Typing tool
|
Complete norovirus genomes
MH218646 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218646 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_177-2_26_01_2016, complete genome. ACCESSION MH218646 VERSION MH218646.1 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_177-2_26_01_2016" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="26-Jan-2016" /note="genotype: GII.P21_GII.3" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17596.1" /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARS KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELTTVTQPE ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVS LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNRKPLPTTDDSKVKKVANIVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTSLLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC PLTLNCDRIENKGKVFDSDVMIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLM CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFRPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHVRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP 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="AWR17597.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIASPLTGQ QNMIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRANDQADTATPRHFGLSWHIQLDNLNGTPYDPAEDIPGP LGIPDFRGKVFGVASQRNPDTTTRAHEAKIDTSSPRFTPKLGSLEISTESDDFELNQP TRFTPVGIGVDHEEDFRQWALPDYAGQLTHNMNLAPAVAPNYPGEQVLFFRSQLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17598.1" /translation="MAGAFVAGLAGDMLTNTVGSLVNAGANAINQTIDFENNRYLQNA SFNHDKEMLNAQVEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKDVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc 121 cctcggggcg cggtctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc 181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aagacgaacc 241 aattatttct tacaacgtca aagggggtgt ttctggtttg cctgagctca caactgtcac 301 ccaaccggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacaa 361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca 421 ttatggctta tacgtagaac gagggttagt gctcggtgtg cacaaaccac cagcagcagt 481 cagccttgct aaggttgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc 541 acagtacctc atttcccctg acactctcag aaagctgcat ggggagacat tcccttacac 601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga atgattcatg 661 gttgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa 721 caggaaaccc ctccccacga cggatgactc caaagtgaaa aaggtggcca atattgtcct 781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc 841 cctaaacatc ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggatctcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagaccttg gtgcatatgg 1141 gctggagatc ctaaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 attggcaatg gtgagatcca tcgaggatgc tgtgctagac cttgaagcca ttgagaacaa 1261 ccatatgaca tctctactta aggataaaga cagccttgca acctacatga ggactcttga 1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg 1381 tacgataaat gccctactgt caagaattgc agctgcccgg tctctagtgc acagggctaa 1441 ggaagagctg tcaagcaggc cccgaccggt cgttgtaatg atttcaggga aaccgggtat 1501 agggaaaacc catctagcta gagagttggc aaagaagatc gcctccacac tcacaggtga 1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga 1621 gagagtcgtt ctctgggacg actatgggat gagcagccct gtccacgacg ccctcagact 1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg 1741 taaagtcttt gacagtgacg tcatgataat aaccaccaat ttggccaacc cagcgccact 1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttccttgtct atgctgatgc 1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac 1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa 1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgcca gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag gttagacgag tatgagctgc agggcccaac 2101 tcctacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga 2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac 2221 tatgacagaa ctcaaacagg cacttaagaa catctcagtc aagaaatgtc agcttgtgta 2281 cggtgggggc acatacacac tcgaatctga tggcaaaggc aatgtgcatg tcgagaaggt 2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcatgtg 2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat 2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acaaacatac agaacctctg 2521 gtccaagcca caagcagaag atctagagga gaccaacaac gaggagggtt gtccaaaacc 2581 caaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg 2641 aaagaacaaa actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga 2701 tgaggagtac gatgagtata agagaatcag ggaagaaaga aatggcaagt actccataga 2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gagcaactga 2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag 2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggttctg agattaggaa 2941 gagaaaccca gatgacttca ggcccaaagg gaaactatgg gctgatgatg acaggagtgt 3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcgc gaatagtcaa 3061 cttcggctca gggtggggct tctgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa 3181 atcaggtgag ttctgccggc tcagattccc aaaaccaatc aggacagatg ttacgggcat 3241 gattttggag gaaggtgccc cagaaggcac tgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gccaccatga aaattcaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga 3421 tttgggcaca actcctggcg attgtggttg tccctacatc tacaagagag ggaacgacta 3481 cgtggtcatt ggagtccaca ctgccgccgc tcgtggagga aacactgtca tctgtgcaac 3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgat aataagggaa cttattgtgg 3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattctggag 3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcctatctgg gtggcaagga 3721 ccctagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac tgaaaccatt 3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat 3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatatg cacaagcgtg 3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac catgtgcgga aaaacgattg 3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat 4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgaactagt 4081 caagactgac aagatctatg gggtggtcaa gaagaggctc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg 4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaagcactcc agatacaagt accattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacctca 4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt 4441 caagatatca atcaacgagg gactgccctc tggtgtccct tgcacttcac aatggaactc 4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaatta gacccagaga aattgacagc aaaactgagg gaatatgggc ttaaaccaac 4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatctgaatg gcctgacctt 4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagctc 4801 aatacttagg cagatgtact ggaccagggg gccaaaccat gaagacccct ttgaaacaat 4861 gataccacac tcccagagac ccatacaact gatgtcatta cttggtgaag ctgcattgca 4921 tggtccgtca ttctacagta aaatcagcaa attggtcatt tcggaactga aagagggtgg 4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgaggt tctcagactt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaac gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag caatagcatc acccctcact ggtcagcaaa 5221 atatgattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag 5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa 5341 atccctattt ggcccatctt gctagaatgt acaatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctatccccc 5461 ccaattttcc agttgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg 5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aacaacttct 5581 ttcattataa tcaagggtct gactcgaggt tacgcctaat tgcaatgcta tatacacctc 5641 ttagagcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctaactagac 5701 ctagtcctga tttctcattc aatttccttg tgccacccac tgtggagtca aagacaaaac 5761 ctttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtgccaa 5821 ttgattccct acacaccagt cccactgaga atattgttgt tcagtgccaa aatgggcgcg 5881 tcacccttga tggtgagctg atgggcacca cccaactctt gccaagccaa atctgtgctt 5941 tcaggggcgt cctcaccaga tcaacaagca gagccaatga ccaggccgat acagcaaccc 6001 ctagacactt tggtctttct tggcacatac aattggataa tctaaatgga accccttatg 6061 atcctgcaga agacatacca ggccccctag ggataccaga tttccgtggc aaagtctttg 6121 gcgtggccag ccagaggaat cctgatacca cgactagggc gcatgaagca aagatagata 6181 cctcttctcc ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctgatg 6241 attttgaact caaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg 6301 aagactttag acagtgggcc ctacccgact acgctggtca gctcacacat aacatgaact 6361 tagccccagc tgttgctccc aactaccctg gtgagcaggt ccttttcttc cgctcacaat 6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctagttccc caagaatggg 6481 tacagcactt ctaccaagag tcagccccct ctcagtccca agtggccctg gtcaggtatg 6541 ttaatcctga cactggtaga gtgttatttg aggccaaatt acataaatta ggtttcatga 6601 ctatagccaa gaatggtgat tctccaataa ctgtcccccc aaatggatac tttaggtttg 6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa 6721 ggattcaata atggctggag cttttgtagc aggattggct ggtgacatgc tcacaaatac 6781 tgtaggatct ttagttaatg caggggctaa tgctattaat caaacaattg attttgaaaa 6841 taatagatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaagt 6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aaacaagggg ttttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cctcgatgtc 7081 gggtggcttt acacaccaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc 7141 ccccaaatcc acacccagta gtgggtcttc agtgaggtca aactcaaccc aaatcactag 7201 cctgagctca cactcgtccg ggtcgtctcg atccagcgga tctacagtta tcagctcaat 7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca 7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctccagctc 7381 aggcacagtc tcaactgtgc ccaaagatgt tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa 7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt //