Typing tool
|
Complete norovirus genomes
MH218689 | GII.17 | ||
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GII.P17 |
ORF1: 5..5113 ORF2: 5094..6716 ORF3: 6716..7495LOCUS MH218689 7562 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_231_20_01_2016, complete genome. ACCESSION MH218689 VERSION MH218689.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7562) AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H., Hartley,J., Harris,K. and Breuer,J. TITLE Norovirus transmission dynamics in a paediatric hospital using full genome sequences JOURNAL Clin. Infect. Dis. (2018) In press PUBMED 29800111 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7562) AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H., Hartley,J., Harris,K. and Breuer,J. TITLE Direct Submission JOURNAL Submitted (17-APR-2018) Division of Infection and Immunity, University College London, 90 Gower St, London, London WC1E 6BT, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 10.1 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7562 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_231_20_01_2016" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="20-Jan-2016" /note="genotype: GII.P17_GII.17" gene 5..5113 /gene="ORF1" CDS 5..5113 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17725.1" /translation="MKMASNDASAAVAGKNNNNDKEKSSSDSLFSNMTVTFKKALGAR PKQPPPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPKIVYKVGEGVSGLPNLTTVA QPDAQNTAYSVPPLSQREAGEAKEPLPGSILEMWDGEIYHYGLYVERGHVLGVHKPPA AISLAKIELTPLSLYWRVVYTPQYLIAPETLKNLSGETFPYTAFDNNCYAFCCWVLDL NDSWLSRRMIQRTTGFFRPYQEWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDI IGKLRPLNILNILATCDWTFAGIVESMILLAELFGVFWTPPDVSAMIAPLLGDYEMQG PEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKW FFPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARK LSTKSASPDIVGTINSLLARIAAARSLVHKAKEELSSRQRPVVVMISGKPGIGKTHLA RELAKKVASTLSGDQRIGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELA DTCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPD IEKAKRDFPGQPDMWKDHYRSDFTHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLI ARASGLLHERMDEFELQGPDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSV KTLDELKQAIKNISIKKCQIVYNGCTYTIESDGKNKVVVEKVQNATVQTNNELVGALH HLRTARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVKRMNISNLWSKPPIEEGDEPEDE GGCPRPRDEGDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREE RNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATL GLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFW VSPSLFITSTHVIPKGTSEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGA PEGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTT PGDCGCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAP ILGPGNSPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPF TEPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKN DYWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWG SDLSTMIRCARAFGGLMDELKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYS RWDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGV PCTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTA KLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWT RGPNHEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVP RQESMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..1003 /gene="ORF1" /product="p48" mat_peptide 1004..2101 /gene="ORF1" /product="NTPase" mat_peptide 2102..2638 /gene="ORF1" /product="p22" mat_peptide 2639..3037 /gene="ORF1" /product="VPg" mat_peptide 3038..3580 /gene="ORF1" /product="Pro" mat_peptide 3581..5110 /gene="ORF1" /product="RdRp" gene 5094..6716 /gene="ORF2" CDS 5094..6716 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17726.1" /translation="MKMASNDAAPSNDGAAGLVPEDNNETLPLEPVAGAAIAAPVTGQ NNIIDPWIRTNFVQAPNGEFTVSARNAPGEVLLNLELGPDLNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD VRNTFFHYNNQPTGRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFQFTYLVPP SVESKTKPFTLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT QLLPSGICAFRGRVTAEPSRSDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGFVFGV ASQRNVGSDAPGSTRAHEVVISTYSPQFVPKLGSVNFKISSDDDFQLQPTKFTPVAIN EEDDDHPFRQWELPDYSGVLTLNMNLAPPVAPNFPGEQLLFFRSFVPCAGGYNQGIVD CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLV VPANGYFRFDSWVNQFYSLAPMGTGNGRRRAQ" gene 6716..7495 /gene="ORF3" CDS 6716..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17727.1" /translation="MAGALIAGLAGDMLTSSVGSLVNAGANAINQRIDFENNKQLQFA SFQHDKEMLQAQVKATKQLQSEMIAIKQGVLAAGGFSPTDAARGAIGAPMTKVLDWSG TRYWAPNSTKTTGYSGQFTSSPVHMPSPNVPQSKPAKPRSIAPSSSSSSVYSMSTQST HLTSGSSSNASSASTKLTNLSSGSSQNRTVEWVNQQRSLSPFMSGALNISHVTPPSSR ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gctggcaaaa acaacaacaa 61 cgacaaggag aaatcttcaa gtgacagctt gttttccaac atgactgtta cttttaagaa 121 agccctcggg gcgcggccta aacaaccgcc cccgggagaa acaaaacaaa tacaaaaacc 181 accaaggcca ccgacaccgg aattggtgaa gagaataccc ccacccccac ccaatggcga 241 ggatgaacca aagatagtgt ataaggtggg agaaggtgtg tctgggctgc ccaacctaac 301 gactgtggca cagcctgacg cacaaaacac agcttatagt gttcccccac ttagccagag 361 agaagccggc gaagctaaag aaccgctgcc tggctccatt ctggaaatgt gggatggtga 421 gatctaccac tatgggctgt atgttgagcg ggggcatgta ctcggagtgc ataaaccacc 481 tgctgcaata agtcttgcca aaattgaatt aacacctctg tctctctact ggagagtggt 541 ttacactccc cagtatttga tagctccaga aactcttaag aacttgagtg gggagacttt 601 cccatacacg gcctttgaca acaactgtta tgccttctgt tgttgggttc tagacctcaa 661 cgactcctgg ctcagcagga gaatgatcca aagaacaact ggcttcttca gaccgtatca 721 ggagtggaac agaaaacctt taccaaccat ggatgaaccg aaaatcaaga aggccgcgaa 781 tgctgttctg tgtgctctct cctcactctt cactagaccc atcaaggaca tcattggaaa 841 gcttagacca ctgaatattc tcaatatact ggcaacttgt gactggactt ttgcaggcat 901 agtggaatct atgatccttc ttgctgaact ctttggggtg ttctggaccc ccccagatgt 961 gtctgcgatg attgctccct tactcggtga ctacgagatg caaggccccg aagacctagc 1021 cgtggaactc gtgcccgtgg taatgggagg aataggtttg gtgttaggat tcaccaagga 1081 aaagatcggc aagatgcttt catcagctgc gaccacgctt agggcctgta aggatctagg 1141 atcttatgga ttggagatac tcaaattggt catgaagtgg ttcttcccca agaaggagga 1201 ggctaatgaa ctagccatgg taagggccat tgaggacgca gtcctggatt tggaggcaat 1261 agaaaacaat cacatgacca cccttctcaa ggataaagac agcttggcca catacatgag 1321 aactcttgac ttggaagaag agaaagcaag gaaactgtcg accaaatcgg cgtcacctga 1381 catcgtgggt acaataaact cattattggc aaggatagca gccgccaggt cactagtcca 1441 caaggctaag gaggagctct cgagcagaca gagacctgtt gttgtaatga tatcaggtaa 1501 accgggtata ggaaagaccc atctggccag agagctagcc aagaaagttg cgtcaacact 1561 gtcaggcgac caaaggattg gactgatacc taggaatggc gtcgaccatt gggacgccta 1621 caagggagaa agggtggttc tgtgggatga ttatggtatg agcaacccta tacaggacgc 1681 actgaggctc caagaattgg ctgacacctg tcctctgacc ctaaattgtg acaggattga 1741 aaacaaagga aaagtgttcg acagtgatgc cataattata acaaccaacc ttgcaaaccc 1801 agcaccacta gattatgtca actttgaggc ctgctctaga cgcatagact