Typing tool
|
Complete norovirus genomes
MF140675 | GII.4 Sydney | ||
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GII.P31 |
ORF1: 1..5077 ORF2: 5058..6680 ORF3: 6680..7483LOCUS MF140675 7483 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2014/GII.Pe-GII.4/Rotterdam/E1300309_p4_d355 ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene, partial cds. ACCESSION MF140675 VERSION MF140675.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7483) 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 7483) 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..7483 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2014/GII.Pe- GII.4/Rotterdam/E1300309_p4_d355" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="02-Apr-2014" /note="genotype: GII.Pe-GII.4" CDS <1..5077 /codon_start=2 /product="ORF1" /protein_id="ATN23721.1" /translation="SAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKEI PPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTAFSV PPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELAP LSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQ RTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILN ILATCDWTFAGVVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPI VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANEL AMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDFEEEKARKLSTKSASPDIV GTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAASL TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDR IENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQ PDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERL DEYELQGPTLTTFNFDRNKILAFRQLAAENKYGLVDTMRVGKQLKDVKTMSDLKQALK NIAIRKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRYYV KCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQMEDTEEMANKDGCLKPKDDEE FVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL QDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKR NPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTH VIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIK RPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYK RGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLS TKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPN VLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGETFTGK LADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIRCAR AFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDVL AAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAH WLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTR PDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFET MIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRF SDLSTWEGDRNLAPSFVNEDGVE" CDS 5058..6680 /codon_start=1 /product="ORF2" /protein_id="ATN23722.1" /translation="MKMASSDANPSDGSAANLVPVVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVLLAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPNIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYRMNLASQNWSNYDPTEEIPAPLGIPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFETNQNTKFTPAGVIQDG STTHRNEPQQWVLPSYSGRSTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6680..