Typing tool
|
Complete norovirus genomes
MH218618 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218618 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_147-2_10_12_2015, complete genome. ACCESSION MH218618 VERSION MH218618.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7548) 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 7548) 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..7548 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_147-2_10_12_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="10-Dec-2015" /note="genotype: GII.P21_GII.3" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17512.1" /translation="MKMASNDASAAAAANSNDDNAKSSSDGVFSNMAVSFKRALGARS KQPPPKDKPPRPPRPPTPELVKSIPPPPPNGEDEPIISYNAEKGVSGLPELTTVTQLE ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANIVLCALSALFTRPIKDIIGK LKPLNVLNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKVGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTNVQTNNELSGALHHLK CARIRYYVKCVQEALYSILQIAGAAFITTRIARRTNIQNLWSKPQAENLEETNNEEGC PKPKNDEEFVISSNDITTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKRTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGEAFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="ORF1" /product="p48" mat_peptide 995..2092 /gene="ORF1" /product="NTPase" mat_peptide 2093..2629 /gene="ORF1" /product="p22" mat_peptide 2630..3028 /gene="ORF1" /product="VPg" mat_peptide 3029..3571 /gene="ORF1" /product="Pro" mat_peptide 3572..5101 /gene="ORF1" /product="RdRp" gene 5085..6731 /gene="ORF2" CDS 5085..6731 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17513.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANSSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGST QLLPSQICAFRGVLIGSTSRASDQADTATPRSFNYYWHIQLDNLNGTPYDPAEDIPCP LGIPDFQGRVFGVASQRNPDTTTRAHEAKIDTTSGRFTPKLGSLEISTESHDFDENEP TRFTPVGIGVDNEAHFKQWALPNYAGQISHNMNLAPAVAPNFPGEQLLFFRSQLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTVA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17514.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSLSGGFTNQTVHRPTPNFRTGQSPKPAPSSGSSVRSNSTQVTNLSS HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacgacga 61 caacgcaaaa tcttcaagtg acggagtatt ttctaatatg gccgtctctt ttaaacgggc 121 cctcggggcg cggtctaaac agccgccccc gaaggacaaa ccaccaaggc ccccaagacc 181 acccacacca gaattggtta aatcaatccc ccccccccca cccaacgggg aggacgaacc 241 aatcatttct tacaacgctg aaaagggtgt ctctggtttg cctgaactta caactgtcac 301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag 361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggatgggg agatctacca 421 ttatggctta tacgtggaac gagggttagt gctaggtgta cacaaaccac cagcagccat 481 cagccttgct aaggttgagc tgaccccttt gtccttgtat tggagaccag tgtacacccc 541 acaatatctc atttcccctg acactctcag aaagttgcat ggggagacgt tcccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggta cttgatttga acgactcatg 661 gctgagcaga aggatgatac aaaggacaac aggattcttc cgaccctacc aggactggaa 721 taggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atattgtcct 781 ctgtgccctc tcagcattgt ttacaagacc aattaaggac attattggga agttgaaacc 841 cctaaacgtc ctcaacatcc tagccacatg tgattggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tgtttggagt tttctggaca cccccagatg tgtctgcaat 961 gatcgctccc ttactgggtg attacgagct gcagggaccc gaggacctcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgttggga ttcaccaaag agaaagtcgg 1081 caaaatgctt tcatcagctg cctcaaccct tagggcatgc aaagatctcg gtgcatatgg 1141 gttggagatc ctcaagttgg tcatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 actggcaatg gtgagatcca ttgaggatgc agtgctagat cttgaggcca ttgagaacaa 1261 ccatatgaca gctctactca aggacaaaga cagccttgca acctacatga ggactcttga 1321 catggaggag gagaaggcga ggaaactttc caccaagtct gcctcgccgg acattgtggg 1381 cacaataaat gccttactat caaggattgc agctgcccga tctctagtgc acagggccaa 1441 ggaggagctg tcaagcaggc cccgaccggt cgtcgtgatg atttcaggga gaccaggtat 1501 aggaaaaacc catttagcta gagagttggc aaagaagatc gcctcctcac tcacaggtga 1561 ccagagggtg ggtctcatcc cacgcaacgg agttgaccac tgggatgcat acaaaggtga 1621 aagagttgtt ctctgggacg actacgggat gagcaaccct atccacgacg ccctcagact 1681 tcaggagctc gctgatacct gtcctcttac actcaactgt gacaggattg agaacaaagg 1741 taaagtcttt gacagtgacg ccataataat aaccaccaat ttagccaacc cagcgccact 1801 ggattatgtc aactttgaag cctgctcaag acgcatagac ttcctcgtct atgctgatgc 1861 ccctgaggtt gagaaggcta aacgggactt tccaggccaa ccagacatgt ggaaagacac 1921 cttcaaacct gatttctcac acataaagct gacattagct ccgcaaggag gttttgataa 1981 gaatggtaac actcctcatg ggaagggtgt catgaagacc ctcactgcca gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac 2101 ccccacaaca ttcaacttcg accgcaataa ggtgcttgct tttaggcaac ttgctgctga 2161 aaacaagtac ggtcttgttg acacaatgag agtcggatca cagctcaaga atgtcaagac 2221 catgacagaa cttaagcagg ctctcaaaaa catctcagtc aagaagtgtc agcttgtgta 2281 tggtggtggc acgtacacac ttgaatctga tggcaaaggc aatgtgcatg tcgagaaggt 2341 gaacaacacc aatgtgcaaa ctaacaacga gctctccgga gctttgcacc atctcaagtg 2401 tgccagaatc aggtactatg ttaagtgtgt ccaggaagct ctctactcca tcttgcaaat 2461 tgccggagct gcattcatca ctacgcgcat tgcaaggcgc acaaacatac aaaacctctg 2521 gtctaaacca caagcagaaa atctggagga gactaacaac gaggagggct gtccaaaacc 2581 taaaaatgat gaagagtttg tcatctcctc taatgacatc acaaccgagg gcaagaaagg 2641 aaagaacaag actggccgtg gcaagaagca cacagccttt tccagcaaag gactcagtga 2701 cgaggagtac gatgagtata aaagaatcag agaagagaga aatggcaagt actccataga 2761 ggaataccta caggacagag acaaatatta tgaggaggtg gccatagcca gggcaactga 2821 ggaagacttc tgtgaagaag aggaggcaaa aatccggcaa aggatattta gaccaacaag 2881 gaaacaacgc aaagaggaaa gggcctctct tggtttggtt acaggttctg agatcaggaa 2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gccgatgatg acaggagcgt 3001 tgactacaat gagaaactta gttttgaggc tccaccaagc atttggtcac gaatagtcaa 3061 ctttggctca ggatggggtt tttgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccaa ggtgcacagg agttctttgg agtgcccatc aaacaaatac aaattcacaa 3181 gtcaggtgag ttctgccggc tcaggttccc aaaaccaatc aggacagatg tcacaggtat 3241 gatcttggag gaaggtgctc cagaaggcac cgttgccacg cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccagaat gggcacccac gcgaccatga aaatccaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agaatatgga 3421 cttgggcaca actcctggcg attgtggttg tccctatatc tacaagagag ggaatgacta 3481 cgtggtcatt ggagtccaca ctgccgccgc tcgtggagga aacactgtca tctgtgcaac 3541 ccaaggaagc gagggtgagg ccacgttaga aggtggtgac aacaagggaa cttattgtgg 3601 agcaccaata ttaggtcctg gaaatgcacc caaactcagc accaaaacca aattctggag 3661 gtcttccacc acccctttgc cgcccggaac ctacgagcca gcttatctgg gcggcaagga 3721 tcctagagta aaaggtggcc cctcactgca acaggttatg agggaccaac taaaaccatt 3781 cactgagccc agaggtaaac cacccaaacc aagcgtgcta gaagctgcca agaggactat 3841 aatcaatgtg cttgagcaaa caatagaccc accccaaaaa tggacatacg cacaggcgtg 3901 tgcatcacta gacaagacca cttctagcgg ccaccctcac cacatgcgga agaacgattg 3961 ctggaatggg gaggccttca caggaaaact ggcagaccaa gcgtcaaagg ctaacctaat 4021 gtttgaggaa ggaaagaaca tgaccccagt ttacacagga gctctaaaag atgagctagt 4081 caagactgat aagatctatg gtaaaatcaa gaaaagactc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgaactca aggcccattg 4201 cgtcacgcta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaaacattcc agatataaat accattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagcg gtgctggctg cagccctgga aataatggtc aaattctcac cagaacccca 4381 tctggcccag gtggttgcag aggacctctt gtcccccagt gtgatggatg tgggtgattt 4441 caagatatca atcaacgagg gattaccctc tggtgttccc tgcacctcac aatggaactc 4501 catcgcccac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaactg gacccagaga aactaacaac aaaattgaag gaatacgggc tgaaaccaac 4681 ccgccctgat aaaacagaag gacccttaat tatctctgaa gacttggatg gcctgacctt 4741 cttacgtaga acggtgaccc gtgatccggc cgggtggttt ggcaaactgg accaaagttc 4801 aatactcagg cagatgtact ggaccaaggg accaaaccat ggggatccct ccgaaacaat 4861 gataccacac tcccaaagac ccatacaact gatgtcattg ttgggtgaag ctgcgttgca 4921 tggtccatcg ttctacagca aaatcagcaa attggtcatc tcagaattga aagagggtgg 4981 aatggatttt tacgtgccca gacaagagcc aatgttcagg tggatgagat tctcagattt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc gcccctcact ggtcagcaaa 5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag 5281 tgtcccctag aaattcccct ggtgaagttc ttcttaattt ggaattgggc ccagaaataa 5341 acccctattt ggcccatctt gccagaatgt ataatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct ggctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc 5461 ccaactttcc aattgacaac ctaagtgcgg cacagatcac aatgtgtcca catgtgattg 5521 tggatgtcag gcagctggaa ccagtcaacc tcccgatgcc tgacgttcgc aacaacttct 5581 ttcattacaa tcaagggtct gattcgagat tgcgcctaat tgcaatgcta tatacacctc 5641 ttagggcaaa cagttctgga gatgatgttt ttactgtgtc ttgcagagtg ctaactagac 5701 ctagccctga tttttcattt aatttccttg tgccacctac tgtggagtca aagacaaaac 5761 cattttcact ccctattctg actatctctg aaatgtccaa ttccaggttc ccagtaccaa 5821 ttgattctct gcacactagt cccactgaga atattgttgt ccagtgtcag aatgggcgcg 5881 ttacccttga tggtgagctg atgggctcca cccaactctt acctagccaa atttgtgctt 5941 tcaggggcgt gctcattgga tcaacaagca gggccagtga ccaggccgac acagcaaccc 6001 ctagatcatt taattattat tggcatatac aattggataa tctaaatgga actccttatg 6061 accctgcaga agatatacca tgccccttag ggataccaga tttccaaggc agagtctttg 6121 gcgtggccag ccagagaaat cctgacacca caactagggc acatgaagca aagatagaca 6181 caacatctgg ccgtttcacc cctaaactag gctcactaga gatttccact gagtctcatg 6241 attttgatga aaacgaacca acaagattca ccccagttgg cattggggtt gacaatgagg 6301 cacactttaa acaatgggct cttcccaact atgctggcca gatctcccac aacatgaact 6361 tagccccagc tgttgccccc aactttcctg gtgagcaact ccttttcttc cgctcacagt 6421 tgccatcctc tggtgggcgg tccaacggga tcctggactg cctggtcccc caagaatggg 6481 tacagcattt ctaccaagaa tcagccccct cccaatctca agtggccctg gttaggtatg 6541 tcaaccctga cactggcaga gtgttatttg aggccaagct gcacaaatta ggtttcatga 6601 ctgtagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg 6661 aatcttgggt gaaccccttt tatacacttg cccccatggg aacagggaat gggcgtagaa 6721 ggattcaata atggctggag cttttatagc aggattggct ggtgatatgc tcacaaacac 6781 tgtagggtct ttagttaatg caggggctaa tgctattaat cagacaattg attttgaaaa 6841 taataaatat ttgcagaatg cttcttttaa tcatgataag gagatgttga atgcacaaat 6901 tgaggcaaca aagaggttac aggctgacat gattgctatc aaacaagggg ttttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg cggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aacgggacga gatactgggc accaggcgcc acctccacaa cttcgttgtc 7081 gggtggcttc acaaatcaaa ccgtacacag acccacacca aattttagaa cgggccagtc 7141 tcccaaaccc gcacccagca gtgggtcttc agtgagatca aactcaaccc aagtcactaa 7201 cctgagttca cactcgtccg ggtcgtctcg atccagcggg tccacagttg tcagctcaat 7261 accatcctcc aacagaacta gggactgggt caaccaacaa aatttcaatt tggaaccaca 7321 tatgcctgga tctcttagga cagcttttgt cactccacca tctagcacag cctctagctc 7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac 7441 acgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa 7501 agattatttt aaatttgatt taaaattagg tttaatctgg aatctttt //