Typing tool
|
Complete norovirus genomes
MH218692 | GII.7 | ||
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GII.P7 |
ORF1: 5..5098 ORF2: 5079..6701 ORF3: 6701..7474LOCUS MH218692 7502 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_236_29_01_2016, complete genome. ACCESSION MH218692 VERSION MH218692.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7502) 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 7502) 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..7502 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_236_29_01_2016" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="29-Jan-2016" /note="genotype: GII.P7_GII.7" gene 5..5098 /gene="ORF1" CDS 5..5098 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17736.1" /translation="MKMASNDATAALGSQKSANDSNNATPSNKEEVGTFSNIKVGFKK MLGAVPKGTKAPSSDQHCPTVKIGPKTLTIPPEPPNGEDTVQFDAKSETIIGLPDLTT VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGKALGVHKPP AAISLATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE LNDTWLNRRCISRTTGFFKPYQSWNRKPLPTIDDGKIKKVANAILCALGSLFSKPIKD LLGKLKPLNLLHLLASCDWTFAGMVETVILMAELFNVFWTPPDVSNFIASLIGDFELQ GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQEL ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP EIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL TARVAGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGTALKS VKTLEDLKVALRDVKFNECEIIYKSSKYRVSSNGKGSVSVDKVEDNASQTVNEVHSAL LRLRQARARYYISCFQDLVYTLIQVAGASFVVSRISRRFCWERWVKPTEAQEVNEFEK EAAQGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTRKQRKEERGVLGLVTG SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL LITTTHVLPKGIKELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV CSVLVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPG KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRG KPPRPAILEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNG ESFTGPLADQASKANLMYEQAKHMQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST QQRSILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ WNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM FRWMRFSDLSTWEGDRNLAPEGVNEDGVE" gene 5079..6701 /gene="ORF2" CDS 5079..6701 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17734.1" /translation="MKMASNDAAPSTDGAAGLVPEINNEVMPLEPVAGASLATPVVGQ QNIIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLAHLARMYNGHAGG MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD IRNNFFHYNQGNDPKLRLIAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP TVESKTKQFTLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT PLLAVNICKFKGEVIAKNGDVRSYRMDMEITNTDGTPIDPTEDTPGPIGSPDFQGILF GVASQRNKNEQNPATRAHEANINTGGDQYAPKLAQVKFFSESQDFEVHQPTVFTPVGV AGDNSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGHELGYMD CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ" gene 6701..7474 /gene="ORF3" CDS 6701..7474 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17735.1" /translation="MASAFFANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGAPMTKLVDWSG TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQSRQPLKVDSPPPSSSSSSVSSVKTQ STTLSGTSRVGSSSQSTLSTRPSTRTSDWVRSQNERLSPFMEGALQTTYVTPPSSRAS SISTVSTVPKEVLDSWTPMFNTHRQPLFAHLRRRGESQI" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cgctgccctt ggcagtcaaa aatctgccaa 61 tgacagtaat aatgccaccc cttctaacaa agaagaggtt ggtacattct ccaacattaa 121 agttggattc aagaaaatgc tgggtgccgt acccaaaggt accaaagcac ccagcagtga 181 tcagcattgc cccacagtta agatcggacc taaaacatta acaatccccc ctgaaccccc 241 aaacggtgag gataccgtac aatttgatgc aaagtcagaa actataattg ggctaccgga 301 cttgacaacg gtgcaaaacg aacacgaaaa tactccatac actgtccccc cattaagtga 361 gagggagcac aggccggcca ctgaaccact tcctggcaca atattggaga tgtgggatgg 421 tgagttttac cattactccg tgtacgtcag cgatggcaaa gctctgggag ttcacaaacc 481 accggcggct ataagtctcg cgacgataga gctcaccccc atatcactct actggagacc 541 cgtctacacc cccaactact tggtctcccc agacacatta aagggccttg ctggtgagaa 601 gttcccctac acggccttta gcaacaactg ttacaacttc tgttgttggg tgcttgagct 661 caacgacact tggcttaaca gaagatgcat ctccagaact accggcttct ttaaaccata 721 ccagtcttgg aataggaaac ctctcccaac tatcgatgat ggaaagatta aaaaggtggc 781 caacgcgatc ctctgcgcac tcggctcgct gttctcaaaa ccaatcaaag atctattagg 841 caaactcaag ccattgaatc tactacactt gctcgcgtct tgtgattgga cgtttgcggg 901 tatggtggag acagtcatct taatggcgga gcttttcaat gtcttctgga ctccgccaga 961 tgtctccaat ttcatagcct ccttgatagg tgattttgaa ttgcaagggc ctgaagattt 1021 ggctgtggag ctcgttcccg tggttatggg tggcataggg atggttctcg gcttcaccgc 1081 tgagaagata ggccgcatgc tgtcgtccgc tgcatcaaca ctgcgggcgt gcaaagacct 1141 agggaactat gcccttgaca tactcaaatt agtcatgaaa tggttcttcc caaagaagga 1201 ggagaaagct gagatggaga ccttgagggc gattgaagat gctgtccttg atatggaagc 1261 tatagggaat aaccacctca caaccctcct caaggacaaa gacagcctca cagctttcat 1321 gaaaaccttg gatctagaag aggagaaggc gaggaaactg tccactaaat catcttcgcc 1381 ggacatagtc ggcaccatta acgccatact agctaggata gctgctgcta ggtccctact 1441 acataaggcc aaagaggaga tgttcagcag gatcagacca gtagtcgtca tgatctcagg 1501 cagacctggc attggaaaaa cccacatggc gagacacttg gctaagagca tcgccaacac 1561 catgagtggc gatcagagag tcggactcgt cccacgcaat ggtgtcgatc actgggacgc 1621 ctacagggga gagagagtgg tcttgtggga tgactacggt atggggagcc ctgttaaaga 1681 cgccctgaca ctgcaagaat tggccgatac gtgtccagtc actttaaatt gtgataggat 1741 cgagaataag gggaagatgt ttgatagtga tgtcatcata atcacgacca acctagtcaa 1801 ccccgcgccc ctcgactatg tgaacttcga ggcgtgttcc aggagagttg atttcctggt 1861 ctatgcagag tcaccagaaa ttgagaaggt caagagagat ttccctggcc agcctgacat 1921 gtggaaagat catttcaagc cagacttttc ccacattaag ctgactctag cccctcaggg 1981 cggttttgac aaaaatggca acaccccaca cggtaagggc accatgcggt ccttgaccca 2041 ggggtcccta actgcgagag ttgcaggcct tgtccatgag aggagggatg agttccagct 2101 ccaaggaaat gacctccaaa catacaattt tgacaccaac agagtctccg catttaggaa 2161 attggccgca gacaacaagt atgggatcat ggagacgatg agagttggca cagcactcaa 2221 gagtgtgaag accttggaag atctcaaagt tgcattgagg gatgtaaaat tcaatgagtg 2281 tgaaataatt tacaagagct ctaagtaccg agtctcttcc aacggtaaag gctcagtctc 2341 tgttgacaaa gttgaagaca atgcttccca gactgtgaac gaggtacact cagcactcct 2401 cagactcagg caggcaaggg