Typing tool
|
Complete norovirus genomes
MH218645 | GII.6 | ||
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GII.P7 |
ORF1: 5..5098 ORF2: 5079..6722 ORF3: 6722..7498LOCUS MH218645 7521 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_176-1_17_12_2015, complete genome. ACCESSION MH218645 VERSION MH218645.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7521) 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 7521) 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..7521 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_176-1_17_12_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="17-Dec-2015" /note="genotype: GII.P7_GII.6" gene 5..5098 /gene="ORF1" CDS 5..5098 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17595.1" /translation="MKMASNDATTAFGSQNSVNDSINTAPSNKEEVGAFSNIKVGFKK MLGAVPKGTKAPSSDQHCPTVKIGTKTLTVPPEPPNGEDTVQFDAKSETVRGLPDLTT VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPP AAISLATIELTPISLYWRPVYTPNYLVHPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE LNDTWLSRRSISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNIFWTPPDVSSFIASLIGDFELQ GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALTLQEL ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP EIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL TARVAGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGTALKS VKTLEDLKVALRDVKFNECEIIYRNSKYRVSSNGKGSVSVDKVEDQASQTANEVGAAL LRLRQARARYYVSCFQDLIYTLIQVAGASFVVNRISKRFCWERWVKPTETQETSEPEK EVAQGRWEVEPKDIETEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTG SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL LITTTHVLPKGIKELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV CSILVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNENLGTYCGAPILGPG KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG KPPRPAVLEEAKKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVKKNDHWNG ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST QQRSILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ WNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM FRWMRFSDLSTWEGDRNLAPEGVNEDGVE" gene 5079..6722 /gene="ORF2" CDS 5079..6722 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17593.1" /translation="MKMASNDAAPSNDGAANLVPEANNEVMALEPVVGASIAAPVVGQ QNIIDPWIRENFVQAPQGEFTVSPRNSPGEMLLNLELGPELNPYLSHLSRMYNGYAGG MQVQVVLAGNAFTAGKIIFAAVPPHFPVENISAAQITMCPHVIVDVRQLEPVLLPLPD IRNRFFHYNQENTPRMRLVAMLYTPLRANSGEDVFTVSCRVLTRPAPDFEFTFLVPPT VESKTKPFTLPILTLGELSNSRFPAPIDMLYTDPNEGIVVQPQNGRCTLDGTLQGTTQ LVPTQICAFRGTLIGQTSRSSDSTDSAPRRRDHPLHVQLKNLDGTQYDPTDEVPAVLG AIDFKGTVFGVASQRDVSGQQVGATRAHEVHINTTDPRYTPKLGSILMYSESEDFVTG QPVRFTPIGMGDNDWHQWELPDYSGHLTLNMNLAPAVAPAFPGERILFFRSIVPSAGG YGSGQIDCLIPQEWVQHFYQEAAPSQSAVALIRYVNPDTGRNIFEAKLHREGFITVAN SGNNPIVVPPNGYFRFEAWVNQFYTLTPMGTGQGRRRNQ" gene 6722..7498 /gene="ORF3" CDS 6722..7498 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17594.1" /translation="MASAFLAGLVGDVITNGVGSLINAGANAVNQKVEYDFNKQLQMA SFKHDKEMLQSQVLATKQLQQEMMNIRQGVLTAGGFSPADAARGAVNAPMTKILDWNG TRYWAPNSMKTTSYSGQFSSSPVHKSPAPSHTALPKSRLQNDSASVYSFPSSASSQST HSTVLSAGTGSSRSTSTSTATPTLSRTSDWVRGQNERLSPFMDGALQTAFVTPPSSKA SSNGTVSTVPKAVLDSWTPMFNTHRQPLFAHLRRRGESQI" ORIGIN 1 gtgaatgaag atggcgtcta atgacgctac cactgccttt ggcagccaaa actctgtcaa 61 tgacagtatc aacaccgccc cttctaataa agaagaggtt ggtgcattct ccaacatcaa 121 agttggtttt aagaaaatgc tgggtgccgt tcccaagggg accaaagcac ccagtagtga 181 tcagcactgc cccacagtta agatcgggac caaaacgtta acagttcccc ctgagccccc 241 aaatggtgaa gacaccgtgc agtttgatgc gaagtcggaa actgtgcgtg ggctaccaga 301 cttaacaacg gtgcagaatg aacacgaaaa cacaccatac actgtccctc cattgagtga 361 aagggagcac agaccagcca ctgagccgct tcctggcaca atactggaga tgtgggatgg 421 tgaattctac cattactccg tgtacgtcag cggtggcaaa gccctagggg ttcacaagcc 481 ccctgcagcg ataagcctcg cgacgataga actcacaccc atatctcttt attggaggcc 541 cgtttacacc cccaactatc tggtccaccc agacacgttg aaaggcctcg ctggtgagaa 601 gttcccctac acggctttca gcaacaactg ttacaacttc tgttgctggg tgcttgagct 661 caatgacacg tggcttagca ggaggagcat ctccaggacc accggcttct tcaaaccata 721 tcagtcttgg aataggaagc cccttccaac cgttgatgat ggaaagatca aaaaggtggc 781 caacgcaatc ctctgcgcac ttgggtcact attttcaaaa ccaatcaagg acctattggg 841 taaacttaaa ccgttgaact tgctgcactt gctcgcatca tgtgactgga cgtttgcggg 901 catagtagag acagttatcc taatggcgga acttttcaac atcttttgga caccgccaga 961 tgtttccagc ttcatagcct ccctgatagg tgattttgaa ttacaggggc ctgaggacct 1021 ggctgtggag cttgtccccg tggtcatggg tggcataggt atggttctcg gcttcactgc 1081 tgagaagata ggccgcatgt tgtcgtccgc cgcatcaaca ctgcgggcat gcaaagactt 1141 ggggaattat gcccttgaca tactgaaact ggttatgaag tggttcttcc caaagaaaga 1201 agagaaagcc gagatggaga ccttaagggc gatcgaggac gccgtcctgg acatggaagc 1261 tataggaaat aaccacctca caaccctcct caaggacaag gatagcctca cggccttcat 1321 gaagactctg gatttagaag aggagaaagc aaggaaactg tccaccaagt catcctcgcc 1381 agacatcgtt ggcactatta atgccatact ggccagaata gctgctgcca ggtccctctt 1441 acataaggct aaggaagaaa tgtttagcag gatcagaccc gtggttgtta tgatctcggg 1501 tagacctggc attggtaaaa cccacatggc aagacacttg gctaagagta tcgccaacac 1561 catgagcggc gaccagagag tagggctagt cccacgcaat ggggtcgacc actgggacgc 1621 ctacagggga gagagggtgg ttttatggga tgattatggc atgggaaacc ctgtcaaaga 1681 tgccctaaca ctgcaagagt tggctgacac ctgcccagta actctaaact gtgataggat 1741 tgagaacaag gggaagatgt tcgacagtga tgtcatcata atcacaacca atttagtcaa 1801 cccagcgccc ctcgattatg taaacttcga ggcgtgctcc agaagggtcg actttctggt 1861 ctatgcagag tcaccagaaa ttgagaaggt taagagagat ttccccggcc aacctgacat 1921 gtggaaggac cattttaaac cagacttttc ccacataaaa ctgaccctag ccccacaggg 1981 tggatttgac aagaacggca acaccccgca tggtaagggc accatgcgat ccttaaccca 2041 ggggtccctg actgcaaggg ttgcaggtct tgttcatgag aggagagacg agtttcagct 2101 ccaggggaat gaccttcaaa catacaactt tgacaccaac agggtctctg catttaggaa 2161 gctggccgcg gacaacaagt atgggatcat ggagacaatg agagtgggta cggcgcttaa 2221 gagtgtcaag accttggaag atctgaaagt tgccctgagg gatgtgaagt tcaatgagtg 2281 tgagataatt tacaggaact ccaaataccg agtctcttcc aatggtaagg gctctgtctc 2341 tgttgacaaa gttgaggacc aagcgtccca gactgcaaac gaagtgggtg cagcactcct 2401 cagacttagg caggcaagag ccaggtacta tgtcagctgc ttccaagatc tcatctacac 2461 tctaatacag gtcgctggag catcattcgt tgtcaacagg atctctaaaa ggttctgttg 2521 ggagagatgg gtcaaaccaa ccgagaccca ggaaacgagc gaacccgaaa aggaagtggc 2581 ccaaggtaga tgggaggttg aacccaagga catagagaca gaaggtaaga agggtaaaaa 2641 caagaaagga agaggcaaga aacacacagc tttctccagc aaaggcctga gtgatgagga 2701 gtatgatgag ttcaaaagaa tcagagaaga aaggaacgga aaatactcca ttgaggaata 2761 cctgcaagac cgggatcgct actatgagga agtggcagtt gcccgggcaa cagaggagga 2821 cttctgtgaa gaggaggagg ccaagataag acaaagaatc ttccgcccca caaagaaaca 2881 gaggaaggaa gaaagggggg ttcttggttt ggtcactggc tcagacatca ggaagaggag 2941 accagacgat tttcaaccga agggcaacct gtgggcagac gacaccagga gtgtggacta 3001 caacgagaga cttgatttcg aggctccccc gagtgtctgg tcaagaatag tcccattggg 3061 cactggttgg ggcttctggg tctcttccaa tctcctgatc acaacaacac acgtcctgcc 3121 taaggggatt aaggaacttt ttggagtcga aatcaaacag attcaaattc ataagtctgg 3181 agagttctgc aggttcaggt tcccgagacc aatcagacca gatgtcacag ggctcgtgtt 3241 ggaggaaggt gctccagaag gcactgtctg ctccatactc gtgaagagac ctacaggtga 3301 gatgatccct ctggcagtga ggatgggcac gcatgcatcc atgaaaatac agggtaggac 3361 cgtcggtggc cagatgggga tgctcctcac aggggcaaat gcaaagaaca tggaccttgg 3421 caccggtcct ggtgactgcg gttgccctta catctacaaa cgtggcaacg atatagttgt 3481 cgcgggtgtc cacaccgcag cagcccgggg aggcaacact gtcatatgtg ccactcaggg 3541 gcaagatggg gaggcagtcc ttgagggaaa tgagaacctt ggcacttact gcggtgcccc 3601 aattttgggt ccaggcaagg cgcccaaact tagcacgaag accaagttct ggcgttcatc 3661 accagacgct ctgccgccag gcacttatga gcctgcctac ttgggaggca aggaccccag 3721 agtggaaaaa ggaccatccc tgcagcaagt catgagggac cagctaaagc ccttcacaga 3781 acccaggggc aagccaccta gacctgcagt cttagaagaa gccaaaaaga cagtgatgaa 3841 tgttctagaa caaaccattg accctgctaa gccatggacc tattcccaag catgtgcctc 3901 actggacaag accacttcca gcggtagccc ccatcatgtc aagaaaaatg accattggaa 3961 tggggaatcc ttcactggcc cccttgcaga ccaagcatcc aaagccaacc tcatgtacga 4021 acaggccaaa cacgtgcagc ccgtgtacac ggccgcactc aaagatgagt tagttaaaac 4081 tgacaagatc tacaaaaaga taaagaaaag gctcttatgg gggtcggacc ttggcacaat 4141 gatcagatgt gccagggcct tcggcggtct catggatagc atgaaggcaa gttgcatagc 4201 cctcccatgt agggtaggaa tgaacatgaa tgaagatggt cccatcatat ttgacaaaca 4261 ttctaagtat aggtaccatt atgatgctga ctattcaagg tgggactcaa cccagcaaag 4321 gagcattctc tcggccgcta tggaagtgat ggtgcggttc tctgccgagc cagagctggc 4381 acaagtggtt gcagaggacc tcctggcacc cagccaactg gatgttggcg actttgtcat 4441 ctcagtacag gagggtctgc catcaggggt cccatgtaca tcacagtgga attcaatagc 4501 acactggatc ctgaccttga gtgcaatggc agaagtgtcg ggtctctcac cagatgttgt 4561 tcaagcccac tcctgtttct cattctacgg tgacgatgag atcgtcagca ctgacatcaa 4621 tcttgatccc atgaagttga cacagaaact cagagaatat ggtctggtcc ccactcgacc 4681 tgacaaaact gagggtcccc tcgtaataac tgaagacctc accggcctaa cgttcctgcg 4741 taggtcaatt gcacgggacc cagctgggtg gtttggaaaa ctggaccaag actcaatcct 4801 cagacagttg tactggacaa ggggccccaa tcatgagaac ccatatgaga gcatggtccc 4861 tcactcccag cgggccacac agcttatggc ccttctcggt gaggcttcac tgcatggccc 4921 ccagttttac aagaaggtta gcaagatggt catcaatgaa atcaaaagtg gtggtctgga 4981 