>7483 /codon_start=1 /product="ORF3" /protein_id="ATN23723.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSAATSVYSNQTTSTRLGSTAGSGTSVSSFPPTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 ttccgctgcc gctgttgcca acagcaacaa cgacatcgca aaatcttcaa gtgacggtgt 61 gttttctaac atggctgtca cttttaagcg ggccctcggg gcgcggccta aacagccgcc 121 cccgaaggaa ataccaccca gacccccgcg accacccaca ccagaattgg tcaaaaagat 181 ccctcctccc ccacccaacg gggaggatga actagtggtc tcctacagcg ccaaagatgg 241 cgtttccgga ctgcctgagc tcaccactgt caggcaaccg gaagaaacca acacggcgtt 301 cagtgtcccc ccactcaacc aaagggagag cagggacgcc aaggagccac taactggaac 361 aatcattgaa atgtgggatg gagaaatcta ccattacggc ctgtacgtgg aacgaggtct 421 tatacttggt gtgcacaagc caccggcagc cattagcctt gccaaggtcg agctagcacc 481 gctctctttg ttctggagac ctgtatacac cccccagtac ctcatctctc cagacactct 541 taggagacta catggagagt cattccccta cactgcattt gacaacaatt gctacgcctt 601 ttgttgttgg gtactagacc taaacgactc atggctaagc aggagaatga ttcagagaac 661 aacaggcttc ttcaggccgt accaggattg gaacaggaaa cccctcccca ctatggatga 721 ttccaaatta aagaaggtag ccaacatatt cttgtgcacc ttgtcttcac tattcaccag 781 gcccattaag gacataatag ggaagttgaa acctcttaac atccttaaca ttctggctac 841 atgtgattgg accttcgcag gcgtagtgga atccttaata ctcttggcag aactctttgg 901 agttttctgg acacccccag atgtgtctgc gatgatcgcc cccttgctag gtgattatga 961 actgcaagga cctgaggacc ttgcagtgga actggtccca atagtgatgg gggggatagg 1021 tttggtgcta ggatttacca aagagaaaat cggaaagatg ctgtcatccg ctgcgtccac 1081 tttaagagct tgtaaagacc ttggtgcata cggactggaa atcttaaaat tggtcatgaa 1141 gtggttcttc ccaaagaaag aggaagcgaa tgaactggct atggtgagat ccatcgagga 1201 tgcagtacta gacctcgagg caattgaaaa caaccacatg accaccctac tcaaggacaa 1261 agacagcttg gcaacctaca tgagaaccct tgactttgag gaggagaaag ccagaaaact 1321 ctcaaccaaa tctgcttcac ccgatattgt gggcacaatc aacgctcttc tggcaagaat 1381 cgctgctgca cgctccctag tgcatcgggc gaaagaagag ctctccagca ggccgagacc 1441 tgtcgttgtg atgatatcgg gaagaccagg gatagggaaa actcaccttg ccagggagct 1501 ggccaagaag atcgcggcct ccctcacagg ggaccagcgt gtgggtctta tcccacgcaa 1561 tggtgtcgac cactgggacg catacaaggg cgaaagagtt gtcctatggg acgactatgg 1621 aatgagcaac cccatccatg acgccctcag gttgcaggag cttgctgaca cttgccccct 1681 cacgctaaat tgtgacagaa ttgagaacaa agggaaagtc tttgacagtg atgccataat 1741 tatcaccacc aatctggcca acccagcacc actggattat gtcaactttg aagcgtgctc 1801 gagacgcatt gatttcctcg tgtacgcaga agcccctgag gtggagaagg caaagcgcga 1861 cttcccaggt caacctgaca tgtggaagaa cgctttcagt cctgacttct cacacataaa 1921 actgtcattg gctccacagg gtggttttga caagaacggc aacaccccgc atggaaaagg 1981 ggtcatgaag accctcacca ctggctccct catcgcccga gcatcagggt tactccatga 2041 gaggctagat gaatatgaac tgcaaggccc aaccctcacc actttcaact ttgaccgcaa 2101 caagatactt gcttttagac agcttgctgc tgaaaacaag tatgggctgg tggacacaat 2161 gagagttgga aaacagctca aggatgtcaa gaccatgtca gacctcaaac aagcactcaa 2221 gaacatcgcg atcaggaagt gccagatagt gtacaatggt ggcacctaca cacttgaggc 2281 tgatggcaag ggtagtgtga aagttgacaa agtgcaaagt gccactgtgc agaccaacaa 2341 tgaactagcc ggtgccctac accacctaag