tcttggtgta 1861 tgcagacgca cctgacatag agaaggctaa gcgtgatttc cctggccaac cagatatgtg 1921 gaaggaccat tacagatcag acttcacaca catcaaactt cagctggcac cacagggagg 1981 ttttgataaa aatggcaaca ccccacacgg caaaggtgtg gtaaagtctc tgacgattgg 2041 ttctctgatc gccagggctt ctggtttact ccacgagaga atggatgaat tcgagctcca 2101 gggccctgac ttgccaacct tcaactttga ccgcaacaaa gtcgccgcct tcagacaatt 2161 agcagctgaa aacaaatatg gtctcatgga cacactgagg gtcggcaacc aactgaaaag 2221 tgtcaagacc ctggatgagc tgaagcaggc cataaagaac atcagtatca agaagtgcca 2281 gatagtgtat aatggatgca cctataccat agaatctgat gggaagaaca aggttgtggt 2341 tgaaaaggtg caaaatgcaa cagttcaaac taacaatgaa cttgtagggg cactccacca 2401 cctgagaact gcaaggataa gatattatgt taaatgcttc caagaagcca tttattctct 2461 actccaaatt gctggtgcag ccttcgtcac ctcacgcatc gtgaagcgca tgaacatctc 2521 aaacctctgg tcgaagccac ccatcgagga gggtgatgag cctgaagatg aaggaggatg 2581 ccccaggccc agggatgaag gtgacctcac tattgactct agggacatta aagtggaagg 2641 gaaaaagggc aagaacaaat ctggccgggg caagaaacat acagccttct catccaaggg 2701 tctcagtgat gaagagtacg acgagtacaa gagaatcaga gaggaaagga atggcaaata 2761 ctcaatagag gaatacctcc aagataggga cagatactat gaagagcttg ccattgctaa 2821 agccactgag gaggacttct gtgaagagga ggaaatcaaa attcgccaga gaatcttccg 2881 acccaccagg aagcagcgga aagaggagag ggccacgctt gggcttgtca caggatcgga 2941 aatcagaaag aggaatccag atgactttaa accaaaagga aaattgtggg ctgatgacaa 3001 caggagcgtg gattacaatg agaggataga ttttgaggct cccccgagtg tttggtctag 3061 gatagtcaac tttggcacag gctggggatt ctgggtttct ccaagtctct ttataacttc 3121 aacacatgtc ataccaaaag gaaccagtga ggcctttgga gtgcccataa accaaatcca 3181 aattcacaaa tctggagaat tttgccgctt gcggtttcca aaaccaatca gaccagacgt 3241 gagtggaatg atcttggaag agggtgcccc tgaaggcact gttgtgtcta ttctcattaa 3301 aaggacgaca ggggagctga tgcctctcgc agtcagaatg gggactcatg ccacaatgaa 3361 aatccagggc agaacggtgg gtggtcagat gggtatgctt ctcactggct caaatgctaa 3421 aagcatggat ctaggcacaa cgccaggtga ctgcgggtgt ccatacatat acaaaagggg 3481 caatgacttc gtggtcattg gggtgcacac tgcagcagca cgtggaggca acacggtcat 3541 atgtgccaca caaggaagtg aaggtgaagc cactcttgaa ggaggtgaca acaagggtac 3601 ttactgtgga gcccccattt tgggacctgg caattcacca aaattgagca caaaaacaaa 3661 attctggaga tcttctaacg caccgcttcc cccaggtact tatgaaccag catatcttgg 3721 tgggagagac ccgcgtgtga agggaggccc atctctgcaa caagttatga gagatcaact 3781 taaacctttt acagagccca gagggaagcc accaaaccca aatgtcctag agtcagcaaa 3841 gaagactatc atcaatgttc tggaacaaac cattgacccc cctcaaaagt ggtcatatgc 3901 tcaagcttgt gcatccctcg acaagacaac ttccagtggg tacccacacc acgtccggaa 3961 gaatgactat tggagtggtg aatccttcac agggaaactt gcagaccagg cttcaaaagc 4021 aaatctcatg tatgaggaag gcaaacacat gcaaccagtc tacaccgcag cactcaaaga 4081 cgagctcgtg aaaactgaca aaatttatgg caagatcaag aaaagactcc tgtggggttc 4141 tgacctctcc accatgattc gatgcgccag agcgtttggt ggtctcatgg atgagctcaa 4201 agcaaattgt atcacactcc ctatcagagt tggtatgaat atgaatgaag atggccccat 4261 aatatttgag aaacactcca ggtacaggta ccactatgac gctgattact cccgttggga 4321 ctccacacaa cagcgggcag tgctggaagc agcacttgaa atcatggtga gattttctgc 4381 tgagccacag ctggcacaaa tagtggcaga ggacctgcta tcaccaagtg tggttgatgt 4441 gggcgatttc aaaatcgcta tcaatgaagg tttaccatca ggtgtgcctt gcacctcaca 4501 atggaattct attgctcact ggttactcac cctgtgtgcc ctttctgaag tgactggatt 4561 aggccctgac atcatacaag ccaactccat gtactctttc tatggtgatg atgagattgt 4621 gagcacagat ataaaattgg acccagagaa attgactgca aaactcaaag aatatggcct 4681 taaacccact cggcctgaca aaactgaggg