Typing tool
|
Complete norovirus genomes
MH218655 | GII.2 | ||
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GII.P2 |
ORF1: 5..5104 ORF2: 5085..6713 ORF3: 6713..7492LOCUS MH218655 7537 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_187_01_10_2015, complete genome. ACCESSION MH218655 VERSION MH218655.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7537) 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 7537) 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..7537 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_187_01_10_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="01-Oct-2015" /note="genotype: GII.P2_GII.2" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17623.1" /translation="MKMASNDASAAAAVNSNNDNTKSSSDGMLNNMAVTLKRALGARP KQPAPREKPPRPPRPPTPELIKRIPPPPPNDGDEPTVVFSTAGGVSGLPELTTVGQPP EANTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS IAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGELFPYTAFENNCYAFCCWVLDLNDS WLSRRMISRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIVLCALSSLFTRPIKDIIGK LKPLNILNILASCDWTFAGIVESLILLAELFDVFWTPPDVSAMIAPLLGDYELQGPED IAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKDEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKNSLAAYMKTLDMEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLVNPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDAYRPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPPLSTFNFDRNKIAAFRQLAAENKYGLVDTMRVGNQLRNVTTM DELKKAIKNITIRKCQIVYGGNTYTLESDGKGRVVVERVQNASVQINNEIAGAVHHLR CARIRYYVKCVQEAIYSLLQIAGTVFVTSRIVSRMNIQNLWSRPLTEDADEATTKEGC PKPRDEEEFVVSSEDIKPEGKKGKNKSGRGKKHTAFSSKGLSDEEYEEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEVKIRQRIFRPTRKQRKEERANLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNERISFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGITEAFGVPIRQVQIHKSGEFCRLRFPKPIRTDVSGMILEEGAPEG TVATILIKRTTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKRTIINVLEQTIDPPQKWTYAQACASLDKTTSSGFPHHVRKNEHW NGESFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKVYGKIKKRLLWGSDL ATMVRCARSFGGLMDELKAHCVTLPIRVGMNMNEDGPIVFEKHSRYRYHYDADYSRWD STQQRAVLAAAMEIMVKFSAEPQLAQIVAEDLLSPSVVDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIVQANSLFSFYGDDEIVSTDIKLDPEKLTGKLR EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQLYWTKGP NHEDPFESMIPHSQRPIQLMSLLGEAALHEPSFYSKISKLVISELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSLVNEDGVE" 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..6713 /gene="ORF2" CDS 5085..6713 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17624.1" /translation="MKMASNDAVPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG IISQRDKQNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ" gene 6713..7492 /gene="ORF3" CDS 6713..7492 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17625.1" /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG TRYWAPGSMRTTSYSGKFTSTAPVRQADFQHTQNRPSSGSSVSSFATQSSRPTLTTTT GSSHGTASSNSTRSTSLSQSTVSRATSRTSDWVRDQNRNLEPYMYGALQTAFVTPPSS RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc tgctgccgct gctgttaaca gcaacaacga 61 caacacaaaa tcttcaagtg acggaatgct taacaacatg gccgtcaccc ttaaacgagc 121 ccttggggcc cggcccaaac agccggcccc gagggaaaaa cccccaagac cccctagacc 181 accaacacca gaactaatta aaagaatccc ccccccacca cctaatgatg gggatgaacc 241 aaccgtggtg tttagcactg caggtggtgt gtctggccta cctgagctca caacagtcgg 301 tcaaccacct gaagctaaca cggcctttag cgtgcctccc cttagccaaa gggaaaacag 361 ggacgctaag gagccgttaa ctggaactat tctggaaatg tgggacgggg agatttatca 421 ctatggactg tatgtggaaa aagggcttgt gttaggcgtg cacaagccac cggctgccat 481 tagcatagcc aaagtggaat taacgcctct ctcactgtat tggaggcctg tgtacacgcc 541 tcagtacctc atatctccag acaccttgag gaaactccac ggtgaactat ttccctatac 601 agcctttgaa aacaactgtt atgccttctg ctgttgggtt ttggacctta acgattcatg 661 gctaagcagg aggatgatta gtaggactac tggctttttc aggccctacc aagagtggaa 721 caggaaaccc ctcccaacta tggatgactc aaaattgaaa aaggtcgcaa acatcgttct 781 atgtgcattg tcatcattgt tcactagacc cattaaggat ataattggca agcttaaacc 841 cctcaacatc ctgaacattc tggcctcgtg cgattggacc ttcgctggca tagttgagtc 901 actaatcctc ttggctgaac tctttgatgt gttctggaca cccccagatg tgtctgcaat 961 gatcgcaccc ctcctcggtg actatgagct acaaggccct gaagacatcg ctgtggagct 1021 cgtacccgtt gtgatgggtg ggataggtct ggtgctggga ttcaccaaag agaaaatagg 1081 taagatgctc tcctctgcag catcaacttt gagggcatgc aaagatcttg gagcctatgg 1141 actggagata ctgaaactag tcatgaaatg gttcttccca aagaaggatg aggccaacga 1201 actggctatg gttagagcca ttgaagacgc tgtattggac ctggaggcca ttgagaacaa 1261 tcatatgacc actctattga aagacaagaa cagccttgca gcctacatga aaaccctgga 1321 catggaagag gaaaaagcta ggaagttatc caccaaatca gcctcccctg acattgtggg 1381 caccataaat gccctgttgg ctaggatcgc tgccgcgcgt tccttagttc atagggccaa 1441 ggaggagctc tccagcaggc caaggccggt cgtcttgatg atctctggca agccagggat 1501 aggaaagacc cacttggcca gagaactggc aaagaaaatc gcctcaacac tcacaggaga 1561 ccagagagtg ggcctcatcc cacggaatgg agttgaccat tgggatgcct acaaaggtga 1621 gagagtggtg ctctgggatg attacgggat gagcaacccc atccacgatg cgctgaggtt 1681 gcaagagctg gcagacacat gtccattgac tctaaattgt gacaggattg aaaacaaggg 1741 gaaagtcttc gacagcgatg cgatcataat taccaccaat ttggtcaatc ccgcgccgct 1801 ggattatgtt aactttgagg cctgctccag acgtatagac ttccttgtgt atgctgatgc 1861 cccagaagtc gagaaagcaa agcgggactt ccccggccaa ccagacatgt ggaaggacgc 1921 ctatcgccct gacttctcac acatcaaact acaacttgca ccacaaggtg ggtttgacaa 1981 aaatggtaac acccctcatg gtaaaggagt gatgaagact ctcaccgcca gctcactggt 2041 tgcgcgtgcc tctggtctct tgcacgagag gctagatgag tacgaattgc aaggtccacc 2101 cctctcaacc ttcaactttg accgcaacaa aattgcagcg ttcagacaac tcgctgctga 2161 aaacaagtat ggtctggtag acacgatgag ggtgggtaac cagctcagaa atgtcacgac 2221 catggatgaa ctcaagaagg ctatcaagaa catcacaatc agaaagtgtc agatagtcta 2281 tggtggcaac acttacacgc ttgagtctga cggcaagggt agagttgtgg ttgagagggt 2341 gcagaacgcc agcgtgcaaa tcaacaatga gatcgctggt gcagtacacc accttagatg 2401 tgccagaata cggtattatg ttaaatgtgt ccaagaggcc atctactcac tcctccaaat 2461 tgctggcacg gtgtttgtca cttcacgcat cgtaagccgc atgaacatcc aaaatttatg 