Typing tool
|
Complete norovirus genomes
MF140653 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5085 ORF2: 5066..6688 ORF3: 6688..7494LOCUS MF140653 7494 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2008/GII.P4-GII.4/Rotterdam/E1300305_p14_d39 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140653 VERSION MF140653.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7494) 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 7494) 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..7494 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2008/GII.P4- GII.4/Rotterdam/E1300305_p14_d39" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="10-Mar-2008" /note="genotype: GII.P4-GII.4" CDS <1..5085 /codon_start=1 /product="ORF1" /protein_id="ATN23655.1" /translation="NDASAAAAANSNNDTAKSSSDKMFSSMAVTFKRALGARPKQPPP REIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTA FSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVE LTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRR MIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLN IINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVEL VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA NELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP DIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREVAKRIA ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN CDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF PGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH ERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELKQ ALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIR YYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATKKDGCPKPKD DEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI RKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFIT STHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTL LIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY IYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAP KLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP KPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF TGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIR CARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQR SVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNS IAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLK PTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDP SESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRW MRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5066..6688 /codon_start=1 /product="ORF2" /protein_id="ATN23656.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTDNDFETHQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRDIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6688..7494 /codon_start=1 /product="ORF3" /protein_id="ATN23657.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGRFSTPQPSGALPGRINPRTPTPARGSSSTSS NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 aacgacgctt ccgctgccgc tgctgctaac agcaacaacg acaccgcaaa atcttcaagt 61 gacaaaatgt tttctagcat ggctgtcact tttaaacgag ccctcggggc gcggcctaaa 121 cagccccccc cgagggaaat accacaaaga cccccacgac cacctactcc agaactggtc 181 aaaaagatcc ctcctccccc gcccaacgga gaggatgaag tagtggtttc ttatagtgcc 241 aaagatggcg tttccggttt acccgagctt tccaccgtca ggcaaccgga agaaaccaat 301 acggccttca gtgtccctcc actcaaccag agggaaaata gagatgctaa ggaaccactg 361 actggaacaa ttctggaaat gtgggatgga gaaatctacc attatggcct gtatgttgag 421 cgaggtcttg tgctgggtgt gcacaaacca ccagctgcca taagcctcgc caaggtcgaa 481 ctaacaccac tctccttgtt ctggagacct gtgtacactc cccagtacct catctctcca 541 gacactctca agaaattaca cggagaaacg tttccctaca cagcctttga caacaattgc 601 tatgcctttt gttgctgggt cctggatcta aatgactcgt ggctgagtag gagaatgatc 661 cagagaacaa ctggcttctt cagaccctac caagactgga ataggaaacc cctccccact 721 atggatgatt ccaaattaaa gaaggtagct aacatattcc tgtgcaccct gtcttcgcta 781 ttcaccaggc ccataaaaga cataatagga aagttaaggc ctctcaacat catcaacatc 841 ctggcttcat gtgattggac tttcgcaggc