Typing tool
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Complete norovirus genomes
MF140696 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5088 ORF2: 5069..6691 ORF3: 6691..7497LOCUS MF140696 7499 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300282_p9_d121 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140696 VERSION MF140696.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7499) 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 7499) 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..7499 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.P4- GII.4/Rotterdam/E1300282_p9_d121" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="20-Dec-2013" /note="genotype: GII.P4-GII.4" CDS <1..5088 /codon_start=1 /product="ORF1" /protein_id="ATN23784.1" /translation="SNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP PREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT AFSVPPLNQRESRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLNR RMIQRTTGFFRPYQDWNRKPLPTIDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKKI AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKNAFSPDFSHIRLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELK QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQNTTVQINNELAGALHHLRSARI RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTNNDGCPKPK DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDMGTTPGDCGCP YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGYPHHVRKNDCWNGES FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL KPTRPDKTEGPLVITEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR WMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5069..6691 /codon_start=1 /product="ORF2" /protein_id="ATN23785.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSDIVVQPQNGRCTTDGVLLGTT QLSSVNICTFRGDVTQVGKSNRYTMNLASPNWNSYDPTEDTPAPLGTPDFVGKIQGML TQTTIPGGSTRAHKATVRTGIADFSPKLGKIQFDTDTSHDLDTNQNTKFTPVGVVQEG DDSHQKEPTQWELPSYSGRGTHNVHLAPAVAPTFPGEQLLFFRSTMPGCGGYPNMNLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGKHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6691..7497 /codon_start=1 /product="ORF3" /protein_id="ATN23786.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQD SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWNGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRAAAPARGSSSMSS KSSIASSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca 61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct 121 aaacagcctc ccccgaggga aataccacaa aggcccccac gaccacccac tccagaactg 181 gtcaaaagta ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttacagt 241 gttaaggatg gtgtttccgg cttgcctgac ctttccaccg ttaggcaacc ggaagaatct 301 aacacagcct tcagtgtccc tccactcaat cagagggaga gtagagatgc taaggagcca 361 cttactggga caattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg 421 gagcgaggtc ttgtactagg cgtgcacaaa ccaccagctg ccatcagcct cgctaaggtt 481 gagctagcac cactctcctt gtactggaga cctgtgtata ctcctcagta cctcatctct 541 ccagacactc tcaagaaatt atccggagaa acgttcccct acacagcctt tgacaacaac 601 tgttatgcct tttgttgctg ggtcctggac ctaaatgact catggctgaa caggagaatg 661 atccagagaa caactggttt ctttaggccc tatcaagact ggaataggaa accccttcct 721 actatagatg actccaaaat aaagaaggta gctaacatat tcctgtgtgc tctgtcctcg 781 ctgttcacca gacccataaa agatataata gggaagataa ggcctcttaa catcctcaac 841 atcttagcct catgtgattg gacttttgca ggcatagtgg agtccctgat actcttggca 901 gaactctttg gagttttctg gacaccccca gatgtgtctg ctatgattgc tcccttactc 961 ggtgactatg agctgcaagg acctgaggac cttgcagtgg agctcgtccc cgtagtgatg 1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct 1081 gccgcgtcca ccttgagagc ttgtaaagac cttggtgcat atgggctaga gatcctgaag 1141 ttggtcatga agtggttctt tccgaagaag gaggaggcaa atgagctggc tatggtgaga 1201 tctatcgagg atgcagttct agatctcgag gcaattgaaa acaaccatat gactaccttg 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 ggcaggccgg ggatagggaa gacccacctc 1501 gctagggaag tggctaagaa gatcgcagcc tcccttacag gagaccagcg tgtgggcctc 1561 atcccacgca atggcgtcga ccattgggat gcgtacaagg gagagagagt cgtcctatgg 1621 gacgattatg gaatgagcaa ccccattcac gacgccctca ggctgcaaga actcgctgac 1681 acttgccccc tcactctaaa ctgtgacagg attgaaaata aaggaaaggt ctttgacagc 1741 gatgtcatca ttatcaccac taatttggcc aacccagcac cactagacta tgtcaacttt 1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctga agtcgagaag 1861 gcgaagcgtg acttcccagg ccagcctgac atgtggaaga acgctttcag tcctgatttc 1921 tcacacataa gactagcact ggccccacag ggtggtttcg acaagaacgg gaacaccccg 1981 catggaaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg agcgtcaggg 2041 ctactccatg agaggttaga tgaatttgaa ctacagggcc cagctctcac caccttcaat 2101 tttgaccgca acaaagtgct tgccttcaga cagcttgctg ctgagaataa atatggattg 2161 atggacacaa tgagggttgg gaaacagctc aaggatgtca aaaccatgcc tgaactcaaa 2221 caagcactca agaatgtctc aatcaagaag tgccaaatag tatatagtgg ttgcacctac 2281 atacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccaaaa caccaccgtg 2341 cagatcaaca atgagctggc tggtgctctg caccatttga ggagcgccag aatcagatac 2401 tatgtcaagt gtgtccagga ggccctatat tccatcattc aaattgctgg ggctgcattt 2461 gtcaccacgc gcattgccaa gcgcatgaac atacaaaacc tatggtccaa accacaagtg 2521 gaaaacacag aggagactac caacaatgac gggtgcccaa aacctaagga tgatgaggag 2581 tttgtcatct catctgacga catcaaaact gagggcaaga aagggaaaaa caagactggt 2641 cgcggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgag 2701 tacaagagga ttagagaaga aaggaatggt aagtactcca tagaagaata ccttcaggac 2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgaa 2821 gaggaggagg ccaagatccg tcaaaggatc tttaggccaa caaggaaaca acgcaaggag 2881 gaaagagctt ctctcggtct ggtcacaggt tctgaaatta ggaaaagaaa cccagatgac 2941 ttcaaaccca aggggaaact gtgggctgac gatgacagga gtgtggacta caatgagaaa 3001 ctcagttttg aggccccacc aagcatctgg tcaagaatag tcaactttgg ttcaggctgg 3061 ggattctggg tctcccccag tcttttcata acatcaaccc atgtcatacc ccagggcgca 3121 aaggagttct ttggagtccc catcaaacaa atacaggtac acaaatcagg cgagttctgt 3181 cgcttgagat tcccaaaacc aatcaggact gatgtgacag gcatgatctt ggaagaaggc 3241 gcacctgagg gtactgtggt cacactactc attaaaaggt ccactgggga actcatgccc 3301 ctagcagcta gaatggggac ccatgcgacc atgaagatcc aagggcgcac tgttggaggc 3361 cagatgggca tgctcctgac agggtccaac gccaagagca tggacatggg tactacacca 3421 ggtgattgcg gctgtcccta tatttacaag agaggcaatg actatgtggt cattggagtc 3481 cacacggctg ccgcacgtgg agggaacact gtcatatgtg ccactcaggg gagtgaagga 3541 gaggctacac ttgaaggtgg tgacaacaag ggaacatatt gtggtgcacc aatcctaggc 3601 ccagggagtg ccccaactct tagcaccaag accaaattct ggagatcatc tacagcgtca 3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccccag agtcaagggt 3721 ggcccttcac tacagcaagt catgagggag cagttgaaac cattcacaga gccaaggggc 3781 aaaccaccaa aaccaagtgt attagaagct gccaagaaga ccatcatcaa tgtccttgag 3841 caaacaattg acccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag 3901 accacttcca gcggttatcc gcaccatgtg cggaaaaacg actgctggaa cggggagtcc 3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaaa 4021 aacatgaccc cagtctacac agctgcactc aaggatgagt tagttaaaac tgacaaaatt 4081 tatggtaaga tcaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt 4141 gctcgggcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcccatt 4201 agagttggca tgaacatgaa tgaggatggc cccatcatct tcgagaggca