gtgcgctaga atcagatact atgttaagtg 2401 cgtccaggag gcactgtatt ccatcatcca aatcgctggg gctgcatttg tcaccacgcg 2461 catcgctaag cgcatgaata tacaggatct ctggtccaag ccacagatgg aagacacaga 2521 agagatggcc aacaaagatg gttgcctaaa acccaaagat gatgaagagt ttgtcgtctc 2581 atccgacgac atcaaaactg agggcaagaa agggaagaac aagtccggcc gtggcaagaa 2641 gcacacagcc ttttcaagta aagggctcag tgatgaggag tacgatgagt acaagagaat 2701 cagagaagaa aggaatggta agtactccat agaagagtac cttcaggaca gagacaagta 2761 ctacgaggag gtggccattg ccagggcaac cgaagaggac ttctgtgaag aagaagaggc 2821 caaaatccgg cagagaattt tcagaccaac aaggaaacaa cgcaaagaag agagggcctc 2881 tctcggcttg gtcacaggct ctgaaatcag gaagagaaac ccagaagact tcaaacccaa 2941 gggaaagctg tgggctgatg atgacagaag tgttgactac aatgagaaac tcaactttga 3001 ggccccacca agcatctggt cgcggatagt caactttggt tcaggctggg gcttctgggt 3061 ctcccccagt ctgtttataa catcaaccca tgtcataccc caaggtgcaa aagagttctt 3121 cggagtctct atcaagcaaa tccagataca caagtcaggt gaattctgcc ggttgagatt 3181 cccaaagcca atcagaactg atgtgacggg catgattcta gaagaaggtg cgcccgaggg 3241 gaccgtggcc acactgctca tcaagagacc aactggagag ctcatgcctc tggcagccag 3301 aatggggacc catgcaacca tgaaaattca ggggcgtaca gttggagggc aaatgggtat 3361 gctcctgaca ggatccaacg ccaagagtat ggacctaggc acaacaccag gcgactgcgg 3421 ctgcccctac atctacaaga gggggaatga ctatgtggtc ataggagtcc atacggccgc 3481 tgcccgtgga ggaaacactg tcatatgtgc cacccagggg agtgagggag aagccacact 3541 tgaaggaggt gacagtaaag ggacatactg tggcgcacca atcttgggcc cagggagcgc 3601 tccgaagctc agtaccaaga ctaagttttg gagatcatcc acaacaccac tcccacctgg 3661 cacctacgaa ccagcctacc tcggtggcaa agaccctaga gtcaaaggtg gcccttcatt 3721 gcaacaagtt atgagggacc agctgaagcc attcacagaa cccagaggca aaccaccaag 3781 accaaatgtg ttggaagctg ccaagaaaac catcatcaat gtccttgagc aaacaattga 3841 tccaccccaa aaatggtcat ttgcgcaagc ttgcgcatcc cttgacaaaa ccacctccag 3901 cggccacccg caccacatgc ggaaaaacga ctgttggaat ggggagacct tcacaggaaa 3961 attggctgat caagcctcca aggccaacct aatgtttgaa gagggaaaga acatgactcc 4021 agtctacaca ggtgcactta aagatgagtt ggtaaagacc gataaagttt atggtaaggt 4081 caagaagagg cttctgtggg gttcagatct ggcgaccatg atacggtgcg cccgagcttt 4141 tggaggcctt atggatgaac tcaaggcaca ctgtgtcaca cttcctgtca gagttggtat 4201 gaacatgaat gaggatggcc ccatcatctt cgagaagcac tccagatata gatatcacta 4261 tgatgctgat tattcccggt gggactcaac acaacaaagg gatgtgctag cagcagcact 4321 agaaatcatg gttaagttct ctccagaacc acacctggcc cagatagttg cagaagacct 4381 cctctcccct agcgtgatgg atgtaggtga ctttcaaata tcaataagtg agggtctccc 4441 ctctggggta ccttgtacct cccagtggaa ttccatcgcc cactggctcc tcactctgtg 4501 tgcactctct gaagtcacgg acctgtcccc tgatatcatt caggccaact cccttttctc 4561 cttctatggt gatgatgaga ttgtgagcac agacataaag ttggacccag agaagctgac 4621 agcaaaactc aaggagtacg ggctgaaacc aacccgcccc gacaaaactg aaggacccct 4681 tgttatctct gaagacctgg atggcctgac attcctccgg agaactgtga cccgtgatcc 4741 agctggctgg tttggaaaat tggaacaaag ttcaattctc aggcaaatgt actggaccag 4801 gggtcccaac catgaagatc catttgaaac aatgatacca cactcccaaa gacccataca 4861 attgatgtcc ttgctgggcg aggctgcact ccacggcccg gcattctata gcaaaattag 4921 caaattagtc