Typing tool
|
Complete norovirus genomes
MH218604 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218604 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_133_26_05_2015, complete genome. ACCESSION MH218604 VERSION MH218604.1 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_133_26_05_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="26-May-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="AWR17470.1" /translation="MKMASNDASAAAAAKSSNDNAKSSSDGVFSNMAVTFKRALGARP KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALRNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQVEDLEETNNEEGC PKPKNDEEFIVSSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRVSINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE 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="AWR17471.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP TRFTPVGIGVDNEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17472.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANVINQKIDFENNKYLQNA SFNHDKEMLNAQVEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKPTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKDVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgca gctgccaaaa gcagcaacga 61 caacgcaaaa tcttcaagtg acggagtatt ttctaatatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc 181 acccacacca gagttggtta aggcaattcc ccctcccccg cccaacgggg aggacgaacc 241 aatcatttct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac 301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacaa 361 agatgcaaag gaacctttga ctggaaccat cctggagatg tgggacgggg agatctacca 421 ttatggctta tacgtagaac gggggttagt gctcggtgta cacaaaccac cagcagccat 481 cagccttgct aaggttgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc 541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagactt tcccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg 661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa 721 caggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtagcca atgttgtcct 781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggaa aattaaaacc 841 cctaaacatt ctcaacatct tagccacatg tgactggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagacg tgtctgcgat 961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggacctcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caagatgctt tcttccgctg cttcaaccct gagagcatgt aaagatctcg gtgcatatgg 1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa 1261 ccacatgaca gctctactca aggataaaga tagccttgca acctacatga gaactcttga 1321 catggaggag gagaaggcga gaaaactctc caccaagtct gcctctccgg atattgtggg 1381 cacgataaat gccttactgt caaggattgc agctgcccgg tctctagtgc acagggctaa 1441 ggaggagctg tcaagtagac cccgaccggt cgttgtaatg atttcaggga aaccgggtat 1501 agggaaaacc catctagcta gagaattggc aaagaagatc gcctccacac tcacaggtga 1561 ccagagggtg ggcctaatcc cacgcaacgg ggtcgaccac tgggatgcat acaaaggtga 1621 aagagtcgtt ctctgggacg actacgggat gagtagcccc gtccacgacg ccctcagact 1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg 1741 taaagttttt gacagtgacg tcataataat aaccaccaat ttagccaacc cagcaccact 1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc 1861 tcctgaagtt gagaaggcta agcgagactt cccaggccaa ccagacatgt ggaaagacac 1921 cttcaagccc gacttctcac acataaaatt ggcattagcc ccacaaggag gttttgacaa 1981 gaatggtaac actcctcatg ggaagggagt tatgaagacc ctcactgcca gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggtccaac 2101 tcccacaaca ttcaacttcg accgcaataa ggtgcttgct tttaggcagc ttgctgctga 2161 aaacaagtac ggtcttgttg acacaatgag ggtcgggtca caactcaaga atgttaaaac 2221 tatgactgaa ctcaagcagg ccctcaggaa catctcagtc aagaaatgtc agcttgtgta 2281 cggtgggggc acatacacac ttgaatctga tggcaaaggc aatgtgcatg tcgaaaaggt 2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg 2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat 2461 tgccggggct gcattcatca ccacgcgcat tgcaaagcgc acaaacatac aaaacctctg 2521 gtccaaacca caagtagaag atctagagga aactaacaac gaggagggtt gtccaaaacc 2581 taaaaatgat gaagaattta tcgtctcctc tgatgacatc aaagctgagg gtaagaaagg 2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga 2701 tgaggagtac gatgagtata agagaatcag ggaagaaaga aatggtaagt actccataga 2761 ggaataccta caggacagag acaaatacta tgaagaggtg gccatagcca gggcaactga 2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag 2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggctctg agatcaggaa 2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gctgatgatg acaggagtgt 3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa 3061 ctttggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa 3181 gtcaggtgag ttctgccggc ttaggttccc gaaaccaatc aggacagatg ttacaggcat 3241 gatcttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga 3421 tttgggcaca actcctggcg attgtggttg tccctatatc tacaagagag ggaacgacta 3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacaccgtca tctgtgcaac 3541 ccaaggaaac gagggtgagg ccatgctaga aggtggtgac aataagggaa cctactgtgg 3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca agttctggag 3661 gtcttctacc acccccctgc cacccggaac ctatgagcca gcttatctgg gtggtaagga 3721 ccctagagtg aaaggtggcc cctcactgca acaggttatg agagaccaac taaaaccatt 3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcta agaagactat 3841 aatcaatgtg cttgagcaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg 3901 tgcatcatta gataagacca cttccagcgg tcaccctcac cacatgcgga agaacgattg 3961 ctggaacggg gactctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat 4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt 4081 caagactgac aagatttatg gggtagtcaa gaagaggctc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aagcccattg 4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaaacactcc agatacaaat accattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacccca 4381 cctggcccag gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt 4441 tagggtatca atcaacgagg gattaccctc tggtgtccct tgcacttcac aatggaactc 4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgagatag tgagcacaga 4621 catcaaatta gacccagaga aattgacagc aaagctgagg gaatacgggc tcaaaccaac 4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatttgaatg gcctgacctt 4741 cttgcggaga acagtgaccc gtgacccggc cggatggttt ggcaaactgg accaaagttc 4801 aatactcaga cagatgtact ggaccaaggg gccaaaccat gaagacccct ttgaaacaat 4861 gataccacac tcccaaagac ccatacaatt gatgtcatta cttggtgaag ctgcattgca 4921 tggtccatca ttctacagta aaatcagcaa attggtcatc tcagaactga aagagggtgg 4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc acccctcact ggccagcaga 5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag 5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa 5341 atccctattt ggcccacctc gctagaatgt ataatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc 5461 ccaattttcc aattgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg 5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct 5581 ttcattataa tcaagggtct gattcaagat tacgcttaat tgcaatgcta tacacacctc 5641 ttagggcaaa caattctggg gatgatgttt ttaccgtgtc ttgtagagtg ctaactagac 5701 ctagtcctga cttctcattc aatttccttg tgccacctac tgtggagtca aagacaaaac 5761 ccttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa 5821 ttgattctct gcacaccagt cccactgaga atattgttgt tcagtgccaa aatgggcgcg 5881 tcacccttga tggtgagttg atgggcacca cccaactctt gcctagccaa atctgtgctt 5941 tcaggggcgt tctcaccaga tcaacaagca gggccagtga ccaagccgat acagcaaccc 6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg 6061 atcctgcaga agatatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg 6121 gcgtggccag ccaaagaaat cctgatgcca cgactagggc acatgaagca aagatagaca 6181 ccacatctgg ccgcttcacc ccaaagctag gctcattgga gatatctact gaatctagtg 6241 actttgacca aaaccaacca acaagattca ccccagttgg cattggagtt gacaatgagg 6301 cagactttca acaatggacc ctacccgact acgctggtca gttcacacac aatatgaacc 6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt 6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggtcccc caagaatggg 6481 tacagcactt ctaccaagag tcagctccct ctcagtctca agtggctctg gttagatatg 6541 ttaaccctga cactggtaga gtgttatttg aggccaagct acacaaatta ggtttcatga 6601 ctatagccaa gaatggtgat tctccaataa ctgttcctcc aaatgggtat tttaggtttg 6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa 6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac 6781 tgtagggtct ttagttaatg caggagctaa tgttattaat cagaaaattg attttgaaaa 6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaagt 6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aagcaagggg tcttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aatggaacga gatactgggc gccaggtgcc acctccacaa cctcgatgtc 7081 gggtggcttt acacatcaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc 7141 tcccaaaccc acacccagca gtgggtcttc ggtgagatca aactcaaccc aaatcactag 7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagttg tcagttcaat 7261 accatcctct aacaggacta gggactgggt taaccaacaa aattttaatt tggaaccaca 7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagcacag cctctagctc 7381 aggcacagtc tcaactgtgc ccaaagatgt tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa 7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt //