Typing tool
|
Complete norovirus genomes
MH218631 | GII.4 Sydney | ||
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GII.P31 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218631 7559 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_161_27_04_2015, complete genome. ACCESSION MH218631 VERSION MH218631.1 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_161_27_04_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="27-Apr-2015" /note="genotype: GII.Pe_GII.4" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17551.1" /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP KQPPPKEIPPRPPRPPTPELVKNIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANRDGC LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLI TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP SLFVTSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW 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="AWR17552.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSHNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17553.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGATAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga 61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc 121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc 181 acccacacca gaattggtca aaaatatccc tcctccccca cccaacgggg aggatgaact 241 agtggtctct tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag 301 acaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag 361 ggacgccaag gagccactaa ctggaacaat cattgaaatg tgggatggag aaatttacca 421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cagcagccat 481 tagccttgcc aaggtcgagc tggcaccgct ctctttgttc tggagacctg tatacacccc 541 ccagtacctc atctctccag acactcttag gagattacat ggagagtcat tcccctacac 601 tgcatttgac aacaattgct acgccttttg ctgttgggta 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 tagctacatg tgactggacc ttcgcaggca tagtggaatc 901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact 1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaatcgg 1081 aaagatgcta tcatccgctg catccacttt aagagcttgc aaagacctag gtgcatacgg 1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga 1201 actggctatg gtgagatcca tcgaggatgc agtactagac ctcgaggcaa ttgaaaacaa 1261 ccacatgact accctgctca aagacaaaga cagcttagca acctacatga gaacccttga 1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg 1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa 1441 agaagaactc tccagcaggc cgagacctgt cgttgtaatg atatcgggaa gaccagggat 1501 agggaaaact caccttgcta gggagctggc caagaagatc gcggcctccc tcacagggga 1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcgt acaagggtga 1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt 1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg 1741 aaaagtcttt gacagtgatg ccataattat caccaccaac ctggccaacc cagcaccact 1801 ggattatgtc aactttgaag cgtgctcgag acgcattgat ttcctcgtgt acgcagaagc 1861 ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc 1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa 1981 gaatggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat 2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc 2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga 2161 aaacaagtat ggactgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac 2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta 2281 caatggtggc acctacacac ttgaggctga tggcaagggt agtgtgaaag ttgacaaagt 2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg 2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat 2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg 2521 gtccaagcca caggtggaag acacagaaga gatggccaac agagatggtt gcctaaaacc 2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag tccggccgtg gtaagaagca cacagccttt tcaagcaaag ggctcagtga 2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga 2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga 2821 agaggacttc tgtgaagaag aagaggccaa aatccgacag agaattttca gaccaacaag 2881 gaaacaacgc aaagaagaga gggcctctct cggcttgatc acaggctctg aaatcaggaa 2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt 3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa 3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttgtaacat caacccatgt 3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa 3181 gtcaggtgaa ttctgccggt tgagattccc aaagccaatc agaaccgatg tgacgggcat 3241 gattctagaa gaaggtgcgc ccgaggggac tgtagccaca 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 aatactgtca tatgtgccac 3541 ccagggaagt gagggagagg ctacacttga aggaggtgac agtaaaggga catactgtgg 3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag 3661 atcatccaca acaccactcc cgcctggcac ctacgaacca gcctacctcg gtggcaaaga 3721 ccctagagtc aaaggtggcc cttcattgca acaagttatg agggaccagc tgaagccatt 3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat 3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cacaagcttg 3901 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgactg 3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat 4021 gtttgaagag ggaaagaaca tgactccggt ctacacaggt gcacttaaag atgagttggt 4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagatctggc 4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg 4201 tgtcacactc cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatcttcga 4261 gaagcactcc agatatagat atcactatga tgctgactat tcccggtggg actcaacaca 4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca 4381 cctggcccag atagttgcag aggacctcct ctcccctagc 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 tgaagccaac 4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gacctggatg gtctgacatt 4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc 4801 aattcttagg caaatgtact ggaccagggg tcccaaccat gaggatccat ttgaaacaat 4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca 4921 cggcccggca ttctacagca aaattagcaa attagtcatt gcagagttga aggaaggtgg 4981 catggatttt tacgtaccca gacaagagcc aatgttcaga 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 ccctggcgga gagttcacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa 5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaactttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 atcattacaa tcaatcaaat gaccccacta ttaagttgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gatgatgtct tcacggtttc ttgccgagtt ctcacgagac 5701 catcccccga ttttgacttc atatttctag tgccacccac agttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggtaggt 5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcccgtcaac atctgcacct 5941 tcagaggaga tgtcacccat atcacaggta gtcataacta cacaatgaat ttggcttctc 6001 aaaattggag caattacgac ccaacagaag aaatcccagc ccctctagga actccagact 6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gtcacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgaaac tgacacaaac catgattttg aagctaacca aaacacaaag ttcaccccag 6241 ttggtgtcat ccaagatggt ggcaccaccc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcctaatg tgcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ctccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgaatg taagcttcat aaatcaggct atgttacagt ggctcacacc 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 agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agcacaaatt gaggcaacca aaaggttaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcggcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccgg gaagagctaa 7141 tcttagggat gctgtccctg ctcggggttc ctccagtaag tcttctaatt cttctactgc 7201 tacttctgtg tactcaaatc aaactacttc aacgagactt ggtgctacag ctggttctgg 7261 taccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg aggatcaaag 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga 7501 gtcacgggcg taatgtgaaa aggcaaaatt gattattttt cttttcttta gtgtctttt //