Typing tool
|
Complete norovirus genomes
MH218656 | GI.2 | ||
---|---|---|---|
GI.P2 |
ORF1: 5..5371 ORF2: 5355..6995 ORF3: 6995..7630LOCUS MH218656 7740 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GI isolate NORO_188_01_10_2015, complete genome. ACCESSION MH218656 VERSION MH218656.1 KEYWORDS . SOURCE Norovirus GI ORGANISM Norovirus GI Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7740) 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 7740) 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..7740 /organism="Norovirus GI" /mol_type="genomic RNA" /isolate="NORO_188_01_10_2015" /host="Homo sapiens" /db_xref="taxon:122928" /country="United Kingdom" /collection_date="01-Oct-2015" /note="genotype: GI.P2_GI.2" gene 5..5371 /gene="ORF1" CDS 5..5371 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17628.1" /translation="MMMASKDVVATNVASNNNANNTSATSRFLSRFRGLGGGASPPSP IKIKSTEMALGLIGRTTPESTGTAGPPPKQQRDRPPRTQEEVQYGMGWSDRPIDQNVK SWEELDTTVKEEILDNHKEWFDAGGLGPCTMPPTYERIRDDSPPGEQVKWSARDGVNI GVERLTTVSGPEWNLCPLPPIELRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTV GVHSPQAAFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLKELENEPWPYAAITNNCF EFCCQVMNLEDTWLQRRLVTSGRFHHPTQSWSQQTPEFQQDSKLELVRDAILAAVNGL VSQPFKNFLGKLKPLNVLNILSNCDWTFMGVVEMVILLLELFGVFWNPPDVSNFIASL LPDFHLQGPEDLARDLVPVILGGIGLAIGFTRDKVTKVMKSAVDGLRAATQLGQYGLE IFSLLKKYFFGGDQTERTLKGIEAAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEE EKARKLSAKNADPHVISSTNALISRISMARSALAKAQAEMTSRMRPVVIMMCGPPGIG KTKAAEHLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNK LQAIADSAPLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVY CSAPEVEQIRRVSPGDTSALKDCFKPDFSHLKMELAPQGGFDNQGNTPFGRGAMKPTT INRLLIQAVALTMERQDEFQLQGKMYDFDDDRVSAFTTMARDNGLGILSMAGLGKKLR GVTTMEGLKNALKGYKISACTIKWQAKVYSLESDGNGVNIKEERNILTQQQQSVCAAS VALTRLRAARAVAYASCIQSAITSILQIAGSALVVNRAVKRMFGTRTATLSLEGPPRE HKCRVHMAKAAGKGPIGHDDVVEKYGLCETEEDEEVAHTEIPSATMEGKNKGKNKKGR GRKNNYNAFSRRGLNDEEYEEYKKIREEKGGNYSIQEYLEDRQRYEEELAEVQAGGDG GIGETEMEIRHRVFYKSKSRKHHQEERRQLGLVTGSDIRKRKPIDWTPPKSAWADDER EVDYNEKISFEAPPTLWSRVTKFGSGWGFWVSSTVFITTTHVIPTSAKEFFGEPLTSI AIHRAGEFTLFRFSKKIRPDLTGMILEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIA SMRIQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVYKRANDWVVCGVHAAATKS GNTVVCAVQASEGETTLEGGDKGHYAGHEIIKHGCGPALSTKTKFWKSSPEPLPPGVY EPAYLGGRDPRVTGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSSLEQVMD TPVPWSYSDACQSLDKTTSSGFPYHRRKNDDWNGTTFIRELGEQAAHANNMYEQAKSM KPMYTAALKDELVKPEKVYQKVKKRLLWGADLGTVVRAARAFGPFCDAIKSHTIKLPI KVGMNSIEDGPLIYAEHSKYKYHFDADYTAWDSTQNRQIMTESFSIMCRLTASPELAS VVAQDLLAPSEMDVGDYVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDV IQSMSYFSFYGDDEIVSTDIEFDPAKLTQVLREYGLKPTRPDKSEGPIIVRKSVDGLV FLRRTISRDAAGFQGRLDRASIERQIYWTRGPNHSDPFETLVPHQQRKVQLISLLGEA SLHGEKFYRKISSKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVN DDGV" gene 5355..6995 /gene="ORF2" CDS 5355..6995 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17626.1" /translation="MMMASKDAPQSADGASGAGQLVPEVNTADPLPMEPVAGPTTAVA TAGQVNMIDPWIVNNFVQSPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLSQMYNG WVGNMRVRILLAGNAFSAGKIIVCCVPPGFTSSSLTIAQATLFPHVIADVRTLEPIEM