Typing tool
|
Complete norovirus genomes
MH218615 | GII.4 Sydney | ||
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GII.P31 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218615 7559 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_144_13_11_2014, complete genome. ACCESSION MH218615 VERSION MH218615.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7559) 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 7559) 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..7559 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_144_13_11_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="13-Nov-2014" /note="genotype: GII.Pe_GII.4" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17503.1" /translation="MKMASNDATAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELITVRQPE ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYIAFDNNCYSFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEVNELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM SDLKQALKNIAIKRCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLNDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFTQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE 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="AWR17504.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQSTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17505.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIDATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 gtgtatgaag atggcgtcta acgacgctac cgctgccgct gttgccaaca gcaacaacga 61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc 121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc 181 acccacacca gagttggtca aaaagatccc tcctccccca cccaacgggg aggatgaact 241 agtggtctct tacagcgcca aagatggcgt ttccggactg cctgagctca tcactgtcag 301 acaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag 361 ggacgccaag gagccactaa ctggaacaat cattgaaatg tgggatggag aaatctacca 421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat 481 tagccttgcc aaggtcgagc tagcaccgct ctctttgttc tggagacctg tatacacccc 541 ccagtatctc atctctccag acactcttag gagattacat ggagagtcat tcccctacat 601 tgcatttgac aacaattgct actccttttg ttgttgggta ttagacctaa acgactcatg 661 gctaagcagg agaatgattc agagaacaac aggcttcttc aggccgtacc aggattggaa 721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtagcca acatattctt 781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc 841 tcttaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc 901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact 1021 agtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaatcgg 1081 aaagatgcta tcatccgctg catccacttt aagagcctgt aaagaccttg gtgcatacgg 1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagtaaatga 1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa 1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga 1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg 1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa 1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat 1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga 1561 tcagcgtgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga 1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt 1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg 1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact 1801 ggattatgtc aactttgaag cgtgctcgag acgcattgat ttcctcgtgt acgcagaagc 1861 ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc 1921 tttcagccct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa 1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat 2041 cgcccgagca tcagggttgc tccatgagag gctagatgaa tatgaactgc aaggtccagc 2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga 2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac 2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaggtgcc agatagtgta 2281 caatggtggc acctacacac ttgaggctga tggcaagggt agtgtgaaag ttgacaaagt 2341 gcaaagcgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg 2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat 2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaacatac agaatctctg 2521 gtccaagcca caggtggaag acacagaaga gatggccaac aaagatggtt gcctaaaacc 2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagtaaag ggctcaatga 2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga 2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga 2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag 2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa 2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt 3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa 3061 ctttggttca ggttggggct tctgggtctc ccccagtctg tttataacat caacccatgt 3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa 3181 gtcaggtgaa ttctgtcggt tgagattccc aaagccaatc agaactgatg tgacgggcat 3241 gattctagaa gaaggtgcgc ccgaggggac cgtggctaca ctgctcatca agagaccaac 3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg 3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga 3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta 3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac 3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaagggga catactgtgg 3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag 3661 gtcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga 3721 ccctagagtc aaaggtggcc cttcattgca acaagttatg agggaccagc tgaagccatt 3781 cacagaaccc agaggcaaac caccaagacc aaacgtgttg gaagctgcca agaaaaccat 3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcattta cgcaagcttg 3901 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgactg 3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat 4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt 4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagatctggc 4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg 4201 tgttacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga 4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca 4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca 4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtgatggatg taggtgactt 4441 tcaaatatca ataagtgagg gtctcccctc tggggtacct tgtacctccc agtggaattc 4501 catcgcccac tggctcctca ctctgtgtgc actctctgaa gtcacggacc tgtcccctga 4561 tatcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga 4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac 4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gacctggatg gcctgacatt 4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc 4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagatccat ttgaaacaat 4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgccctcca 4921 cggcccggca ttctatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg 4981 catggatttt tacgtaccca gacaagagcc aatgttcagg tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacgg 5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa 5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag 5521 tagatgttag gcaactagaa cctgtgttaa ttcccttacc cgatgttagg aataacttct 5581 atcattacaa tcaatcaaat gactccacca ttaagttgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac 5701 catcccccga ttttgatttt atatttctag tgccacccac agttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggtaggt 5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atatgcacat 5941 tcagaggaga tgtcacccac atcgcaggta gtcgtaacta cacaatgaat ttggcttctc 6001 aaaattggag caattatgac ccaacagaag aaattccagc ccctctagga actccagatt 6061 ttgtggggaa gatccaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgaaac tgacacagac catgattttg aagctaacca aagcacaaag ttcaccccag 6241 ttggtgtcat ccaagatggt ggcaccactc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcctaatg tgcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttttac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg taagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttttaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc actataatgg ctggagcttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc 6841 cttccaattt agcagtaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agcacaaatt gatgccacta aaaggctaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccccca accatcgggg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggttc ctctagtaag tcttctaatt cttctactgc 7201 tacttctgtg tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg 7261 taccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg aggatcaaag 7321 taggaatttg tcacctttta tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga 7501 gtcacgggcg taatgtgaaa agacaaaatt gattatcttt cttttcttta gtgtctttt //