atagtggagt ccttgatact cttggcagag 901 ctctttggag tcttctggac acccccagat gtgtctgcga tgattgcccc cttactcggt 961 gatttcgagt tacaaggacc tgaggacctt gtagtggagc tcgtccctgt agtaatgggg 1021 ggaattggtc tggtgctagg attcaccaaa gagaagattg gaaaaatgtt gtcatctgct 1081 gcgtccacct tgagagcttg taaagatctc ggtgcatacg ggctagagat cctaaagtta 1141 gtcatgaagt ggttcttccc gaagaaagag gaggcaaatg aactggctat ggtgagatcc 1201 attgaggatg cagtactgga ccttgaggca attgaaaaca accatatgac caccttgctc 1261 aaagacaaag acagtctggc aacctacatg agaacccttg acctcgagga agagaaagcc 1321 agaaaactct caaccaaatc tgcttcacct gacatcgtgg gcacaatcaa cgcccttctg 1381 gcgagaatcg ccgctgcacg ctccctggtg caccgagcga aggaggagct ttccagcaga 1441 ccaagacctg tagtcttgat gatatcaggc aaaccaggga tagggaaaac ccaccttgct 1501 agggaagtgg ctaagagaat cgcagcctcc ctcacaggag accagcgtgt aggcctcatc 1561 cctcgcaatg gcgtcgatca ctgggatgcg tacaaggggg agagggtcgt cctatgggac 1621 gactatggaa tgagcaatcc catccacgac gcccttaggc tgcaagaact cgctgacact 1681 tgccccctta ctctaaattg tgacaggatt gagaataaag gaaaggtctt tgacagcgat 1741 gtcatcatta tcactactaa tctggccaac ccagcaccac tggattatgt caactttgaa 1801 gcgtgctcga ggcgcatcga tttccttgtg tatgcagaag cccccgaggt cgaaaaggcg 1861 aagcgtgact tcccgggcca acctgacatg tggaaaaacg ctttcagttc tgatttctca 1921 cacataaaat tggcactggc tccacaaggt ggctttgata agaacgggaa caccccacac 1981 gggaagggcg tcatgaagac tctcaccact ggctccctca ttgcccgggc atcagggctg 2041 ctccatgaga gattggatga gtttgaacta cagggcccag ctcttaccac cttcaacttt 2101 gaccgcaaca aagtgcttgc cttcaggcag cttgctgctg aaaacaaata tgggttgatg 2161 gacacaatga aagttgggag gcagctcaag gatgtcaaaa ccatgccaga acttaaacaa 2221 gcactcaaaa acatctcaat caagaagtgc cagattgtgt atagtggttg cacctacaca 2281 cttgagtctg atggcaaggg caatgtgaaa gttgacagag ttcagagcac ctccgtgcag 2341 accaacaatg agttggctgg cgccctgcat catctgaggt gcgccagaat caggtactat 2401 gtcaagtgtg tccaggaggc cctgtattct atcatccaga ttgctggggc tgcatttgtc 2461 actacgcgca ttatcaagcg tgtgaacatt caagacttat ggtcaaagcc acaagtggaa 2521 aacacagagg aggctaccaa aaaggacggg tgcccaaaac ccaaagatga tgaggagttc 2581 gtcatttcat ctgacgacat caaaactgag ggtaagaaag ggaagaacaa gactggccgt 2641 ggcaagaagc acacagcctt ctcaagtaaa ggtctcagtg atgaagagta tgatgagtac 2701 aagagaatta gagaggaaag gaatggcaag tactccatag aagagtacct tcaggacagg 2761 gacaaatact atgaggaggt ggccattgcc agggcgaccg aggaagactt ctgtgaagag 2821 gaggaggcca agatccggca aaggatcttc agaccaacaa ggaaacaacg caaggaagaa 2881 agagcttctc tcggtttagt cacaggttct gaaattagga aaagaaaccc agaagacttc 2941 aagcccaagg ggaaactatg ggctgacgat gacagaagtg tggactacaa tgagaaactc 3001 agttttgagg ccccaccaag catttggtca aggatagtca actttggttc aggttggggc 3061 ttctgggtct cccctagcct gttcataaca tcaacccacg tcatacccca gggcgcgaag 3121 gagttctttg gggtccccat caaacaaatt caggtacaca agtcaggcga attctgtcgc 3181 ttgaggttcc caaaaccaat caggactgat gtgactggca tgatcctgga agaaggtgcg 3241 cccgaaggca ccgtggtcac actactcatc aaaaggtcta ctggagaact catgccccta 3301 gcagccagaa tggggaccca tgcaaccatg aaaattcaag ggcgcactgt tggaggtcag 3361 atgggcatgc ttctgacagg atccaacgcc aaaagcatgg atctaggcac cacaccaggt 3421 gattgcggct gtccctacat ctacaagaga ggaaatgact atgtggtcat tggagtccac 3481 acggctgccg ctcgtggggg aaacactgtc atatgtgcca cccagggggg cgagggggaa 3541 gctacacttg aaggtggtga cagtaaggga acatactgtg gtgcaccaat cctaggccca 3601 gggagtgccc cgaaacttag caccaaaacc aaattctgga gatcatccac agcaccactc 3661 ccacctggca cctatgaacc agcctacctt ggtggcaagg accccagagt caagggtggc 3721 ccttcgttgc agcaagtcat gagggaccag ctgaaaccat ttacagagcc caggggtaag 3781 ccaccaaagc caagtgtgtt agaagctgcc aagaaaacca tcatcaatgt ccttgaacaa 3841 acaattgacc cacctgagaa gtggtcgttc gcacaagctt gcgcgtccct tgacaagacc 3901 acttctagcg gccatccgca ccatatgcgg aaaaacgact gctggaacgg ggagtccttc 3961 acaggcaagc tggcggacca ggcttccaag gccaacctga tgtttgaaga agggaagaac 4021 atgaccccag tctacacagg tgcacttaag gatgaattag tcaaaactga caaaatttat 4081 ggcaagatca agaagaggct tctctggggc tcggatttag caaccatgat ccggtgcgct 4141 cgagcattcg gaggcctaat ggatgaactc aaagcgcact gtgtcacact