 /codon_start=1 /product="ORF3" /protein_id="ATN23720.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFNSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 cgcttccgct gccgctgttg ccaacagcaa caacgacatc gcaaaatctt caagtgacgg 61 tgtgttttct aacatggctg tcacttttaa gcgggccctc ggggcgcggc ctaaacagcc 121 gcccccgaag gaaataccac ccagaccccc gcgaccaccc acaccagaat tggtcaaaaa 181 gatccctcct cccccaccca acggggagga tgaactagtg gtctcttaca gcgccaaaga 241 tggcgtttcc ggactgcctg agctcaccac tgtcagacaa ccggaagaaa ccaacacggc 301 gttcagtgtc cccccactca accaaaggga gagcagggac gccaaggagc cactaactgg 361 aacaatcatt gaaatgtggg atggagaaat ctaccattac ggcctgtacg tggaacgagg 421 tcttatactt ggtgtgcaca agccaccggc agccattagc cttgccaagg tcgagctagc 481 accgctctct ttgttctgga gacctgtata caccccccag tatctcatct ctccagacac 541 tcttaggaga ttacatggag agtcattccc ctacactgca tttgacaaca attgctacgc 601 cttttgttgt tgggtattag acctaaacga ctcatggcta agcaggagaa tgattcagag 661 aacaacaggc ttcttcaggc cgtaccagga ttggaacagg aaacccctcc ccactatgga 721 tgattccaaa ttaaagaagg tagccaacat attcttgtgc actttgtctt cactattcac 781 cagacccatt aaggacataa tagggaagtt gagacctctt aacatcctta acattctggc 841 tacatgtgat tggaccttcg caggcatagt ggaatcctta atactcttgg cagaactctt 901 tggagttttc tggacacccc cagatgtgtc tgcgatgatc gcccccttgc taggtgatta 961 tgaactgcaa ggacctgagg accttgcagt ggaactggtc ccaatagtga tgggggggat 1021 aggtttggtg ctaggattta ccaaagagaa aatcggaaag atgctatcat ccgctgcatc 1081 cactttaaga gcttgtaaag accttggtgc atacggactg gaaatcttaa aattggtcat 1141 gaagtggttc ttcccaaaga aagaggaagc gaatgaactg gctatggtga gatccatcga 1201 ggatgcagta ctagacctcg aggcaattga aaacaaccac atgaccaccc tactcaaaga 1261 caaagacagc ttggcaacct acatgagaac ccttgacttt gaggaggaga aagccagaaa 1321 actctcaacc aaatctgctt cacccgatat tgtgggcaca atcaactctc ttctggcaag 1381 aatcgctgct gcacgctccc tagtgcatcg ggcgaaagaa gagctctcca gcaggccgag 1441 acctgtcgtt gtgatgatat cgggaagacc agggataggg aaaactcacc ttgccaggga 1501 gctggccaag aagatcgcgg cctccctcac aggggaccag cgtgtgggtc ttatcccacg 1561 caatggtgtc gaccactggg acgcatacaa gggcgaaaga gttgtcctat gggacgacta 1621 tggaatgagc aaccccatcc atgatgccct caggttgcag gagcttgctg acacttgccc 1681 cctcacgcta aattgtgaca gaattgagaa caaagggaaa gtctttgaca gtgatgccat 1741 aattatcacc accaacctgg ccaacccagc accactggat tatgtcaatt ttgaagcgtg 1801 ctcgagacgc attgatttcc tcgtgtacgc agaagcccct gaggtggaga aggcaaagcg 1861 cgacttccca ggtcaacctg acatgtggaa gaacgctttc agtcctgact tctcacacat 1921 aaaactgtca ttggctccac agggtggttt tgacaagaac ggcaacaccc cgcatggaaa 1981 aggggtcatg aagaccctca ccactggctc cctcatcgcc cgagcatcag ggttactcca 2041 tgagaggcta gatgaatatg aactgcaagg cccagccctc accactttca actttgaccg 2101 caacaagata cttgctttta gacagcttgc tgctgaaaac aagtatgggc tgatggacac 2161 aatgagagtt ggaaaacagc tcaaggatgt caagaccatg tcagacctca aacaagcact 2221 caagaacatc gcgatcaaga agtgccagat agtgtacaat ggtggcacct acacacttga 2281 ggctgatggc aagggtagtg tgaaagttga caaagtgcaa aatgccactg tgcagaccaa 2341 caatgaacta gccggtgccc tacaccacct aaggtgcgct agaatcagat actatgttaa 2401 gtgcgtccag gaggcactgt attccatcat