Typing tool
|
Complete norovirus genomes
MF140639 | GII.4 Sydney | ||
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GII.P31 |
ORF1: 1..5064 ORF2: 5045..6667 ORF3: 6667..7468LOCUS MF140639 7468 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2014/GII.Pe-GII.4/Rotterdam/E1300287_p10_d462 ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene, partial cds. ACCESSION MF140639 VERSION MF140639.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7468) 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 7468) 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..7468 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2014/GII.Pe- GII.4/Rotterdam/E1300287_p10_d462" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="01-May-2014" /note="genotype: GII.Pe-GII.4" CDS <1..5064 /codon_start=1 /product="ORF1" /protein_id="ATN23613.1" /translation="VANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKEIPPRP PRPPTPELVKKIPPPPPNGGDELVVSYNAKDGVSGLPELTTVRQPEETNTAFSVPPLN QRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELAPLSLF WRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTG FFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILNILAT CDWTFAGIVESLILLAELFGAFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGG IGLVLGFTKEKIGKILSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVR SIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTIN ALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHFAREVANKVAASLTGDQ RVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENK GKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMW KNAFSSDFSHMKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEYE LQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQALKNITI KKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRYYVKCAQ EALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEIVNKDGCLKPKDDEEFVVS SDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRD KYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPED FKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQ GAKEFFGVPIKQIQIHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVTLLIKRPTG ELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGND YVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLSAKTK FWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPNVLEA AKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQ ASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLATMIRCARAFGG LMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDVLAAAL EIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAHWLLT LCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTHPDKT EGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFETMIPH SQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLS TWEGDRNLAPSFVNEDGVE" CDS 5045..6667 /codon_start=1 /product="ORF2" /protein_id="ATN23614.1" /translation="MKMASSDANPSDGSTVSLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAVPPNFPTECLSPSQVTMLPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCSTDGVLLGTT QLSPVNICTFRGDVTQITGSSTYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTVGSTRGHKATVRTGSADFAPKLGRVRFETDTNNDFEVNQNTKFTPVGVIQDG DTAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAP" CDS 6667..>7468 /codon_start=1 /product="ORF3" /protein_id="ATN23615.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSRKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPTTARTRSWVEDQSRNLSPFMSGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESR" ORIGIN 1 gttgccaaca gcaacaacga catcgcaaaa tcttcaagtg acggtgtgtt ctctaacatg 61 gctgtcactt ttaagcgggc cctcggggcg cggcctaaac agccgccccc gaaggaaata 121 ccacccagac ccccgcgacc acccacacca gaattggtca aaaagatccc tcctccccca 181 cccaacgggg gggatgaact agtggtctcc tacaatgcca aagatggcgt ttccggactg 241 cctgagctca ccactgtcag acaaccggaa gaaaccaaca cggcgttcag tgtcccccca 301 cttaaccaaa gggagagcag ggacgccaag gagccactaa ctggaacaat cattgaaatg 361 tgggatggag aaatctacca ttacggcctg tacgtggaac gaggtcttat acttggtgtg 421 cacaagccac cggcagccat tagccttgcc aaggtcgagc tagcaccgct ctctttgttc 481 tggagacctg tatacacccc ccagtatctc atctctccag acactcttag gagattacat 541 ggagagtcat tcccctacac tgcatttgac aacaattgct acgccttttg ctgttgggta 601 ttagacctaa acgactcatg gctaagcagg agaatgattc agagaacaac aggcttcttt 661 aggccgtacc aggattggaa caggaaaccc ctccccacta tggatgattc caaattaaag 721 aaggtagcca acatattctt gtgcactttg tcttcactat tcaccagacc cattaaggac 781 ataataggga agttgaaacc tcttaacatc cttaacattc tggctacatg tgattggacc 841 ttcgcaggca tagtggaatc cttaatactc ttggcagaac tctttggagc tttctggaca 901 cccccagatg tgtctgcgat gatcgccccc ttgctaggtg attatgaact gcaaggacct 961 gaggaccttg cagtggaact ggtcccagta gtgatggggg ggataggttt ggtgctagga 1021 tttaccaaag agaaaatcgg aaagatacta tcatccgctg catccacttt aagagcttgt 1081 aaagaccttg gtgcatacgg actggaaatc ttaaaattgg tcatgaagtg gttctttcca 1141 aagaaagagg aagcaaatga actggctatg gtgagatcca tcgaggatgc agtactagac 1201 ctcgaggcaa ttgaaaacaa ccacatgacc accctactca aagataaaga cagcttggca 1261 acctacatga gaacccttga ccttgaggag gagaaagcca gaaaactctc aaccaaatct 1321 gcttcacccg atattgtggg cacaatcaac gctcttctgg caagaatcgc tgctgcacgc 1381 tccctagtgc atcgggcgaa agaagagctc tccagcaggc tgagacctgt cgtagtgatg 1441 atatcgggaa agccagggat agggaaaact cactttgcca gggaggtggc caacaaggtc 1501 gcggcctccc tcacagggga ccagcgtgtg ggtcttatcc cacgcaatgg cgtcgaccac 1561 tgggacgcat acaagggcga aagagttgtc ctatgggacg actatggaat gagcaacccc 1621 atccatgatg ccctcaggtt gcaggagctt gctgacactt gccccctcac gctaaattgt 1681 gacagaattg agaacaaagg gaaagtcttt gacagtgatg ccataattat caccaccaat 1741 ctggccaacc cagcaccact ggattatgtc aactttgaag cgtgctcgag acgcattgat 1801 ttcctcgtgt acgcagaagc ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa 1861 cctgacatgt ggaagaacgc tttcagttct gacttctcac acatgaaact gtcattggct 1921 ccacaaggtg gttttgacaa gaacggcaac accccgcatg gaaaaggtgt catgaagacc 1981 ctcaccactg gctccctcat cgcccgagca tcagggttac ttcatgagag gctagatgaa 2041 tatgaactac aaggcccagc cctcaccacc ttcaactttg accgcaacaa gatacttgct 2101 tttagacagc ttgctgctga aaacaagtat gggctgatgg acacaatgag agttggaaaa 2161 cagctcaagg atgtcaagac catgtcagac ctcaaacaag cactcaagaa catcacgatc 2221 aagaagtgcc agatagtgta caatggtggc acctacacac ttgaggctga tggcaagggt 2281 agtgtgaaag ttgacaaagt gcaaagtgcc actgtgcaga ccaacaatga actagccggt 2341 gccctacacc acctaaggtg cgctagaatc agatactatg ttaagtgcgc ccaggaggca 2401 ctgtattcca tcatccaaat cgctggggct gcattcgtca ccacgcgcat cgctaagcgc 2461 atgaatatac agaatctctg gtccaagcca caggtggaag acacagaaga gatagtcaac 2521 aaagatggtt gcctaaaacc caaagatgat gaagagtttg tcgtctcatc cgacgacatc 2581 aaaactgagg gcaagaaagg gaagaacaag tccggccgtg gcaagaagca cacagccttt 2641 tcaagtaaag ggctcagtga tgaggagtac gatgagtaca agaggatcag agaagaaagg 2701 aatggtaagt actccataga agagtacctt caggacagag acaagtacta cgaggaggtg 2761 gccattgcca gggcaaccga agaggacttc tgtgaagaag aagaggccaa aatccggcag 2821 agaattttta gaccaacaag gaaacaacgt aaagaagaga gggcctctct cggcttggtc 2881 acaggctctg aaatcaggaa gagaaaccca gaagacttca aacccaaggg aaagttgtgg 2941 gctgatgatg acagaagtgt tgactacaat gagaaactca attttgaggc cccaccaagc 3001 atctggtcgc ggatagtcaa ctttggttca ggctggggct tctgggtctc tcccagtctg 3061 tttataacat caacccatgt cataccccaa ggtgcaaaag agttcttcgg agtccctatt 3121 aagcaaatcc agatacacaa gtcaggtgaa ttctgccggt tgagattccc aaggccaatc 3181 agaactgatg tgacgggcat gattctagaa gaaggtgcgc ccgagggaac cgtggtcaca 3241 ctgctcatca agagaccaac tggagagctc atgcctctgg cagccagaat ggggacccat 3301 gcaaccatga aaatccaggg gcgcacagtt ggggggcaaa tgggtatgct cctgacagga 3361 tccaacgcca agagtatgga cctaggcaca acaccaggcg actgcggatg cccctacatc 3421 tacaagaggg ggaatgacta cgtggtcata ggagtccata cggccgctgc ccgtggagga 3481 aacactgtca tatgtgccac ccagggaagt gagggagaag ccacacttga aggaggtgac 3541 agtaaaggga catactgtgg cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt 3601 gccaagacta agttttggag gtcatccaca acaccactcc cacctggcac ctacgaacca 3661 gcctacctcg gtggcaaaga ccctagagtc aaaggtggcc cttcattgca acaagttatg 3721 agggaccagc tgaagccatt cacagaaccc agaggcaaac caccaagacc aaatgtgttg 3781 gaagctgcca agaaaaccat catcaatgtc cttgagcaaa caattgatcc accccaaaaa 3841 tggtcatttg cgcaagcttg cgcatccctt gacaaaacca cctccagcgg ccacccgcac 3901 cacatgcgga aaaacgactg ttggaatggg gagtccttca caggaaaatt ggctgaccag 3961 gcctccaagg ccaacctaat gtttgaagag ggaaagaaca tgactccagt ctacacaggt 4021 gcacttaaag atgagttggt aaagaccgac aaagtttatg gtaaaatcaa gaagaggctt 4081 ctgtggggtt cagatctggc gaccatgata cggtgcgccc gagcttttgg aggccttatg 4141 gatgaactca aggcgcactg tgtcacactt cctgtcagag ttggtatgaa catgaatgag 4201 gatggcccca tcatctttga gaagcactcc agatacagat atcactatga tgctgattat 4261 tcccggtggg actcaacaca acaaagggat gtgctagcag cagcactaga aatcatggtt 4321 aagttctctc cagaaccaca cctggcccag atagttgcag aagacctcct ttcccctagc 4381 gtgatggatg taggtgactt tcaaatatca ataagtgagg gtctcccctc tggggtacct 4441 tgtacctccc agtggaattc catcgcccac tggctcctca ctctgtgtgc actctctgaa 4501 gtcacaaacc tgtcccctga tatcattcag gccaactccc ttttctcctt ctatggtgat 4561 gatgagattg taagcacaga cataaagttg gacccagaga agctgacagc aaagctcaag 4621 gagtacgggc tgaaaccaac ccaccccgac aaaactgaag gacccctcgt tatctctgaa 4681 gacctggatg gcctgacatt cctccggaga actgtgaccc gtgatccagc tggctggttt 4741 ggaaagttgg aacaaagttc aattctcagg caaatgtact ggaccagggg tcccaatcat 4801 gaagatccat ttgaaacaat gataccacac tcccaaagac ccatacaatt gatgtccttg 4861 ctgggcgagg ctgcactcca cggcccggca ttctatagca aaattagcaa attagtcatt 4921 gcagagttga aggaaggtgg catggatttt tacgtgccca gacaagagcc aatgttcaga 4981 tggatgagat tctcagatct gagcacgtgg gagggcgatc gcaatctggc tcccagtttt 5041 gtgaatgaag atggcgtcga gtgacgccaa cccatctgat gggtccacag tcagcctcgt 5101 cccagaggtc aacaatgagg ttatggctct ggagcccgtt gttggtgccg ccattgcggc 5161 acctgtagcg ggccaacaaa atgtaattga cccctggatt agaaataatt ttgtacaagc 5221 ccctggtgga gagtttacag tatcccccag aaacgctcca ggtgaaatac tatggagcgc 5281 gcccttgggc cctgatctaa atccctatct gtcccatttg gccagaatgt acaatggtta 5341 tgcaggtggt tttgaagtgc aggtagttct cgcggggaac gcgttcaccg ccgggaagat 5401 catatttgca gcggtcccac caaattttcc aactgaatgt ttgagcccca gccaggtcac 5461 tatgctcccc catataatag tagatgttag gcaattagaa cctgtgttga ttcccttacc 5521 cgatgttagg aataattttt atcattacaa tcaatcaaat gactccacca ttaagttgat 5581 agcaatgttg tatacaccac ttagggctaa taatgctggg gatgatgtct tcacagtctc 5641 ttgccgagtt ctcacgagac catcccccga ttttgatttc atatttttag tgccacccac 5701 agttgagtca agaactaaac cattctctgt cccagtttta actgttgagg agatgaccaa 5761 ttcaagattc cccattcctt tggaaaagtt gttcacgggt cccagcagta cctttgttgt 5821 ccaaccacaa aacggtaggt gctcgactga tggcgtgctc ctaggcacca cccagctgtc 5881 tcctgtcaac atctgcacct tcagaggaga tgtcacccag atcacaggta gtagtaccta 5941 cacaatgaat ttggcttctc aaaattggag caactatgac ccaacagaag aaatcccagc 6001 ccctctggga actccagatt ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag 6061 gacagttggc tcaacacgcg gccacaaagc cacagtgcgc actgggagcg ccgactttgc 6121 tccaaaactg ggtagagttc gatttgaaac tgacacaaac aatgattttg aagttaacca 6181 aaatacaaag ttcaccccag ttggtgtcat ccaagatggt gacaccgccc accgaaatga 6241 accccaacag tgggtgctcc caagttactc aggcagaaac actcctaatg tacatctggc 6301 ccccgctgta gcccccactt ttccgggtga gcaacttctc ttcttcagat ccaccatgcc 6361 cggatgcagc gggtacccca acatggattt ggactgtctg ctcccccagg aatgggtgca 6421 gtacttctac caagaggcag ccccagcaca atctgatgtg gctctgctga gatttgtgaa 6481 tccagacaca ggtagggttt tgtttgagtg taagcttcat aaatcaggct atattacagt 6541 ggctcacact ggccaacatg atttggttat cccccccaat ggttatttta ggtttgattc 6601 ctgggttaat cagttttaca cgcttgcccc catgggaaat ggaacggggc gtagacgtgc 6661 accataatgg ctggagcttt ctttgctgga ttggcatctg atgtccttgg ctctggactt 6721 ggttccctta tcaatgctgg ggctggggcc atcaaccaaa aagttgagtt tgaaaataac 6781 agaaaattgc aacaagcatc cttccaattt agcagcaatc tacaacaggc ttcctttcaa 6841 catgacaaag agatgctcca agcacaaatt gaggccacca aaaggctaca acaggaaatg 6901 atgaaagtca aacaggcaat gctcctagag ggtgggtttt ctgagacaga tgcagcccgc 6961 ggggcaatca acgcccccat gacaaaagtt ttggactgga gtgggacaag gtactgggct 7021 cccgatgcta ggaccacaac atacaatgca ggccgctttt ccacccctca accatcgggg 7081 gcactgccag gaagagctaa tcttagggat gctgtccctg ctcggggttc ctccagaaag 7141 tcttctaatt cttccactgc tacttctgtg tactcaaatc aaactacttc aacgagactt 7201 ggttctacag ctggttctgg taccagtgtc tcgagcttcc cgacaactgc aaggactagg 7261 agctgggttg aggatcaaag taggaatttg tcacctttca tgagtggggc ccacaacata 7321 tcgtttgtca ccccaccatc tagcagatcc tctagccaag gcacagtctc aaccgtgcct 7381 aaagagattt tggactcctg gactggcgct ttcaacacgc gcaggcagcc actcttcgct 7441 cacattcgta agcgagggga gtcacggg //