ccagatacta catcagctgc ttccaagacc tcgtctacac 2461 tcttatacag gttgccgggg catcatttgt tgtcagtagg atctccagaa ggttctgctg 2521 ggaaaggtgg gtcaaaccga ccgaggccca ggaggtgaat gagttcgaaa aggaagcggc 2581 ccaaggtaga tgggaaattg agcccaagga cacagaacca gaaggcaaga agggtaagaa 2641 caagaaagga aggggcaaga aacacacagc cttctctagc aaaggtctga gtgatgaaga 2701 gtatgacgag ttcaagagga tcagggaaga aagaaatgga aagtactcca ttgaggaata 2761 cctgcaggac cgagaccgct attatgaaga agtagcagtt gctcgggcaa cagaggagga 2821 cttctgtgaa gaggaagagg ccaagataag acaaaggatt ttccgcccga caaggaaaca 2881 gaggaaggag gaaaggggcg tgcttggctt ggtcaccggc tcagacatca gaaagaggag 2941 accagacgat ttccaaccaa aaggtaacct gtgggcagac gacaccagaa gtgtagacta 3001 caatgaaagg cttgattttg aagcaccccc gagtgtctgg tcaagaatag tcccattagg 3061 cactggttgg gggttttggg tttcatccaa ccttttgatc acaacaacac acgtcctgcc 3121 taaagggatt aaggaactct ttggagttga aatcaaacaa attcaaattc ataaatctgg 3181 agagttttgc aggtttagat tcccaagacc tatcaggcca gatgttacag gactcgtgct 3241 ggaggagggc gccccagagg gcactgtctg ttctgtactc gtgaaaagac ccacaggtga 3301 aatgatcccc cttgcagtga ggatgggcac acacgcatcc atgaaaatac agggcaggac 3361 cgttggtggc cagatgggaa tgcttctcac aggagcaaac gcaaagaaca tggatcttgg 3421 caccggccct ggtgactgcg gttgccccta catctacaaa cgtggcaacg acattgttgt 3481 tgcgggcgtc cacaccgcag cagcccgggg aggcaacact gtaatatgtg ccacccaagg 3541 gcaagatggg gaagcagtcc ttgagggaaa tgaggatctt ggtacctact gtggtgcccc 3601 aattctgggc cctggtaagg cgcctaaact cagcacgaag accaagttct ggcgctcatc 3661 accagatgcc ctgccacctg gcacatatga acctgcttac ctaggaggca aagaccctag 3721 agtggaaaaa ggcccctccc tgcaacaagt catgagagac cagttgaggc cctttacaga 3781 acccagaggc aagccaccta gacctgcaat cttagaggaa gccaaaaaga cagtgatgaa 3841 tgttctagag caaaccattg accctgccaa gccatggtcc tattcgcagg catgtgcctc 3901 attggacaaa actacctcta gtggtagtcc ccaccacgtt aagaaaaatg accactggaa 3961 tggggagtcc ttcactggtc cccttgcgga tcaggcttct aaagccaacc tcatgtatga 4021 gcaggccaaa catatgcagc ccgtgtatac ggccgcactt aaagatgagc ttgttaagac 4081 tgataagatc tacaagaaga taaagaagag gcttctatgg gggtcagacc ttggcacaat 4141 gatcaggtgc gccagggctt ttggtggtct catggacagc atgaaggcaa gttgtatagc 4201 tcttccttgc agggtgggaa tgaacatgaa tgaagatggc cccatcatat ttgacaaaca 4261 ctctaagtac aggtaccact atgatgctga ctattctagg tgggactcaa cccaacaaag 4321 gagcattctc tctgccgcta tggaagtgat ggtgcggttt tctgctgaac cagaattggc 4381 acaagtggtt gcagaggacc ttttggcacc tagccagctt gatgttggcg actttgtcat 4441 ctcagttcag gagggcctgc catcaggagt cccatgcaca tcacaatgga attcaatagc 4501 gcactggata ctcactttga gtgcgatggc agaagtgtca ggtctctcac cagatgttgt 4561 tcaagctcac tcttgttttt cattttatgg ggacgatgag atcgtcagca ctgatatcaa 4621 ccttgacccc atgaagttaa cacaaaaact cagggagtat ggcctggttc ccacccggcc 4681 tgacaaaact gaaggtcccc tcgtcataac tgaagacctc actggcctga cgttccttcg 4741 taggtcgatt gctcgggacc cagctggctg gtttggaaaa ctagaccaag attcaatcct 4801 caggcaactg tactggacaa gggggcctaa ccatgagaac ccgtacgaga gcatggttcc 4861 tcattcccag cgggccacac aactcatggc ccttcttggt gaggcctcgt tgcatggtcc 4921 tcaattttac aagaaagtta gcaaaatggt catcaatgaa attaagagtg