tcaaatcgct ggggctgcat tcgtcaccac 2461 gcgcatcgct aagcgcatga atatacagaa tctctggtcc aagccacagg tggaagacac 2521 agaagagatg gccaacaaag atggttgcct aaaacccaaa gatgatgaag agtttgtcgt 2581 ctcatccgac gacatcaaaa ctgagggcaa gaaagggaag aacaagtccg gccgtggcaa 2641 gaagcacaca gccttttcaa gtaaagggct cagtgatgag gagtacgatg agtacaagag 2701 aatcagagaa gaaaggaatg gtaagtactc catagaagag taccttcagg acagagacag 2761 gtactacgag gaggtggcca ttgccagggc aaccgaagag gacttctgtg aagaagaaga 2821 ggccaaaatc cggcagagaa ttttcagacc aacaaggaaa caacgcaaag aagagagggc 2881 ctctctcggc ttggtcacag gctctgaaat caggaagaga agcccagaag acttcaaacc 2941 caagggaaag ctgtgggctg atgatgacag aagtgttgac tacaatgaga aactcaactt 3001 tgaggcccca ccaagcatct ggtcgcggat agtcaacttt ggttcaggct ggggcttctg 3061 ggtctccccc agtctgttta taacatcaac ccatgtcata ccccaaggtg caaaagagtt 3121 cttcggagtc cctatcaagc aaatccagat acacaagtca ggtgaattct gccggttgag 3181 attcccaaag ccaatcagaa ctgatgtgac gggcatgatt ctagaagaag gtgcgcccga 3241 ggggaccgtg gtcacactgc tcatcaagag accaactgga gagctcatgc ctctggcagc 3301 cagaatgggg acccatgcaa ccatgaaaat tcaggggcgc acagttggag ggcaaatggg 3361 tatgctcctg acaggatcca acgccaagag tatggaccta ggcacaacac caggcgactg 3421 cggctgcccc tacatctaca agagggggaa tgactacgtg gtcataggag tccatacggc 3481 cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag gggagtgagg gagaagccac 3541 acttgaagga ggtgacagta aagggacata ctgtggcgca ccaatcttgg gcccagggag 3601 cgctccgaag ctcagtacca agactaagtt ttggagatca tccacaacac cactcccacc 3661 tggcacctac gaaccagcct acctcggtgg caaagaccct agagtcaaag gtggcccttc 3721 attgcaacaa gttatgaggg accagctgaa gccattcaca gaacccagag gcaaaccacc 3781 aagaccaaat gtgttggagg ctgccaagaa aaccatcatc aatgtccttg agcaaacaat 3841 tgatccaccc caaaaatggt catttgcgca agcttgcgca tcccttgaca agaccacctc 3901 cagcggccac ccgcaccaca tgcggaaaaa cgactgttgg aatggggagt ccttcacagg 3961 aaaattggct gatcaagcct ccaaggccaa cctaatgttt gaagagggaa agaacatgac 4021 tccagtctac acgggtgcac ttaaagatga gttggtaaag accgataaag tttatggtaa 4081 ggtcaagaag aggcttctgt ggggttcaga tctggcgacc atgatacggt gcgcccgagc 4141 ttttggaggc cttatggatg aactcaaggc acactgtgtc acacttcctg tcagagttgg 4201 tatgaacatg aatgaggatg gccccatcat ctttgagaag cactccagat atagatatca 4261 ttatgatgct gattattccc ggtgggactc aacacaacaa agggatgtgc tggcagcagc 4321 actagaaatc atggttaagt tctctccaga accacacctg gcccagatag ttgcagaaga 4381 cctcctttcc cctagcgtga tggatgtagg tgacttccaa atatcaataa gtgagggtct 4441 cccctctggg gtaccttgta cctcccagtg gaattccatc gcccactggc tcctcactct 4501 gtgtgcactc tctgaagtca cggacctgtc ccctgatatc attcaggcca actccctttt 4561 ctccttctat ggtgatgatg agattgtaag cacagacata aagttggacc cagagaagct 4621 gacagcaaag ctcaaggagt acgggctgaa accaacccgt cccgacaaaa ctgaaggacc 4681 ccttgttatc tctgaagacc tggatggcct gacattcctc cggagaactg tgacccgtga 4741 tccagctggc tggtttggaa aattggaaca aagttcaatt ctcaggcaaa tgtactggac 4801 caggggtccc aaccatgaag atccatttga aacaatgata ccacactccc aaagacccat 4861 acaattgatg tccttgctgg gcgaggctgc actccacggc ccggcattct atagcaaaat 4921 tagcaaatta gtcattgcag agttgaagga aggtggcatg gatttttacg