ttctaggtac 4261 acatatcact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg 4321 gcagcagctc tcgaaatcat ggttaaattc tctccagaac cacatttggc ccaggtagtc 4381 gcagaagacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac 4441 gagggtcttc cctctggggt gccttgcacc tctcaatgga actccatcgc ccactggctt 4501 ctcactctct gtgcgctctc tgaagtcaca aacctatccc ctgacacaat acaggctaat 4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca 4621 gagaaattga cagcaaagct cagagaatat gggttaaaac cgacccgccc tgacaaaact 4681 gaaggacccc ttgtcatcac tgaagacctg aatggcctaa ctttcctgcg gagaactgtg 4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg 4801 tactggacta ggggtcccaa ccatggagac ccatctgaaa caatgattcc acactcccaa 4861 agacccatac aattgatgtc cctactgggg gaggccgctc tccacggccc agccttttac 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 gccgccattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg 5221 gattagaaat aattttgtac aagcccctgg tggagagttt acagtatccc ctagaaacgc 5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaacccct acctttccca 5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg 5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaatt tcccaactga 5461 aggtttgagc cccagtcaag tcactatgtt tccccatata atagtggatg ttaggcaatt 5521 ggaacctgtg ttgattccct tacccgatgt taggaataat ttctaccatt ataatcaatc 5581 aaatgactcc accattaaat tgatagcaat gttgtataca ccacttaggg ctaataatgc 5641 tggggacgat gtcttcacag tctcttgtcg agtcctcacg agaccatccc ccgattttga 5701 ttttatattt ttggtgccac ctacagttga atcaagaact aaaccattct ctgtcccagt 5761 tctaactgtt gaagagatga ccaattcaag gttccccatc cctttggaaa agttgttcac 5821 aggccccagt agtgacatcg tagttcaacc acaaaatggc aggtgcacga ctgatggcgt 5881 gctcctaggt actacccaat tgtcctctgt caacatctgc accttcagag gggatgtcac 5941 ccaagttgga aaatctaaca gatacacaat gaatttggcc tccccaaatt ggaacagtta 6001 cgatccaaca gaagataccc cagcccctct aggaactcca gatttcgtgg ggaagattca 6061 aggtatgctc acccaaacca caatcccagg tggctcgacc cgcgcccaca aggccacagt 6121 gcgcactggg atcgccgact tttctccgaa actgggtaaa attcaatttg acactgacac 6181 aagtcatgat cttgacacca accagaacac aaagttcacc ccagtcggcg ttgtccagga 6241 aggtgatgat tcccaccaga aagaacccac acaatgggag ctcccaagct attcaggcag 6301 aggcactcat aatgtacacc tggcccccgc tgtagcccct actttcccgg gcgagcagct 6361 cctcttcttc agatctacta tgcccggatg tggcgggtac cccaacatga atttggactg 6421 tctactccct caggaatggg tgcagtactt ctaccaggag gcagccccag cacaatctga 6481 tgtagctctg ttgagatttg tgaatccaga tacaggtagg gttttatttg aatgtaagct 6541 tcataaatca ggctatgtta cagtggctta cactggcaaa catgatttgg ttatcccccc 6601 taatggttat tttagatttg attcctgggt caaccagttc tacactcttg cccccatggg 6661 aaatggaacg gggcgtagac gtgcattata atggctggag ctttctttgc tggattggca 6721 tctgatgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggtcatcaac 6781 caaaaagttg attttgaaaa taatagaaaa ttacaacaag attccttcca atttagtagc 6841 aatctccaac aagcttcctt tcaacatgac aaagagatgc tccaagcaca aattgaggcc 6901 accaaaaagt tgcaacagga aatgatgaga gttaaacaag caatgctcct agagggtgga 6961 ttctctgaga cagatgcagc ccgtggggca atcaacgccc ccatgacaaa agttttggac 7021 tggaatggaa caaggtactg ggctcccgat gccaggacta caacatacaa tgcaggccgc 7081 ttttccaccc ctcaaccctc gggggcacca ccaggaaggg ctaatcttag ggctgctgcc 7141 cccgcccggg gctcctctag tatgtcttct aaatcttcta ttgcttcttc tgtgtattca 7201 aatcaaacca cctcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc 7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa tttgtcacct 7321 ttcatgaggg gggcccacaa catctcgttt gtcaccccac catctagcag atcctctagc 7381 caaggcacag tctcaaccgt gcccaaagaa attttggact cctggactgg cgctttcaac 7441 acgcgcaggc agcctctctt cgctcacatt cgtaagcgag gggagtcacg ggtgtaatg //