attgcagagt tgaaggaagg tggcatggat ttttacgtac ccagacaaga 4981 gccaatgttc agatggatga gattctcaga tctgagcacg tgggagggcg atcgcaatct 5041 ggctcccagt tttgtgaatg aagatggcgt cgagtgacgc caacccatct gatgggtccg 5101 cagccaacct cgtcccagtg gtcaacaatg aggttatggc tctggagccc gttgttggtg 5161 ccgccattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg attagaaata 5221 attttgtaca agcccctggt ggagagttta cagtatcccc tagaaacgct ccaggtgaaa 5281 tactatggag cgcgcccttg ggccctgatc taaatcccta cctatcccat ttggccagaa 5341 tgtacaatgg ttatgcaggt ggttttgaag tgcaggtact tctcgcgggg aacgcgttca 5401 ccgccgggaa ggtcatattt gcagcagtcc caccaaattt tccaactgaa ggcttgagcc 5461 ccagccaggt cactatgttc cccaatatag tagtagatgt taggcaatta gaacctgtgt 5521 tgattccctt acccgatgtt aggaataatt tctatcatta caatcaatca aatgacccca 5581 ccattaagtt aatagcaatg ttgtacacac cacttagggc taataatgct ggggatgatg 5641 tcttcacagt ttcttgccga gttctcacga gaccatcccc cgattttgat ttcatatttc 5701 tagtgccacc cacagttgag tcaagaacta aaccattctc tgtcccaatt ttaactgttg 5761 aggagatgac caattcaaga ttccccattc ctttggaaaa gttgttcacg ggtcccagca 5821 gtgcctttgt tgtccaacca caaaacggta ggtgcacgac tgatggcgtg ctcctaggca 5881 ccacccaact gtctcctgtc aacatctgca ccttcagagg agatgtcacc catatcacag 5941 gtagtcgtaa ctacagaatg aatttggctt ctcaaaattg gagcaattat gacccaacag 6001 aagaaatccc agcccctcta ggaattccag attttgtggg gaagattcaa ggcgtgctca 6061 cccaaaccac aaggacagat ggctcaacac gcggccacaa agccacagtg tacactggga 6121 gcgccgactt tgctccaaaa ctgggtagag ttcaatttga aactgacaca gaccatgatt 6181 ttgaaactaa ccaaaacaca aagttcaccc cagctggtgt catccaagat ggtagcacca 6241 cccaccgaaa tgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga agtactccta 6301 atgtgcatct ggcccccgct gtggccccca cttttccggg tgagcaactt ctcttcttca 6361 gatccaccat gcccggatgc agcgggtacc ccaacatgga tttggactgt ctgctccccc 6421 aggaatgggt gcagtacttc taccaagagg cagccccagc acaatctgat gtggctctgc 6481 taagatttgt gaatccagac acaggtaggg ttttgtttga gtgtaagctt cataaatcag 6541 gctatgttac agtggctcac actggccaac atgatttggt tatccccccc aatggttatt 6601 ttaggtttga ttcctgggtc aaccagtttt acacgcttgc ccccatggga aatggaacgg 6661 ggcgtagacg tgcactataa tggctggagc tttctttgct ggattggcat ctgatgtcct 6721 tggctctgga cttggttccc ttatcaatgc tggggctggg gccatcaacc aaaaagttga 6781 gtttgaaaat aacagaaaat tgcaacaagc atccttccaa tttagcagca atctacaaca 6841 ggcttccttt caacatgaca aagagatgct ccaagcacaa attgaggcca ccaaaaagct 6901 acaacaggaa atgatgaaag ttaagcaggc aatgctccta gagggtgggt tctctgagac 6961 agatgcagcc cgcggggcaa tcaacgcccc catgacaaaa gctttggact ggagcgggac 7021 aaggtactgg gctcccgatg ctaggacaac aacatacaat gcaggccgct tttccacccc 7081 tcaaccatcg ggggcactgc caggaagagc taatcttagg gatgctgtcc ctgctcgggg 7141 ttcctccagt aagtcttcta attcttctgc tgctacttct gtgtactcga atcaaactac 7201 ttcaacgaga cttggttcta cagctggttc tggtaccagt gtctcgagct tcccgccaac 7261 tgcaaggact aggagttggg ttgaggatca aagtaggaat ttgtcacctt tcatgagggg 7321 ggcccacaac atatcgtttg tcaccccacc atctagcaga tcctctagcc aaggcacagt 7381 ctcaaccgtg cctaaagaga ttttggactc ctggactggc gctttcaaca cgcgcaggca 7441 gccactcttc gctcacattc gtaagcgagg ggagtcacgg gcg //