gccgctggtg attagtgaag acctgaatgg 4741 gttgactttc ctccgccgaa cagtcacccg tgatccagca ggttggtttg gaaagttgga 4801 ccaaaactcc atcctcaggc aattgtactg gacaagagga cccaaccatg aagaccccag 4861 tgagaccatg ataccacacg cacagaggcc tgtgcagctc atggcactac taggagaatc 4921 ctccctacat ggaccctcat tttacagcaa ggtcagcaaa ctggtcatat ctgaacttaa 4981 agagggggga atggattttt atgtgcccag acaagagtca atgttcaggt ggatgaggtt 5041 ctcagatcta agcacatggg agggcgatcg caatctggct cccagttttg tgaatgaaga 5101 tggcgtcgaa tgacgccgct ccatctaatg atggtgctgc tggtctcgta ccagaggaca 5161 acaacgagac ccttccccta gaaccagttg cgggcgcagc tatagccgca cccgtcactg 5221 gccaaaacaa cataattgac ccctggatta gaacaaattt tgtgcaagca ccaaatggag 5281 agtttacagt gtcagccaga aacgctcctg gagaagtttt attaaatcta gagttgggcc 5341 ctgatttaaa cccttattta gctcatttgt caaggatgta caatgggtat gctggtggag 5401 tggaagttca ggttctcctg gcagggaacg cgttcactgc cggaaagatc ctcttcgccg 5461 ccgtcccgcc aaatttccca gtggaattct taagcccagc ccagattact atgctcccac 5521 atttaatagt agatgtcagg actcttgaac caattatgat cccactccct gatgttcgga 5581 atacattctt ccattataac aatcagccca ccggccgtat gagattagtg gctatgctct 5641 atacccctct tagatctaat ggctcaggtg atgatgtctt tactgtttct tgcagggttt 5701 tgactaggcc cactcctgat tttcagttca cttatttagt gccaccttct gttgaatcta 5761 agaccaagcc ttttacctta cctattttaa ccctttctga gctcacaaat tcgaggttcc 5821 cagtccccat cgattcgctt ttcaccgccc agaataatgt gttgcaggtg cagtgtcaaa 5881 atggcaggtg cacacttgat ggtgagttac aaggcacaac ccagttgctc ccatctggca 5941 tctgtgcatt cagaggacgg gtgacagcag aacctagccg tagtgacagg tggcacatgc 6001 aactgcaaaa tctcaatggc acaacatatg acccaactga tgatgtgcca gccccgctgg 6061 gtacacctga cttcaagggc ttcgtgtttg gggtggcaag tcaaagaaat gtgggtagtg 6121 atgcgcctgg ctcaaccagg gctcatgagg tggtgatttc aacctatagt ccccaatttg 6181 tccccaaatt aggttctgtc aattttaaaa ttagcagtga tgatgatttc caattgcagc 6241 cgacaaaatt cacaccagtg gccatcaatg aagaagatga tgaccacccg ttcagacaat 6301 gggaactacc agactattca ggggtgctta ccttgaatat gaaccttgcc cccccggttg 6361 cgccaaattt ccctggtgaa caattattat tcttcagatc ttttgtgcca tgcgcaggag 6421 gttataacca aggtattgta gattgtctta ttccccaaga atggatccaa catttctatc 6481 aggaatcagc gccctcccag tcagacgtgg ctctaatcag gtatgtcaac cccgacacgg 6541 ggcgcacact gtttgaagca aaattgcaca gatctggtta cattactgtg gctcactctg 6601 gagactatcc tcttgttgtt ccggctaatg gatactttag atttgattct tgggtaaatc 6661 agttttactc actcgcccca atgggaactg ggaatgggcg aaggagggct cagtaatggc 6721 tggagctttg attgcaggat tggcaggcga catgctcacg tcatctgtgg gctccctggt 6781 gaacgcaggg gcaaacgcca tcaaccaaag gatagatttt gaaaacaaca aacaactcca 6841 gtttgcttcc tttcagcatg ataaagagat gctccaagcg caggtgaagg caaccaagca 6901 gctgcaatct gaaatgatag ccataaaaca aggggtttta gccgcaggcg gcttttcccc 6961 cactgatgca gcaagggggg ccattggtgc acccatgaca aaggtgcttg attggtctgg 7021 cactcgatac tgggcaccca attccacaaa gacaactggt tattcgggac aattcacctc 7081 ttcacctgtg catatgccta gcccaaatgt tccacaatca aaacctgcaa agcctaggtc 7141 tatagctcct tcctcttctt ctagtagtgt ctatagcatg tctactcaat caactcatct 7201 aacatctggc tcctctagta atgcttcttc tgcctccaca aaattaacaa acttaagctc 7261 tggctcctct caaaacagaa cagtagagtg ggtgaaccaa cagaggagtc ttagcccttt 7321 catgagtggc gcactcaata tctcacatgt cacaccaccc tcaagtaggg cttccagttc 7381 tgggacggtc tcaaccgtgc ccaaggaagt tttggactcc tggacgtctg cgtttaacac 7441 acacagacag ccgctcttcg cacacctcag agtgaggggg gagtcacgtg tttagtgaaa 7501 agaaataatt ggctataatg tgatttcttt aataaatttg gctaatttgt atcttttaaa 7561 aa //