Typing tool
|
Complete norovirus genomes
MH218612 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218612 7564 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_141_02_11_2014, complete genome. ACCESSION MH218612 VERSION MH218612.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7564) 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 7564) 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..7564 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_141_02_11_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="02-Nov-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="AWR17494.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKGGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCAMSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP 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="AWR17495.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAHLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVIHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17496.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcccccccc gagggaaaaa ccacaaagac ccccacgacc 181 acctacacca gaactggtta aaaatattcc ccccccccca cccaacggag aggatgaaat 241 agtggtttct tatagtgtca aaggtggtgt ttccggcttg cctgaccttt ccaccgtcag 301 gcagccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag 361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt actaggcgtg cacaaaccgc cagctgccat 481 cagcctcgct aaggttgagt tagcaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagaaacat tcccctacac 601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg 661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa 721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtggcta acatatttct 781 gtgtgctatg tcctcgctat tcaccaggcc cataaaagat ataataggga agataaggcc 841 tcttaacatc ctcaacatct tagcctcatg tgattggacc tttgcgggca tagtggagtc 901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct 1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg 1081 gaaaatgttg tcatcagctg cgtccacctt aagagcttgc aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttaa tcatgaagtg gttcttcccg aagaaggagg aggcaaatga 1201 gctggctata gtgaggtcca tcgaggatgc agtcctggat ctcgaagcaa ttgaaaacaa 1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga 1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg 1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa 1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat 1501 agggaagacc tacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga 1561 ccagcgtgtt ggtctcatcc cacgcaatgg cgtcgaccat tgggatgcgt ataaggggga 1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagccccact 1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtat atgcagaagc 1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa 1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat 2041 tgcccgggca tcagggttac tccatgagag gctagatgaa tttgaactgc agggcccagc 2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga 2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac 2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgtc aaatagtgta 2281 tagtggttgc acctacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaggat 2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat 2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg 2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc 2581 taaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga 2701 tgaagagtac gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga 2761 agagtacctt caggacaggg acaaatatta tgaggaggtg gccattgcca gggcgactga 2821 ggaagacttc tgtgaagagg aggaagccaa gatccgacaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaggaaa gagtctctct cggtttagtc acaggttctg aaattaggaa 2941 aagaaaccca gatgatttta aacccaaggg gaaattgtgg gctgacgatg acaggagtgt 3001 ggactacaat gagaaactca gttttgaggc cccgccaagc atttggtcaa gaatagtcaa 3061 ctttggttca ggctggggat tctgggtctc ccccagcttg ttcataacat caacccatgt 3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa 3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat 3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac 3301 tggggaactt atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg 3361 gcgcactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga 3421 cctgggtact acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta 3481 tgtggtcatt ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac 3541 ccaggggagt gaaggagagg ctacacttga gggtggtgac aacaagggga catactgtgg 3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag 3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt 3781 cacagagccc aggggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat 3841 cattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg 3901 cgcgtctctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtttgaagag gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt 4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctttggggct cggacttggc 4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg 4201 tgtcacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca 4321 acagagagcc gtgttggcag cagctctaga aatcatggta aaattctccc cagaaccaca 4381 tttggctcag gtagtcgctg aagaccttct ttctcctagc gtggtggacg tgggcgactt 4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacaaacc tgtctcctga 4561 taccatacag gctaattctc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgagacaat 4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttttacagta aaattagcaa attggtcatt gcagagctaa aagaaggtgg 4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaacgagg 5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tgtcccccag aaacgctcca ggtgaaatac tatggagcgc gcacttaggc cctgatttaa 5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgagac 5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggtaggt 5881 gcacgactga tggcgtgctc ctaggcacca cccaattgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcatccac attacaggta gtcgtaacta cacaatgaat ttggcttctc 6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga gctccagatt 6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag ggcagatggc tcaacacgcg 6121 gccacaaggc tacggtgtac actgggagcg ccgactttgc tccaaaactg ggcagagttc 6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcataatg ttcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc ttctttagat ccaccatgcc cggatgtagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg taaacttcat aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgt agtataatgg ctggagcttt 6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc 6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag aaatgctcca 6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgaaacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggttc ctctagtaaa tcttctaact cttctactgc 7201 tacttcagtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg 7261 taccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag 7321 taggaatttg tctcctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta aacgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt ttttagtgtc 7561 tttt //