Typing tool
|
Complete norovirus genomes
MH218644 | GII.6 | ||
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GII.P7 |
ORF1: 5..5098 ORF2: 5079..6722 ORF3: 6722..7498LOCUS MH218644 7550 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_174-1_13_11_2015, complete genome. ACCESSION MH218644 VERSION MH218644.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7550) 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 7550) 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..7550 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_174-1_13_11_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="13-Nov-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="AWR17592.1" /translation="MKMASNDATTAFGSQNSVNDSINTTPSYKEEVGTFSNIKVGFKK MLGAVPKGTKAPSSDQHCPTVKIGTKTLTVPPEPPNGEDTVKFDAKSETVRGLPDLTT VQNEHENTPYTVPPLSEREHRPAAEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPP AAISLATIELTPISLYWRPVYTPNYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE LNDTWLSRRSISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFGIFWTPPDVSSFIASLIGDFELQ GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLAAFMKTLDLEEEKAR KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALTLQEL ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP EIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTHGSL TARVAGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGTALKG VKTLEDLKVALRDVKFNECEIIYRSSKYRVSSNGKGSVSVDKVEDQTSQTANEAGAAI LRLRQARARYYVSCFQDLVYTLIQVAGASFVVNRISKRFCWERWVKPTETQETSEPEK EVAQGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTG TDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL LITTTHVLPKGIKELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV CSILVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNENLGTYCGAPILGPG KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG KPPRPAVLEEAKKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNG ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST QQRSILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ WNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVISEIKSGGLEFYVPRQEAM FRWMRFSDLSTWEGDRNLAPEGVNEDGVE" gene 5079..6722 /gene="ORF2" CDS 5079..6722 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17590.1" /translation="MKMASNDAAPSNDGAANLVPEATNEVMALEPVVGASIAAPVVGQ QNIIDPWIRENFVQAPQGEFTVSPRNSPGEMLLNLELGPELNPYLSHLSRMYNGYAGG MQVQVVLAGNAFTAGKIIFAAVPPHFPVENISAAQITMCPHVIVDVRQLEPVLLPLPD IRNRFFHYNQENTPRMRLVAMLYTPLRANSGEDVFTVSCRVLTRPAPDFEFTFLVPPT VESKTKPFTLPILTLGELSNSRFPAPIDMLYTDPNEAIVVQPQNGRCTLDGTLQGTTQ LVPTQICSFRGTLISQTSRSADSTDSAQRVRNHPLHVQLKNLDGTPYDPTDEVPAVLG AIDFKGTVFGVASQRNTTGGSIGATRAHEVHIDTTNSRYTPKLGTVLMYSESDDFDNG QPTRFTPIGMGDDDWRQWELPEYSGHLTLNMNLAPAVAPAFPGERILFFRSVVPSAGG YGSGHIDCLIPQEWVQHFYQEAAPSQSAVALIRYVNPDTGRNIFEAKLHREGFITVAN SGNNPIVVPPNGYFRFEAWVNQFYTLTPMGTGQGRRRVQ" gene 6722..7498 /gene="ORF3" CDS 6722..7498 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17591.1" /translation="MAGAFLAGLAGDAITSGVGSLINAGANAINQKVEYDFNKQLQLA SFKHDKEMLQSQVLATKQLQQEMMNIRQGVLSAGGFSPTDAARGAVNAPMTKILDWNG TRYFAPNSMKTTSYSGQFSSNPVHRQPTLPPSASPKIKANSDSASVYSSISTAPSQST HSTALTAGSSSSRTTSSSAVASTLSRTSDWVRGQNERLSPFMDGALQTAFVTPPSSKA SSYGSVSTVPKAVLDSWTPMFNTHRQPLFAHVRRRGESQI" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cactgccttt ggcagccaaa actctgtcaa 61 tgacagtatc aacaccaccc cttcttataa agaagaggtt ggtacattct ccaacatcaa 121 agttggtttt aagaaaatgc tgggtgccgt tcccaagggg accaaagcac ccagtagtga 181 tcagcactgc cccacagtta agatcgggac caagacatta acagttcccc ctgagccccc 241 aaatggtgaa gacaccgtga agtttgatgc gaagtcggaa actgtgcgcg ggttgccaga 301 cttgacaacg gtgcagaatg aacacgaaaa cacaccatat actgtccccc cattgagtga 361 aagagagcac agaccagctg ctgaaccgct tcctggcaca atactggaaa tgtgggatgg 421 tgaattctac cattactctg tgtacgtcag cggtggcaaa gccctagggg ttcataaacc 481 ccctgcagcg ataagcctcg cgacgataga gctcacaccc atatctcttt attggaggcc 541 cgtttacacc cccaactatc tggtctgccc agacacgttg aagggccttg ctggtgagaa 601 gttcccctac acggccttca gcaacaactg ttacaacttc tgttgctggg tgcttgagct 661 caatgacacg tggcttagca ggagaagcat ctctaggacc accggcttct tcaaaccata 721 ccagtcttgg aataggaaac cccttccaac cgttgatgat ggaaagatca aaaaggtggc 781 caacgcaatt ctctgtgcac ttggatcact gttttcaaaa ccaatcaagg acctattggg 841 caaacttaaa ccattgaact tgctgcactt gctcgcatca tgtgactgga cgtttgcggg 901 tatagtagag acagtcatcc taatggcgga acttttcggc atcttttgga caccgccaga 961 tgtttccagt ttcatagcct ccctgatagg tgattttgaa ttgcaagggc ctgaggacct 1021 ggctgtggag cttgtacccg tggtcatggg tggcatagga atggttctcg gctttactgc 1081 tgagaagata ggccgcatgc tatcgtccgc tgcatcaaca ctgcgggcgt gcaaagactt 1141 ggggaactat gctcttgaca tattgaaact ggttatgaag tggttcttcc caaagaaaga 1201 agagaaagcc gagatggaaa ccctgagggc gattgaggat gccgtcctgg acatggaagc 1261 tataggaaat aaccatctca cgaccctcct caaggacaag gatagcctcg cggctttcat 1321 gaagactcta gatctagaag aagagaaggc aaggaagctg tccaccaagt catcctcgcc 1381 agacattgtc ggcaccatta atgccatact tgctagaata gctgctgcca ggtccctctt 1441 gcacaaggct aaagaagaaa tgttcagcag gatcagaccc gtggttgtca tgatctcggg 1501 tagacctggt attggcaaaa cccacatggc aagacacttg gctaagagta tcgccaacac 1561 catgagcggc gaccagagag tgggactcgt cccacgcaac ggggttgatc attgggacgc 1621 ctacagggga gagagggtgg ttttatggga tgattatggc atgggaaacc ctgtcaaaga 1681 tgccctaacg ctgcaagagc tggccgacac ctgcccagta actctaaact gtgataggat 1741 tgagaacaag gggaagatgt ttgacagtga tgtcatcata atcacgacca atttagtcaa 1801 cccagcgccc ctcgattatg taaacttcga ggcgtgctcc agaagggtcg actttctggt 1861 ctatgcagag tcaccagaaa ttgagaaggt taagagagac tttcccggcc aacctgacat 1921 gtggaaggac cattttaagc cggatttttc ccacataaaa ctgactctag ccccacaggg 1981 tgggtttgac aagaatggca acaccccgca tggtaagggc accatgcgat ccctaaccca 2041 tgggtccctg actgcaaggg ttgcaggtct tgtccatgag aggagagacg agtttcagct 2101 ccaggggaac gaccttcaaa catataactt tgataccaac agagtctctg catttaggaa 2161 gctggccgca gacaacaagt atgggatcat ggagactatg agagtgggca cagcgcttaa 2221 gggtgtcaag accttggaag atctgaaagt tgcactgagg gatgtgaagt tcaatgagtg 2281 tgagataatt tacagaagct caaaataccg agtctcttcc aatggtaaag gttctgtctc 2341 tgttgacaaa gttgaggacc agacatccca gaccgcaaac gaagcgggtg cagcaatcct 2401 tagactcaga caggcaagag ccagatacta tgtcagctgc ttccaagacc tcgtttacac 2461 tctaatacag gtcgccggag catcattcgt tgtcaacagg atctctaaaa ggttctgctg 2521 ggagagatgg gtcaaaccaa ccgagaccca ggaaacgagt gaacccgaaa aggaagtggc 2581 ccaaggcaga tgggagattg agcccaagga cacagaacca gaaggtaaga agggtaagaa 2641 caagaaagga agaggcaaga aacacacagc tttctccagt aaaggcttga gtgatgagga 2701 gtatgacgag ttcaagagaa tcagagaaga aaggaacgga aaatactcca ttgaggaata 2761 cctgcaagac cgggatcgct actatgagga agtggcagtt gcccgggcga cagaggagga 2821 cttctgtgaa gaggaggagg ccaagataag acaaagaatc tttcgcccca caaagaaaca 2881 gaggaaggaa gaaagggggg tgcttggttt ggttactggc acagacatca ggaagagaag 2941 accagacgat tttcaaccga agggcaacct gtgggcagac gacactagga gtgtggacta 3001 caacgagaga cttgatttcg aggctccccc gagtgtctgg tcaagaatag tcccattggg 3061 cactggctgg ggcttctggg tctcatcaaa cctcctgatc acaacaacgc acgtcctacc 3121 taaggggatt aaagaactct ttggagttga gatcaaacag attcagattc ataagtctgg 3181 ggagttctgc aggttcagat tcccaagacc aattagacca gatgtcacag ggctcgtgtt 3241 ggaggaaggc gctccagaag gcactgtctg ctccatactc gtaaagagac ctacaggtga 3301 gatgatcccc ctggcagtga ggatgggcac gcatgcatcc atgaaaatac agggtaggac 3361 cgttggtggc cagatgggaa tgctcctcac aggggcaaat gcgaagaaca tggatcttgg 3421 caccggtcct ggtgactgcg gttgccctta catctacaaa cgtggcaatg atatagttgt 3481 cgcgggtgtt cacaccgcag cagcccgggg aggcaacact gtcatatgtg ccactcaagg 3541 gcaagatggg gaagcagtcc ttgagggaaa tgagaacctt ggcacttact gcggtgctcc 3601 aatcttgggt ccaggcaagg cgcccaaact cagcacgaag accaagttct ggcgttcatc 3661 accagacgct ttgccgccag gcacttatga gcctgcctac ttgggaggta aggaccctag 3721 agtggaaaaa ggaccatccc tgcagcaagt catgagggac cagctaaaac ctttcacaga 3781 gcccaggggc aagccaccta gacctgcagt cttagaagaa gccaaaaaga cagtgatgaa 3841 tgttctagag caaaccattg accctgctaa accgtggacc tattcccaag catgtgcctc 3901 actggacaag accacttcca gtggtagccc ccatcatgtc aggaaaaatg accattggaa 3961 tggagaatcc ttcactggcc ccctcgcaga ccaagcatcc aaagccaacc tcatgtacga 4021 gcaggccaaa catgtgcagc ccgtgtacac ggccgcactc aaagatgaac tagtcaaaac 4081 tgataagatc tacaagaaga taaagaaaag gctcttatgg gggtcggatc ttggtacaat 4141 gatcaggtgt gccagggcct ttggcggtct catggatagc atgaaggcaa gctgcatagc 4201 cctcccatgt agggtaggaa tgaacatgaa tgaagatggc cccatcatat ttgacaaaca 4261 ttctaaatat aggtaccatt atgatgctga ctattccagg tgggactcaa cccagcaaag 4321 gagcattctc tcggccgcta tggaagtgat ggtgcggttc tctgctgaac cagagctggc 4381 acaagtggtt gcagaggacc tcctggcacc cagccaacta gatgttggcg atttcgtcat 4441 ctcagtccag gagggcctgc catcaggagt cccatgcaca tcacaatgga attcaatagc 4501 acactggatc ctaaccttga gtgcaatggc agaagtatcg ggtctctcac cagatgttgt 4561 tcaagcccac tcctgtttct cattctacgg tgatgatgag atcgtcagca ctgacatcaa 4621 ccttgatccc atgaagttga cacagaagct cagagagtat ggcctggtcc ccacccgacc 4681 tgacaaaact gagggtcccc tcgtaataac tgaggatctc accggcctaa cgttcctgcg 4741 taggtcaatt gcacgggacc cagctgggtg gtttggaaag ttggaccaag actcaatcct 4801 cagacagttg tactggacaa gaggccccaa ccatgagaac ccatatgaga gcatggtccc 4861 tcattcccag cgggccacac aacttatggc ccttctcggt gaggcctcac tgcatggtcc 4921 ccagttttac aagaaagtta gcaagatggt tattagtgag atcaaaagtg gtggtctgga 4981 attctatgtg