gtggtctgga 4981 gttttacgtg cccagacaag aggccatgtt caggtggatg agattctctg acctcagcac 5041 gtgggagggc gatcgcaatc ttgctcccga aggtgtgaat gaagatggcg tcgaatgacg 5101 cagccccatc tactgatggt gcagcaggcc tcgtaccaga gatcaacaat gaggtcatgc 5161 cccttgagcc cgtggctggt gcatcgctgg cgacaccagt tgtcgggcaa caaaatataa 5221 ttgatccctg gataagaaat aattttgtac aggctcctgc aggtgagttt acagtttccc 5281 ctagaaattc ccctggtgag attttgcttg atttggagtt ggggccagaa ctgaacccct 5341 atctcgctca tctggcccgt atgtacaatg ggcacgctgg tggcatggaa gtgcaaattg 5401 tgctggctgg gaacgcgttc acagctggca agatcatatt tgctgccatc cccccagggt 5461 tcccatatga aaatttgtca ccttcacaga tcacaatgtg ccctcatgtt ataattgatg 5521 ttagacaatt agaaccagtt ctattaccta tgccagatat tagaaataac ttcttccatt 5581 acaatcaggg caatgacccg aaattgagat tgatagctat gctctatacc cctctaaggg 5641 ctaacaattc tggtgatgat gtgttcacag tttcttgtag ggtcctcact aaaccgtcac 5701 ctgattttga attcacattt ttggtccccc ctacggttga atctaagacc aaacagttca 5761 cattgcccat cctcaaaata tcagagatga ccaactcaag atttccagtg ccagtggaaa 5821 tgatgtatac agccaggaat gagaaccaag ttgtgcaacc acagaatggt agggtcacac 5881 ttgatggtga actattaggc accacaccct tgctggctgt caacatctgc aagttcaagg 5941 gggaggttat tgctaagaat ggagatgtga gatcctatag gatggacatg gaaattacca 6001 acactgatgg cactccaatt gaccccacgg aagacacacc tggtcccatt ggttcacctg 6061 actttcaagg tatacttttt ggcgttgcca gccaacgcaa caagaatgaa caaaaccccg 6121 ccacgagagc ccatgaagcc aacattaata ctggtgggga ccaatatgcc cccaaattgg 6181 cccaagtgaa attcttttca gagtcccagg atttcgaggt gcaccagccc acagttttca 6241 ccccagttgg tgtggcaggc gacaactccc accctttcag acagtgggtc ctgcctcgat 6301 acggcggaca tctcaccaac aacacccact tggctccagc ggtggccccc ctgtttccag 6361 gtgagcagat tctgttcttt agatcacaaa tacccagctc aggcggccat gaattgggct 6421 acatggactg ccttgtccca caagaatggg tccaacactt ctatcaagaa gctgccacag 6481 ctcagtctga agtggcactc ataaggttca ttaacccaga cactggcaga gtcctctttg 6541 aggccaagtt acacaagcaa ggctttataa ctgtggctca tactggtgat aacccaattg 6601 tcatgccacc aaatgggtac ttcagatttg aagcctgggt caatcagttt tactcactcg 6661 cccccgtggg aactgggaat gggcgcagga ggatccaata atggctagtg ctttctttgc 6721 aaatttggca ggaggcgttg cctccaatgg aattagttca cttataaatg ctggggctaa 6781 tgctattaac caaaaggttg agtttgatta taataaacaa ctccaaaatg catccttctc 6841 tcatgataaa gaaatgctcc aagctcaaat tgaagccacc aaacgtctgc aacaagagat 6901 gattgacata aaacaagggg tgctgacagc tgcgggattc tctcccacgg atgccgcgag 6961 gggttcagtc ggcgcaccaa tgacaaaatt agttgattgg agtggcacta gatattgggc 7021 acctggtgcc atgaggacaa ctggctattc agggactttt actcatttgc cccctgtgca 7081 gtctgcttca tatgtcaaca atcaaagtag acaacctctt aaagtagatt ctcctcctcc 7141 ttcttcgagt agttcttctg tttcttctgt taaaacacaa tcaactaccc tctcaggcac 7201 ctcaagggtg ggctcatcat ctcagtcgac cctgtcgacc aggccgagca caaggacatc 7261 tgattgggtg cgcagccaga atgaaaggtt gagtcccttc atggaaggag cgttgcaaac 7321 aacgtatgta acgccaccat ccagtagggc atcaagtatc agcacagtct cgaccgtgcc 7381 gaaagaggtt ttggactcct ggacgcctat gtttaacact cacaggcagc cactcttcgc 7441 ccatttgcgt aggcgagggg agtcacagat ttagtgaaaa gattggttag gaaagttgat 7501 ta //