2521 gtccaggcca ttaactgaag atgcagatga ggccaccacg aaagaggggt gccctaaacc 2581 tagggatgaa gaagaatttg tcgtctcctc agaagatatc aagccagagg gcaagaaagg 2641 taaaaacaag agtggccggg gcaagaaaca cacggcattc tcaagcaaag gtctcagtga 2701 tgaggagtac gaagagtaca aaaggattag agaggagaga aatggcaaat actccataga 2761 ggaataccta caggatagag acaagtacta tgaagaggtg gccattgcca gggcaactga 2821 agaagacttc tgtgaagaag aagaggttaa gattcgtcag aggatcttca ggccaactag 2881 aaagcaacgc aaggaagaaa gagccaacct tggcctcgtc accggatctg agatcaggaa 2941 gaggaaccca gatgacttta aaccaaaagg aaagctgtgg gccgacgatg ataggagcgt 3001 cgactacaac gaaagaatca gctttgaggc cccaccaagc atttggtcta gaattgtcaa 3061 ctttggttct ggatgggggt tttgggtgtc acctagcctc ttcataacat caacacatgt 3121 cataccccaa ggcataactg aagcctttgg tgtacccata aggcaagtgc aaatacacaa 3181 atcgggcgaa ttctgtcgcc tgagattccc aaaacccatc aggacagatg tgtcaggtat 3241 gatactggag gagggagcgc ctgaaggcac tgttgccacc atactcatca agagaaccac 3301 tggagaactg atgccccttg cagcaagaat gggcacccac gcgaccatga ggatacaagg 3361 acgcacggtg ggcggccaaa tgggaatgct gctcactgga tccaatgcaa agagcatgga 3421 tctcggcacc acgcctggtg actgtgggtg tccctatatt tacaaaaggg gtaatgatta 3481 catagtcatt ggagttcaca cagcagctgc ccgtggcgga aacactgtca tctgcgccac 3541 acaaggtagt gagggtgagg ccacactcga gggtggtgac aacaaaggga catactgtgg 3601 ggcaccaatc ctaggacccg ggagtgcccc gaaactgagc actaagacca aattctggag 3661 gtcctctaca acaccactcc cacccggcac atacgagccg gcatatctgg gaggaaaaga 3721 cccccgagtc aaaggtggac catctctgca acaagtcatg cgagatcaac tgaagccatt 3781 caccgaaccc cgtggtaaac caccaaaacc aagtgtcctt gaagctgcca aaaggacaat 3841 tatcaatgtg ctagagcaaa caatagaccc cccacagaag tggacgtacg cgcaagcgtg 3901 cgcatctctt gacaaaacca catctagtgg gtttccccac cacgtgcgca aaaacgagca 3961 ctggaatggg gaatctttca caggaaaatt ggctgatcag gcatcaaaag caaacctaat 4021 gtttgaagag ggaaagcaca tgactccagt ttacacagct gcccttaagg atgagttggt 4081 caaaactgag aaggtgtatg ggaaaataaa gaagaggttg ctttggggct ctgatctggc 4141 cacaatggtg cggtgcgcgc gctcttttgg tggtttgatg gacgaactta aggcccactg 4201 tgtaacactt ccgataaggg ttggcatgaa tatgaatgaa gatggaccaa tagtctttga 4261 gaaacactcc agatacaggt atcactatga tgcagactat tccaggtggg attcaacaca 4321 gcagagagcc gtcctggctg cggccatgga gattatggtt aaattctcag cagaaccaca 4381 actagcccaa atagttgcag aggatctact gtcgcctagt gtagttgatg tgggcgactt 4441 caaaatttcc atcaacgaag ggttaccatc aggtgtccct tgcacctctc aatggaactc 4501 cattgcacac tggctcctca ccttgtgtgc cctttctgaa gttacagatc tctctcccga 4561 tattgtgcaa gccaactccc tcttctcctt ctatggtgat gatgaaattg tgagtacaga 4621 tattaaatta gacccagaaa agttgacggg gaagttgaga gaatacggcc tcaaacccac 4681 tcggcctgac aagactgagg gccccctgat cattagcgag gacctgaatg gcctgacctt 4741 cttgaggaga accgtcaccc gtgaccctgc aggatggttt ggcaaactgg accagagctc 4801 tatactcagg caattgtatt ggaccaaggg tcctaatcat gaagacccct ttgagtcaat 4861 gattccacac tcccagaggc ccatacaact catgtcactc ttgggcgaag cagcactgca 4921 tgaaccatcg ttttacagca agatcagcaa gcttgtgata tctgagttga aagaaggtgg 4981 aatggatttt tacgtgccca ggcaagaacc catgttcagg tggatgagat