Typing tool
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Complete norovirus genomes
MF140690 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5088 ORF2: 5069..6691 ORF3: 6691..7497LOCUS MF140690 7497 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2012/GII.P4-GII.4/Rotterdam/E7800011_p8_d0 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140690 VERSION MF140690.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7497) 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 7497) 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..7497 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2012/GII.P4- GII.4/Rotterdam/E7800011_p8_d0" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="29-Jun-2012" /note="genotype: GII.P4-GII.4" CDS <1..5088 /codon_start=1 /product="ORF1" /protein_id="ATN23766.1" /translation="SNDASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPP PREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPELSTVRQPEESNT AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSR RMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGRIRPL NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELK QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQINNELAGALHHLRSARI RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSKDGCLKPK DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE IRRRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVMGMILEEGAPEGTVVT LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGES FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI RCARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR WMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5069..6691 /codon_start=1 /product="ORF2" /protein_id="ATN23767.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVLLAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVIHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6691..7497 /codon_start=1 /product="ORF3" /protein_id="ATN23768.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSEADAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATAPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacatcgc aaaatcttcg 61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct 121 aaacagcctc ccccgaggga aaaaccacaa agacccccac gaccacctac tccagaactg 181 gtcaaaaata ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttatagt 241 gtcaaggatg gtgtttccgg cttgcctgaa ctttccaccg tcaggcaacc ggaagaatct 301 aacacggcct tcagtgtccc tccacttaat cagagggaga atagagatgc taaggagcca 361 cttactggaa caattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg 421 gagcgaggcc ttgtactagg tgtgcacaaa ccaccagctg ccatcagcct cgctaaggtt 481 gagctagcac cactctcctt gtactggaga cctgtgtaca ctcctcagta cctcatctct 541 ccagacactc tcaagaaatt atccggagaa acgttcccct acacagcctt tgacaacaac 601 tgctatgcct tttgttgctg ggtcctggac ctaaatgact cgtggctgag caggagaatg 661 atccagagaa caactggttt cttcaggccc taccaagact ggaataggaa accccttccc 721 actatggatg actccaaaat aaagaaggta gctaacatat tcctgtgtgc tctgtcctcg 781 ctgttcacca gacccataaa agatataata gggaggataa ggcctcttaa catcctcaac 841 atcttagcct catgtgattg gacttttgca ggcatagtgg agtccctgat actcttggca 901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttgctt 961 ggtgactacg agctacaagg acctgaggac cttgcagtgg agctcgtccc cgtagtgatg 1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct 1081 gctgcgtcca ccttgagagc ttgtaaagac cttggtgcat atgggctaga gatcctaaag 1141 ttggtcatga agtggttctt cccgaagaag gaggaggcaa atgagctggc tatagtgagg 1201 tctatcgagg acgcagtcct agatctcgag gcaattgaaa acaaccatat gaccaccttg 1261 ctcaaagaca aagacagtct ggcaacctat atgagaacac ttgaccttga ggaggagaaa 1321 gccaggaaac tctcaaccaa gtctgcctca cccgacatcg tgggcacaat caacgccctc 1381 ctggcgagaa tcgctgccgc acgttctctg gtgcatcgag cgaaggagga gctttccagc 1441 agaccaagac ctgtggtgtt gatgatatca ggcaggccag gaatagggaa gacccacctc 1501 gctagggaag tggctaagag aatcgcagcc tcccttacag gagaccagcg tgtgggcctc 1561 atcccacgca atggcgtcga ccattgggat gcatacaagg gagagagggt cgtcctatgg 1621 gacgattatg gaatgagcaa ccctatccac gatgccctca ggctgcaaga actcgctgac 1681 acttgccccc tcactctaaa ctgtgacagg attgaaaata aaggaaaggt ctttgacagc 1741 gatgtcatca ttatcaccac taatctggcc aacccagcac cactggacta tgtcaacttt 1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctga agtcgaaaag 1861 gcgaagcgtg acttcccagg ccagcctgac atgtggaaga acgctttcag ttctgatttc 1921 tcacacataa aactagcact ggccccacag ggtggtttcg ataagaacgg gaacaccccg 1981 cacggaaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg 2041 ctactccatg agaggttaga tgaatttgaa ctacagggcc cagctctcac caccttcaat 2101 ttcgatcgca ataaagtgct tgcctttaga cagcttgctg ctgaaaataa atatggattg 2161 atggacacaa tgagggttgg gaaacagctc aaggatgtca gaaccatgcc agaactcaaa 2221 caagcactca agaatgtctc aatcaagaag tgccaaatag tgtatagtgg ttgcacctac 2281 atacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccaaag cgccgccgtg 2341 cagatcaaca atgagctggc tggtgccctg caccatttga ggagcgccag aatcagatac 2401 tatgtcaagt gtgtccagga ggccctgtat tccatcattc aaattgctgg ggctgcattt 2461 gtcaccacgc gcattgccaa gcgcatgaac atacaaaacc tatggtccaa gccacaagtg 2521 gaaaacacag aggagactac cagcaaggac gggtgcctaa aacctaagga tgatgaggag 2581 tttgtcattt catccgacga catcaaaact gagggtaaga aagggaagaa caagactggc 2641 cgcggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgag 2701 tacaagagga ttagagaaga aaggaatggc aagtactcca tagaagagta ccttcaggac 2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgaa 2821 gaggaggagg ccaagatccg gcaaaggatc tttaggccaa caaggaaaca acgcaaggag 2881 gaaagagcct ctctcggtct ggtcacaggc tctgaaatta ggagaagaaa cccagatgat 2941 ttcaaaccca aggggaaatt gtgggctgac gatgacagga gtgtggacta caatgagaaa 3001 ctcagttttg aggccccacc aagcatctgg tcgagaatag tcaactttgg ttcaggctgg 3061 ggattctggg tctcccccag tctgttcata acatcaaccc atgtcatacc ccagggcgca 3121 aaggagttct ttggagtccc catcaaacaa atacaggtac acaagtcagg cgagttctgt 3181 cgcttgagat tcccaaaacc aatcaggact gatgtgatgg gcatgatctt agaagaaggc 3241 gcacctgagg gcaccgtggt cacactactc atcaaaaggt ccactgggga actcatgccc 3301 ctagcagcta ggatggggac ccatgcgacc atgaagatcc aagggcgcac tgttggaggc 3361 cagatgggca tgcttctgac aggatccaac gccaagagca tggacctggg tactacacca 3421 ggtgattgtg gctgccccta tatctacaag agaggtaatg actatgtggt cattggagtc 3481 cacacggctg ccgcacgtgg gggaaacact gtcatatgtg ccacccaggg gagtgaagga 3541 gaggctacac ttgaaggtgg tgacaacaag gggacatact gtggtgcacc aatcctaggc 3601 ccagggagtg ccccaactct tagcaccaag accaaattct ggagatcgtc tacagcatca 3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccctag agtcaagggt 3721 ggcccttcac tacagcaagt catgagggaa cagttgaagc cattcacaga gccaaggggc 3781 aagccaccaa aaccaagtgt attagaagct gccaagaaga ccatcatcaa tgtccttgag 3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag 3901 accacttcca gtggtcatcc gcaccacgtg cggaaaaacg actgctggaa cggagagtcc 3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag 4021 aacatgaccc cagtctacac agctgcgctc aaggacgagt tagttaaaac tgacaaaatt 4081 tatggtaaga tcaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt 4141 gctcgagcat tcggaggcct aatggatgaa ttcaaagcac actgtgtcac gcttcccatt 4201 agagttggca tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac 4261 acatatcact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg 4321 gcagcagctc tcgaaatcat ggttaaattc tccccagaac cacatttggc tcaggtagtc 4381 gcggaagacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac 4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt 4501 ctcactctct gtgcactctc cgaagtcaca aacctatctc ctgataccat acaggctaac 4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca 4621 gagaaattga cagcaaagct cagagaatat gggttaaaac caacccgccc tgacaaaact 4681 gaaggacccc ttgtcatctc tgaagacctg aatggcctaa ctttcctgcg gagaactgtg 4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg 4801 tactggacta ggggtcccaa tcatggagac ccatctgaaa caatgattcc acactcccaa 4861 agacccatac aattgatgtc cctactgggg gaggccgctc tccacggccc agccttttat 4921 agcaaaatca gcaagttggt cattgcagag ctaaaagaag gtggcatgga tttttacgtg 4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc 5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc 5101 tgatgggtcc acagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc 5161 cgtagttggt gccgctattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg 5221 gattagaaac aattttgtac aagcccctgg tggagagttt acagtatccc ctagaaacgc 5281 tccaggtgaa atattatgga gcgcgccctt aggccctgat ctgaatccct acctttctca 5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtac tcctcgcggg 5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaatt tcccaactga 5461 aggtttgagc cccagccagg tcactatgtt cccccatata atagtagatg ttaggcaatt 5521 ggaacctgtg ttgatcccct tacccgatgt taggaataat ttttaccatt ataatcaatc 5581 aaatgacccc actatcaaat tgatagcaat gctgtacaca ccacttaggg ctaataatgc 5641 tggggacgat gtcttcacag tttcttgtcg agttctcacg agaccatccc ccgattttga 5701 tttcatattt ttggtgccac ccacagttga atcaagaact aaaccattct ctgtcccagt 5761 tttaactgtt gaggagatga ccaattcaag gttccccatt cctttggaaa agttgttcac 5821 gggccccagt agtgcctttg ttgttcaacc acaaaatggc aggtgcacga ctgatggcgt 5881 gctcctaggt actacccaac tgtcccctgt aaacatctgc accttcagag gggatgtcat 5941 ccacattcca ggcagtcgta actacacaat gaatttggcc tcccaaaatt ggaacagtta 6001 cgatccaaca gaagaaatcc cagcccctct aggaactcca gatttcgtgg ggaagattca 6061 aggtgtgctc acccaaacca caaggacaaa tggctcgacc cgcggccaca aagctacagt 6121 gtacactggg agcgccgact tttctccaaa actgggtaga gttcaatttg ccactgacac 6181 agacaatgat tttgaaacta accaaaacac aaagttcacc ccagtcggtg tcatccagga 6241 tggtagtacc accccccgaa atgaacctca acaatgggtg ctcccaagtt actcaggcag 6301 aaacattcat aatgtgcacc tggcccccgc tgtagccccc actttcccgg gcgagcagct 6361 cctctttttc agatctacta tgcccggatg cagcgggtac cccaacatgg atttggactg 6421 tctgctcccc caggaatggg tgcagtactt ctaccaggag gcagccccag cgcaatctga 6481 tgtggctctg ttgagatttg tgaatccaga cacaggtagg gttttgtttg agtgtaagct 6541 ccataaatca ggctatgtta cagtggctca cactggccaa catgatttgg ttatcccccc 6601 caatggttat tttagatttg attcctgggt caaccagttc tacacacttg cccccatggg 6661 aaatgggacg gggcgtagac gtgcattata atggctggag ctttctttgc tggattggca 6721 tctgacgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggccatcaac 6781 caaaaagttg aatttgaaaa taatagaaaa ttgcaacaag cttccttcca atttagtagc 6841 aatctacaac aagcttcctt tcaacatgac aaggagatgc tccaagcaca aattgaggcc 6901 accaaaaagt tgcaacagga aatgatgaga gttaaacaag caatgctcct agagggtgga 6961 ttctctgagg cagatgcagc ccgtggggca atcaacgccc ccatgacaaa aactttggac 7021 tggagcggga caaggtactg ggctcccgat gctaggacta caacatataa tgcaggccgc 7081 ttttccaccc ctcaaccctc gggggcacta ccaggaagag ctaatcttag ggctactgcc 7141 cccgcccggg gttcctccag cacgtcttct aactcttcta ttgctacttc tgtgtattca 7201 aatcaaacca cttcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc 7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa tttgtcacct 7321 ttcatgaggg gggcccataa catctcgttt gtcaccccac catctagcag atcctctagc 7381 caaggcacag tctcaaccgt gcccaaagaa gttttggact cctggactgg cgctttcaac 7441 acgcgcaggc agcctctctt cgctcacatt cgcaagcgag gggagtcacg ggcgtaa //