attttatgtg cccagacaag aggccatgtt cagatggatg agattctctg acctcagcac 5041 atgggagggc gatcgcaatc ttgctcccga gggtgtgaat gaagatggcg tcgaatgacg 5101 ctgctccatc gaatgatggt gctgccaacc tcgtaccaga ggccaacaat gaggttatgg 5161 cacttgaacc ggtggtggga gcctcaattg cagctcctgt tgtcggccaa caaaatataa 5221 ttgacccctg gattagagaa aattttgtcc aagcaccaca gggtgagttc accgtctcac 5281 cgaggaactc gcctggtgag atgctattaa atcttgaatt gggcccagaa ctcaaccctt 5341 acctgagtca cctgtcccgc atgtataacg ggtatgctgg tggcatgcag gttcaggtgg 5401 tcctagctgg gaatgcgttc acagctggga aaatcatctt tgccgccgtg ccaccacatt 5461 ttcccgtaga aaatattagt gcagctcaaa taactatgtg cccccatgta attgtcgatg 5521 tgagacaact tgaaccagta cttctgcccc ttcctgacat aaggaacagg ttcttccatt 5581 acaaccagga gaacaccccc cggatgagac ttgtggctat gctttacacc cccctaaggg 5641 ccaactctgg tgaagatgtg tttactgttt cttgtagggt tttgacccga cctgcccctg 5701 attttgaatt tactttcctg gtaccaccaa ctgttgaatc aaagactaaa cctttcacac 5761 tgcccatatt aactcttggt gagctatcta actccaggtt cccagcccca atagatatgt 5821 tgtacactga cccaaatgag ggaatcgtag tccaaccaca aaatggcaga tgcactcttg 5881 atggcactct gcaaggcacc acacaactgg tccccaccca aatttgtgct ttcaggggca 5941 cactaattgg ccaaacatca agatcttcag actcaaccga ctcagcccct cggagaaggg 6001 atcacccact ccatgtgcaa ttaaagaatc ttgatggcac gcagtacgac ccaactgatg 6061 aagtgccagc agtccttggt gccattgact tcaaggggac tgtctttggg gtggccagtc 6121 agagagatgt gtcaggacaa caagtgggag caactcgagc tcatgaagtg cacatcaaca 6181 caaccgatcc taggtacaca ccaaaactgg ggtccattct catgtactca gagtcggaag 6241 actttgtgac tggacagccg gtccgcttca cacccatagg aatgggtgac aacgactggc 6301 accagtggga gctgcctgac tactctggac acctaaccct gaacatgaac cttgccccag 6361 cagtcgctcc tgctttcccg ggcgagagga ttcttttctt caggtcaata gtcccgtctg 6421 ctggtggcta tgggtctgga caaatagatt gcctcatacc acaggagtgg gttcagcatt 6481 tctaccagga agctgcacca tcccaatctg ccgtggcact catcaggtat gtcaatcctg 6541 acacaggcag gaacatcttt gaggctaaat tgcacaggga aggtttcatc accgtggcaa 6601 attctggtaa taaccccatt gttgtccccc ctaatgggta ttttaggttt gaggcttggg 6661 tgaaccaatt ttatactttg acccccatgg gaactggtca ggggcgtaga aggaatcaat 6721 aatggctagt gcttttcttg caggtcttgt tggcgacgtc ataacaaatg gcgttggatc 6781 tctaataaat gctggagcta atgcagttaa tcagaaagtt gaatatgatt tcaataaaca 6841 gcttcaaatg gcatcgttta aacatgataa agagatgttg caatcacaag tgttggcaac 6901 caaacagttg cagcaggaga tgatgaacat aaggcagggg gtgttgaccg ctggcggctt 6961 ctcccccgcg gatgctgcta gaggggccgt caatgcccca atgacaaaga ttttggactg 7021 gaatggcacc agatattggg cacctaacag catgaaaacc acaagttatt caggacagtt 7081 ttctagcagc cctgttcaca agtcccctgc tccttctcac actgctttgc caaagagtag 7141 attgcaaaac gattctgcta gtgtatatag ctttccttcc tctgcttcct cacaatcaac 7201 ccattcaaca gtactgtcag caggaaccgg gtcttctagg tccacctcca catctacagc 7261 gacccctacc ttgtctagaa ccagcgactg ggttagggga cagaacgaga ggctcagccc 7321 gtttatggat ggtgctctcc aaactgcctt tgtcacacct ccatcgagca aagcttcttc 7381 aaatggtacg gtctcaaccg ttcccaaagc tgttttggac tcctggaccc ctatgttcaa 7441 cacacatagg cagcctctct tcgcccatct acgtagacga ggggagtcac aaatttagtg 7501 aaaagagtga ttaggttttc t //