tctcggattt 5041 gagcacgtgg gagggcgatc gcaatcttgc tcccagtctt gtgaatgaag atggcgtcga 5101 atgacgccgt tccatctact gatggtgcag ccggcctcgt gccagaaagt aacaatgagg 5161 tcatggctct tgaacccgtg gctggtgccg ccttggcagc cccagtcacc ggtcaaacaa 5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccccaatggt gaattcacag 5281 tttctccccg taatgcccct ggtgaagtgc tattgaatct agagttgggt ccagaattaa 5341 atccttatct ggcacattta gcaagaatgt ataacgggta tgccggtggg atggaggtgc 5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtcttcgcc gctgtaccac 5461 ctcacttccc ggttgaaaac cttagcccac agcaaatcac catgttccct catgtgatta 5521 tagatgtaag gaccttagaa cctgttttat taccacttcc tgatgttagg aacaatttct 5581 tccactacaa tcagaaagat gatcctaaaa tgagaattgt ggctatgctt tacacccccc 5641 ttaggtctaa tggttcaggt gatgatgtgt tcacagtctc ctgcagggtg ttgactagac 5701 cctcccctga ttttgatttc acatatctgg tgccaccaac agtggaatct aaaacaaaac 5761 cattcactct cccaatcctc acacttgggg aactttccaa ttctaggttc ccagtgtcca 5821 tagaccagat gtacaccagc cccaatgagg ttatatcagt gcagtgtcaa aatggtagat 5881 gcacattgga cggggagctt caggggacaa cacaactcca agtcagtggt atttgtgctt 5941 tcaaggggga agtgaccgcc catttgcacg acaatgacca cctatataat gtcaccatca 6001 caaacctgaa tgggtccccc tttgacccct ccgaggacat ccctgcccct ctgggcgtgc 6061 ctgatttcca gggaagggtc tttggtatca tctcccaaag agacaaacag aatagccctg 6121 ggcacaatga accagcaaac aggggacacg acgctgtggt tcctacttac acagcacagt 6181 acaccccaaa attgggtcag attcaaattg gcacatggca gaccgacgat ctcacagtca 6241 accaaccagt caaatttacc ccagttggtc tcaatgacac tgaacatttt aaccaatggg 6301 tggtccccag atacgctggt gccctaaacc tcaacacaaa tcttgcccct tctgttgctc 6361 cagtgtttcc aggagagcgt ctgcttttct tcagatcata tattcctctc aagggtggtt 6421 atggaaatcc agccattgat tgcctactac cacaagagtg ggtgcaacac ttctaccagg 6481 aggctgcccc atcaatgagt gaggtggccc ttgtcagata catcaacccg gacactggtc 6541 gggcactgtt tgaggccaag ctccacagag ctggtttcat gacagtctcg agcaacacca 6601 gtgccccggt ggttgtgcct gccaatggat acttcagatt tgactcttgg gtgaatcaat 6661 tctattctct cgcccccatg ggaactggaa atgggcgtag aagggttcaa taatggctgg 6721 agcttttgta gctggtcttg caggggacgt gctcagcaat gggctcagtt cattaattaa 6781 tgcaggtgct aatgcaataa atcagagggc agaatttgat tttaatcaga aattacagca 6841 aaattctttt aatcatgata aggagatgtt gcaggctcag attcaggcaa ctaagcagct 6901 gcaggcagac atgatggcta ttaaacaggg ggtcctgacc gctggcggct tttcccctgc 6961 tgatgcagcc agaggtgccg tgaatgcgcc catgacacag gcgctggact ggaacggtac 7021 aaggtattgg gcaccaggct ctatgaggac cacatcttat tctgggaaat ttacatcaac 7081 cgccccagtg agacaggccg actttcagca cacccaaaac cggccatcga gtggctcttc 7141 tgtgtcctcc tttgccactc aatcttcgag gccaactctg accacaacca ctgggtcctc 7201 acatggcaca gcctcatcaa attcaactcg cagcacgagc ctctcccaat caacggtctc 7261 tagagctaca tctaggacta gtgattgggt tagagatcaa aatagaaatt tggaacccta 7321 tatgtatggt gccttacaga cagcctttgt caccccaccc tccagcaggg cgtctgatgg 7381 gacagtctca accgtcccaa agggtgtttt ggactcctgg acacctgcgt tcaacacccg 7441 caggcagccg ctctttgcac acctccgtaa gaggggggag tcacaagctt agtgaaaagg 7501 tggaaaattt gtttagaata aattgatttt acctttt //