tacccagaca 4981 agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg gcgatcgcaa 5041 tctggctccc agttttgtga atgaagatgg cgtcgagtga cgccaaccca tctgatgggt 5101 ccgcagccaa cctcgtccca gaggtcaaca atgaggttat ggctctggag cccgttgttg 5161 gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc tggattagaa 5221 ataattttgt acaagcccct ggtggagagt ttacagtatc ccctagaaac gctccaggtg 5281 aaatactatg gagcgcgccc ttgggccctg atctaaatcc ctacctatcc catttggcca 5341 gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aattctcgcg gggaacgcgt 5401 tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa ttttccaact gaaggcttga 5461 gccccagcca ggtcactatg ttcccccata tagtagtaga tgttaggcaa ctagaacctg 5521 tgttgattcc cttacccgat gttaggaata atttctacca ttacaatcaa tcaaatgacc 5581 ccaccattaa gttgatagca atgttgtata caccacttag ggctaataat gctggggatg 5641 atgtcttcac agtttcttgc cgagttctca cgagaccatc ccccgatttt gatttcatat 5701 ttctagtgcc acccacagtt gagtcaagaa ctaaaccatt ctctgtccca gttttaactg 5761 ttgaggagat gaccaattca agattcccca ttcctttgga aaagttgttc acgggtccca 5821 gcagtgcctt tgttgtccaa ccacaaaacg gtaggtgcac gactgatggc gtgctcctag 5881 gcaccaccca actgtctcct gtcaacatct gcaccttcag aggagatgtc acccatatca 5941 caggtagtcg taactacaca atgaatttgg cttctcaaaa ttggagcaat tatgacccaa 6001 cagaagaaat cccagcccct ctaggaactc cagattttgt ggggaagatt caaggcgtgc 6061 tcacccaaac cacaaggaca gatggctcaa cacgcggcca caaagccaca gtgtacactg 6121 ggagcgccga ctttgctcca aaactgggta gagttcaatt tgaaactgac acagaccgtg 6181 attttgaagc taaccaaaac acaaagttca ccccagttgg tgtcatccaa gatggtagca 6241 ccacccaccg aaatgaaccc caacagtggg tgctcccaag ttactcaggc agaaatactc 6301 ctaatgtgca tctggccccc gctgtagccc ccacttttcc gggtgagcaa cttctcttct 6361 tcagatccac catgcccgga tgcagcgggt accccaacat ggatttggac tgtctgctcc 6421 cccaggaatg ggtgcagtac ttttaccaag aggcagcccc agcacaatct gatgtggctc 6481 tgctgagatt tgtgaatcca gacacaggta gggttttgtt tgagtgtaag cttcataaat 6541 caggctatgt tacagtggct cacactggcc aacatgattt ggttatcccc cccaatggtt 6601 attttaggtt tgattcctgg gtcaaccagt tttacacgct tgcccccatg ggaaatggaa 6661 cggggcgtag acgtgcacta taatggctgg agctttcttt gctggattgg catctgatgt 6721 ccttggctct ggacttggtt cccttatcaa tgctggggct ggggccatca accaaaaagt 6781 tgagtttgaa aataacagaa aattgcaaca agcatccttc caatttaaca gcaatctaca 6841 acaggcttcc tttcaacatg acaaagagat gctccaagca caaattgagg ccaccaaaag 6901 gctacaacag gaaatgatga aagttaagca ggcaatgctc ctagagggtg ggttctctga 6961 gacagatgca gcccgcgggg caatcaacgc ccccatgaca aaagctttgg actggagcgg 7021 gacaaggtac tgggctcccg atgctaggac cacaacatac aatgcaggcc gcttttccac 7081 ccctcaacca tcgggggcac tgccaggaag agctaatctt agggatgctg tccctgctcg 7141 gggttcctcc agtaagtctt ctaattcttc tactgctact tctgtgtact caaatcaaac 7201 tacttcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga gcttcccgtc 7261 aactgcaagg actaggagtt gggttgagga tcaaagtagg aatttgtcac ctttcatgag 7321 gggggcccac aacatatcgt ttgtcacccc accatctagc agatcctcta gccaaggcac 7381 agtctcaacc gtgcctaaag agattttgga ctcctggact ggcgctttca acacgcgcag 7441 gcagccactc ttcgctcaca ttcgtaagcg aggggagtca cgggc //