Typing tool
|
Complete norovirus genomes
MH218699 | GII.4 Sydney | ||
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GII.P31 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218699 7560 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_39_26_08_2014, complete genome. ACCESSION MH218699 VERSION MH218699.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7560) 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 7560) 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..7560 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_39_26_08_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="26-Aug-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="AWR17755.1" /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAVARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEGLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSRISKLVIAELKEGGMDFYVPRQE 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="AWR17756.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHVVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHTTGSHNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17757.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQEQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTHNAGRFSTPQPSGALPGRANLKDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaata gcaacaacga 61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc 121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc 181 acccacacca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact 241 agtggtctct tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag 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 ctccttgttc tggaggcctg tatacacccc 541 ccagtatctc atctctccag acactcttag gagattacat ggagagtcat tcccctacac 601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg 661 gctaagcagg agaatgattc agagaacaac aggcttcttc aggccgtacc aggattggaa 721 caggaaaccc ctccccacta tggatgattc taaattaaag aaggtagcca acatattctt 781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc 841 tcttaacatc ctcaacattc tggctacatg tgattggacc 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 aagagcttgt aaagaccttg gtgcatacgg 1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga 1201 actggctatg gtgagatcca tcgaggatgc agtactagac ctcgaggcaa ttgaaaacaa 1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga 1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg 1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa 1441 agaagagctt tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat 1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga 1561 ccagcgtgtg 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 ccctgaggtt gagaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc 1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa 1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat 2041 tgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc 2101 cctcaccacc ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga 2161 aaacaagtat gggctgatgg acacaatgag ggttggaaaa cagcttaagg 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 aaagatggtt gcttaaaacc 2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagtaaag ggctcagtga 2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga 2761 agagtacctt caggacagag acaagtacta cgaggaggtg gccgttgcca gggcaaccga 2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag 2881 gaaacaacgc aaagaagaga gggcttctct cggcttggtc acaggctctg aaatcaggaa 2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt 3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa 3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccacgt 3121 cataccccaa ggcgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa 3181 gtcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat 3241 gattctagaa gaaggtgcgc ccgagggtac cgtggccaca 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 ccagggaagt gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg 3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag 3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga 3721 ccctagagtc aaaggtggcc cttcattgca acaagttatg agggaccagc tgaagccatt 3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat 3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg 3901 cgcgtccctt 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 tgtcacactt 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 ctacggtgat gatgagattg taagcacaga 4621 cataaagttg gacccagaga agctgacagc aaagctcaag gagtacgggc tgaaaccaac 4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa ggcctggatg gcctgacatt 4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc 4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagacccat ttgaaacaat 4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca 4921 cggcccggca ttctatagca gaattagcaa 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 acccgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag 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 catgtagtag 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac 5701 catcccccga ctttgatttc atatttctag tgccacccac agttgagtca agaaccaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggtaggt 5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct 5941 tcagaggaga tgtcacccat accacaggta gtcataacta cacaatgaat ctggcttctc 6001 aaaattggag caattatgac ccaacagaag aaatcccagc ccctctagga actccagatt 6061 ttgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag 6241 ttggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcctaatg tgcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcagcttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggtct 6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttttaca 6661 cgcttgcccc catgggaaac ggaacggggc gtagacgtgc actataatgg ctggagcttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaactgc aacaagcatc 6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agaacaaatt gaggccacca aaaggctaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgacgcta ggactacaac 7081 acacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa 7141 tcttaaggat gctgtccctg ctcggggttc ctccagtaag tcttctaatt cttctactgc 7201 tacttctgtg tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg 7261 taccagtgtc tcgagcttcc cgtcaactgc aagaactagg agctgggttg aggatcaaag 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg 7441 gactggcgct tttaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga 7501 gtcacgggcg taatgtgaaa agacaaaaat tgattatctt tcttttcttt agtgtctttt //