tcctatcaga 4201 gttggtatga atatgaatga ggatggcccc atcatcttcg agaaacattc caggtacaga 4261 taccactatg atgctgatta ctctcggtgg gattcaacac aacagagaag cgtgctggca 4321 gctgctctag aaatcatggt taaattctcc tcagaaccac atttggccca ggtagtcgca 4381 gaagaccttc tttcccctag cgtggtggat gtgggtgact tcacaatatc aatcaacgag 4441 ggtcttccct ctggggtgcc ctgcacctcc caatggaact ccatcgccca ctggcttctc 4501 actctctgtg cactctccga agttacaaat ttgtccccag acatcataca ggctaattct 4561 ctcttctcct tctatggtga tgatgaaatt gttagtacag acataaaatt agacccagag 4621 aagttgacag caaagcttaa ggaatatgga ttgaagccaa cccgccctga caaaactgaa 4681 ggacctcttg ttatttctga agacttagat ggtttgactt tcctgcggag aactgtgacc 4741 cgcgacccag ctggttggtt tggaaaactg gagcagagct caatactcag gcaaatgtac 4801 tggactaggg gccccaacca tgaagatcca tctgaatcaa tgattccaca ctctcagaga 4861 cccatacaat tgatgtcctt actgggagag gccgcactcc acggcccaac attctacagt 4921 aaaatcagca aattagtcat tgcagagcta aaagaaggtg gtatggattt ttacgtgccc 4981 aggcaagagc caatgttcag atggatgaga ttctcagatc tgagcacgtg ggagggcgat 5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg aatgacgcca acccatctga 5101 tgggtccgca gccaacctcg tcccagaggt cagcaatgag gttatggctt tggagcccgt 5161 tgtcggtgcc gctattgcgg cgcctgtagc gggccaacaa aatgtaattg acccctggat 5221 tagaaataat tttgtacaag cccctggtgg agagttcaca gtatccccta gaaacgctcc 5281 aggtgaaata ctatggagcg cgcccttagg ccctgatctg aatccctacc tatctcattt 5341 ggccagaatg tataatggtt acgcgggtgg ctttgaagtg caggtgatcc tcgcggggaa 5401 cgcgttcacc gccggaaaaa ttatatttgc agcagtccca ccaaattttc caactgaagg 5461 cctgagtccc agccaggtca ctatgttccc ccacataata gtggatgtta ggcaattgga 5521 acctgtgctg atccctttac ctgatgttag gaataacttc tatcactata atcagtcaaa 5581 tgattctacc attaaattga tagcaatgct gtatacacca cttagggcca ataatgctgg 5641 ggaagatgtc ttcacagtct cttgtcgagt cctcacgagg ccgtcccctg attttgattt 5701 tatatttttg gtgccaccca cagttgagtc aagaactaaa ccatttactg tcccaatctt 5761 aactgttgaa gaaatgacca attcaagatt ccccattcct ttggaaaagt tgttcacggg 5821 tcccagcggt gcctttgttg tccaaccaca aaatggcagg tgcacgactg atggcgtgct 5881 cttaggcacc acccaactgt ctcctgtcaa catctgcacc ttcagagggg atgtcaccca 5941 cattgctggt tctcgtaatt acacaatgaa cttggcatct ctaaattgga acaattatga 6001 cccaacagag gaaattccag cccctctggg aactccagat ttcgtgggaa agatccaagg 6061 tgtgctcact caaaccacaa agggagatgg ctcgacccgt ggccataaag ctacagttta 6121 cactgggagt gcccccttta ctccaaagct gggcagtgtc caattcagta ctgatacaga 6181 caatgatttt gaaactcacc aaaacacaaa attcacccca gtcggtgtca tccaggatgg 6241 tagcaccacc caccgaaatg aaccccaaca atgggtgctc ccaagttatt caggtagaga 6301 tatccataat gtacacctag cccctgctgt agcccccact tttccgggtg aacaacttct 6361 tttcttcagg tccaccatgc ccggatgcag cgggtatccc aacatggatt tggattgcct 6421 actcccccag gagtgggtgc agcacttcta ccaagaggca gctccagcac aatctgatgt 6481 ggccctattg agatttgtga atccagacac aggtagggtc ctgtttgagt gcaaacttca 6541 taaatcaggc tatgtcacag tggctcacac cggccagcat gatttggtca tcccccccaa 6601 tggctatttt aggtttgatt cctgggttaa tcaattctac acacttgccc ccatgggaaa 6661 tggaacgggg cgtagacgtg ctttataatg gctggagctt tctttgctgg attggcatct 6721 gatgtccttg gctctggact tggttcccta atcaatgctg gggctggggc tatcaaccaa 6781 aagattgatt ttgaaaataa cagaaaattg cagcaagctt ccttccagtt tagcagtaat 6841 ctacaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat tgaggccact 6901 aaaaagttgc aacaggaaat gatgaaagtc aaacaggcaa tgctcttaga aggtggattc 6961 tctgaaacag atgcagcccg tggggcaatc aacgccccca tgacaaaggc tttggactgg 7021 agcggaacaa ggtactgggc ccctgatgct aggattacaa catacaatgc aggtcgcttt 7081 tccacccctc aaccttcggg ggcactgcca ggaagaatca atcccaggac tcctaccccc 7141 gctcggggct cctccagcac atcttctaat gcttctactg ctacttctat atattcaaat 7201 caaactgttt caacgagact tggttctaca gctggttctg gcaccaatgt ctcgagtctc 7261 ccgtcaactg caaggactag gagttgggtt gaggatcaaa acagaaattt gtcacctttc 7321 atgagggggg ctcacaacat atcgtttgtc accccaccat ctagcagatc ctctagccaa 7381 ggcacagtct caaccgtgcc taaagaagtt ttggactcct ggactggcgc tttcaacacg 7441 cgcaggcagc ctctcttcgc tcacattcgt aggcgagggg agtcacgggt gtaa //