Typing tool
|
Complete norovirus genomes
MH218698 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218698 7571 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_38_09_08_2014, complete genome. ACCESSION MH218698 VERSION MH218698.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7571) 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 7571) 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..7571 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_38_09_08_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="09-Aug-2014" /note="genotype: GII.P4_GII.4" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17752.1" /translation="MKMASNDASAAAVASSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKIELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDNSKIKKVADIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE 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..6707 /gene="ORF2" CDS 5085..6707 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17753.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICSFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAYTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17754.1" /translation="MAGAVFAGLASDVLSSGLGSLINAGAGAINQTIEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIETTKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTVTSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctagca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc 181 acctactcca gaactggtta agaatatccc ccctcccccg cccaacgggg aagatgaaat 241 agtggtctct tatagtgtca aaaatggtgt ttccggcttg cctgaccttt ctaccgtcag 301 gcaaccggaa gaaaccaaca cagccttcag tgtccctcca ctcaatcaga gggagaatag 361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagccgccat 481 cagccttgct aagattgagc tggcaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagagacgt tcccctacac 601 agcctttgat aacaactgtt atgccttttg ttgctgggtt ctggacctga atgactcgtg 661 gctgagcaga agaatgatcc agagaacaac tggtttcttc agaccctatc aggactggaa 721 taggaaaccc cttcccacta tggacaactc caagataaag aaggtagctg acatatttct 781 gtgtgccctg tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc 841 tcttaatatc ctcaacatct tggcctcatg tgattggacc tttgcaggta tagtggagtc 901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct 1021 tgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg 1081 gaaaatgttg tcatctgctg cgtccacttt gagggcttgc aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttag tcatgaaatg gttcttccca aagaaggagg aggcaaatga 1201 gctggctatg gtgagatcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa 1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga 1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg 1381 tacagtcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa 1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat 1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga 1561 tcagcgtgtg ggcctcgtcc cacgcaatgg tgtcgaccat tgggacgcgt acaaggggga 1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaataaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact 1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt atgcagaggc 1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgataa 1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctctctcat 2041 tgcccgggca tcagggctac tccatgagag gttggatgaa tttgaactgc agggcccagc 2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga 2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac 2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta 2281 tagtggctgc acttacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacagaat 2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt tcaggaagcc ctgtattcca tcatccaaat 2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctgtg 2521 gtccaagcca caagtggaaa acacagagga gactaccagt aaggacgggt gcccaaaacc 2581 caaggatgat gaggagttcg tcatttcatc cgacgacatc aaaaccgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagcattc tcaagcaaag gtctcagtga 2701 tgaagagtat gatgaataca agaggattag agaagaaagg aatggcaagt actctataga 2761 agagtacctt caggacagag acaaatacta tgaggaggtg gccattgcca gggcgactga 2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaggaaa gagtctctct tggtctggtc acaggctctg aaattaggaa 2941 aagaaaccca gatgacttca aacccaaggg aaaattgtgg gctgacgatg acaggaatgt 3001 ggactacaat gagaaactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa 3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt 3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa 3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat 3241 gatcttggaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca agaggtccac 3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg 3361 gcgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga 3421 cctgggtaca acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta 3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac 3541 ccaagggagt gaaggggagg ctacacttga gggtggtgac aacaagggga catactgtgg 3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaaaacca aattctggag 3661 atcgtccaca gcaccacttc cacctggtac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt 3781 cacagagccc aggggcaagc caccaaaacc aagtgtacta gaagctgcca agaagaccat 3841 cattaatgtc cttgagcaaa caattgatcc accagagaaa tggtcgttcg cacaagcttg 3901 cgcgtccctt gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtatgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttggt 4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggatctggc 4141 aaccatgatt cggtgcgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg 4201 tgtcacactc cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca 4321 acagagagcc gtgctggcag cagctctgga aatcatggtt aaattctccc cagaaccaca 4381 tttggctcag gtagtcgcgg aagaccttct ttcccccagc gtggtggacg tgggcgactt 4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga 4561 taccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaga aattgacagc aaaactcaga gaatatgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgc catctctgaa gacctggatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat 4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctaggggagg ccgctctcca 4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg 4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa 5341 acccctacct atcccattta gccagaatgt acaatggtta tgcaggtggc tttgaagtgc 5401 aggtaattct cgcggggaat gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac catgttcccc catatagtgg 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 atcattataa ccaatcaaat gactccacca ttaagctgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gacgatgttt tcacagtttc ttgccgagtt ctcacaagac 5701 catcccccga ttttgatttc atatttttgg tgccccccac agttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgctcct 5941 tcagagggga tgtcacccat atcacaggca gtcacaacta cacaatgaat ttggcttctc 6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctaggg actccagact 6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga acctcaacag tgggtgctcc 6301 ctagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgcctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctga gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg caagcttcat aaatcaggct atattacagt ggcttacact ggccaacacg 6601 atttggttat cccccccaat ggttatttta gatttgattc ttgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagctgt 6721 ctttgctgga ttggcatctg atgtccttag ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa caattgagtt tgaaaataac agaaaattgc aacaagcatc 6841 attccaattt agcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agcacaaatt gagactacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcca ggaccacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcttctaact cttctactgt 7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg 7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gattattctt cctttttctt tagtgtcttt 7561 taaaaaaaaa a //