cccagacaag aggccatgtt cagatggatg agattctctg acctcagcac 5041 atgggagggc gatcgcaatc ttgctcccga gggtgtgaat gaagatggcg tcgaatgacg 5101 ctgctccatc gaatgatggt gctgccaacc tcgtaccaga ggccaccaat gaggttatgg 5161 cacttgagcc ggtggtggga gcctcaattg ctgctcctgt cgtcggccaa caaaatataa 5221 ttgacccctg gattagagaa aattttgttc aggcaccaca gggtgagttt actgtttcac 5281 caaggaactc acctggtgag atgcttctaa atcttgaatt aggccctgag ctcaaccctt 5341 atctgagtca cttgtcccgc atgtacaacg gctatgctgg tggtatgcag gttcaggtgg 5401 tcctagctgg gaatgcgttc acagctggta aaatcatctt tgccgccgtc ccaccacatt 5461 tccctgttga gaacattagt gcagcccaaa tcacaatgtg cccccatgta attgttgatg 5521 taagacagct tgagccagtg cttttgcccc ttcctgacat taggaataga ttctttcatt 5581 ataatcagga aaataccccc cggatgagac ttgtggctat gttgtataca ccccttagag 5641 caaattctgg tgaggatgtg tttacggtgt cttgcagagt tctgacccgc cctgcccccg 5701 actttgagtt cacgtttttg gtgccaccaa ctgtggagtc aaagactaag ccctttacac 5761 ttcctattct gactcttgga gagctgtcca actctagatt ccccgctccg atagacatgt 5821 tgtacactga ccccaatgag gcaattgtgg tgcaaccaca aaatggcagg tgcactctag 5881 atggaacact tcaagggacc acccaactgg tacccaccca aatttgctcc ttcaggggca 5941 cgctaattag ccagacgtcg aggtctgcag attcaactga ttcagctcaa cgggtgagga 6001 accaccctct ccacgttcag ctgaagaacc tcgatgggac accatatgac cctacagatg 6061 aggtgccagc agttttgggt gccatagatt tcaaaggaac tgtgtttggg gtcgctagcc 6121 aaagaaacac cacagggggc tctataggag caacccgcgc ccatgaagtg cacatagaca 6181 ccacaaactc tagatatacc ccaaagcttg gcactgtgtt gatgtattct gaatctgatg 6241 attttgataa tggacaaccc acccgcttca cccccattgg catgggagac gatgattggc 6301 gccaatggga attgcccgaa tattctggtc acctcactct taacatgaat ttggcccccg 6361 cagttgcccc tgcttttcct ggcgagcgca ttctcttctt cagatcagtg gtgccgtctg 6421 ctggtggcta tggatcaggt cacatagatt gcctcatccc acaggagtgg gttcagcatt 6481 tctaccagga ggccgctcca tcacagtccg cggtggctct tatcagatat gtcaaccctg 6541 acactggaag aaacatcttt gaggcaaaac tgcatagaga agggttcatc actgtggcaa 6601 attctggaaa caaccccata gttgtgcccc caaatggtta cttcaggttt gaggcctggg 6661 tcaatcaatt ctacacactc acccccatgg gaactggaca ggggcgcaga agagttcaat 6721 aatggcagga gctttcttag ctggattagc aggtgacgcc ataacaagtg gtgtcgggtc 6781 cctaatcaat gctggggcca atgcaattaa ccaaaaggta gagtatgact ttaataaaca 6841 gctccaattg gcatccttca aacatgacaa agagatgttg caatcacaag tactggccac 6901 taaacagctc cagcaggaga tgatgaacat aaggcaaggg gtcttgtccg ctggcggctt 6961 ttcccctaca gacgccgcga gaggtgctgt gaacgcgccg atgacaaaaa ttttggattg 7021 gaatggaaca aggtactttg ccccaaatag tatgaagaca accagttatt cgggccagtt 7081 ttccagcaac cctgtgcata ggcaacccac tttaccccct tctgcatccc caaaaattaa 7141 ggctaatagt gattctgcta gtgtatatag ttctatatct actgctcctt cacaatcaac 7201 tcactcaacg gctttgactg cggggtctag ctcatctagg acaacatcct cttctgcagt 7261 agcttccacc ctatccagga ctagtgactg ggtgagagga caaaatgaaa ggcttagccc 7321 gttcatggat ggtgctctcc aaacagcttt tgtcacacca ccatcgagca aagcttcatc 7381 atatgggtcg gtctcaaccg ttcccaaagc tgttttggac tcctggactc ctatgttcaa 7441 tacccatagg cagcctctct tcgctcatgt gcgcaggcga ggggagtcac agatttagtg 7501 aaaagattga ttaggttttc tttctttctt ctttcccttt tctttctttt //