PLEDVRNVLYHTNDNQPTMRLVCMLYTPLRTGGGSGSSDSFVVAGRVLTAPSSDFSFL FLVPPTIEQKTRAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQ LLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMR ISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPST PPGTDINLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPC LLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQ QLPLNGVFLFVSWVSRFYQLKPVGTASTARGRLGVRRI" gene 6995..7630 /gene="ORF3" CDS 6995..7630 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17627.1" /translation="MAQAIIGAIAASAAGSALGAGIQAGAEAALQSQRYQQDLALQRN TFEHDKDMLSYQVQASNALLAKNLNTRYSMLVAGGLSSADASRAVAGAPVTQLIDWNG TRVAAPRSSATTLRSGGFMAVPMPVQPKSKALQSSGFSNPAYDTSTVSSRTSSWVQSQ NSLRSVSPFHRQALQTVWVTPPGSTSSSSVSSTPYGVFNTDRMPLFANLRR" ORIGIN 1 gtgaatgatg atggcgtcga aagacgtcgt tgcaactaat gttgcaagca acaacaatgc 61 taacaacact agtgctacat ctcggttttt atcgagattt aggggcttag gaggtggcgc 121 aagcccccct agccctataa aaatcaaaag tacagaaatg gctctggggt taattggcag 181 aacgacccca gaatcaacgg ggaccgctgg tccaccgccc aaacaacaga gagaccgacc 241 tcctagaact caggaggagg tccagtatgg tatggggtgg tccgacaggc ccattgatca 301 aaacgtcaaa tcatgggaag agcttgacac cacagttaag gaagagatcc tagacaacca 361 caaagaatgg tttgacgctg gtggtttggg cccttgcaca atgcctccaa catatgaacg 421 gatcagggat gacagtccac ctggtgaaca ggttaaatgg tccgcacgtg atggagtcaa 481 cattggagtg gaacgcctca caacagtgag tgggcctgag tggaatcttt gccccttacc 541 ccccattgaa cttaggaaca tggaaccagc tagtgaaccc actattggag atatgataga 601 attctacgaa ggccacatct atcattactc catatacatt gggcaaggca aaacagtcgg 661 cgtccattct ccacaggcgg cattttcagt ggctagagtg accatccagc ccatagccgc 721 ttggtggaga gtttgttaca taccccaacc caagcataga ctgagttacg accaactcaa 781 ggaactggag aatgagccat ggccatacgc ggccataacc aataattgtt ttgaattctg 841 ctgtcaagtc atgaaccttg aggacacgtg gctgcaaagg cgactggtca cgtcgggcag 901 attccaccac cccacccagt cgtggtcaca gcagacccct gagttccaac aagatagcaa 961 gttagagttg gttagggacg ccatattagc tgcagtgaat ggtcttgttt cgcagccctt 1021 taagaacttc ttgggtaaac tcaaacccct caacgtgctt aacatcctgt ctaactgtga 1081 ttggaccttc atgggggtgg tggaaatggt catactatta cttgaactct ttggtgtgtt 1141 ctggaacccg cctgatgtat ccaattttat agcgtccctt cttcctgatt tccatcttca 1201 gggacctgaa gacttggcac gagatctagt cccagtgatt cttggtggta taggattagc 1261 cattgggttc accagggaca aagtcacaaa ggtcatgaag agtgctgtgg atggtcttcg 1321 agctgccaca caactgggac agtatggatt agaaatattc tcactgctca agaaatactt 1381 ctttgggggg gaccagactg agcgtaccct caaaggcatt gaggcagcag tcatagatat 1441 ggaggtactg tcgtccactt cagtgacaca gctagtgagg gacaaacagg cagcaaaggc 1501 ctatatgaac atcttggaca atgaagaaga gaaggccagg aagctctctg ctaaaaacgc 1561 tgacccacat gtgatatcct caacaaatgc cctaatatcg cgcatatcca tggcacgatc 1621 tgcattggcc aaggcccagg ctgagatgac cagtcgaatg cgaccagttg tcattatgat 1681 gtgtggccca cctgggattg ggaagaccaa ggctgctgag cacctagcta agcgtctagc 1741 caatgagatc agaccaggtg gtaaggtggg gttggttccc cgtgaagctg tcgaccactg 1801 ggacggttat catggtgagg aagtgatgct gtgggatgac tatggcatga caaaaataca 1861 agacgattgt aataaactcc aggccattgc tgattcggcc cccctcacat taaattgtga 1921 taggattgaa aataaaggaa tgcagttcgt ttcagatgca atagtcatca ccaccaacgc 1981 cccaggcccc gcccctgtgg actttgtcaa ccttggacca gtgtgtagac gggtcgactt 2041 tttggtgtac tgctctgccc cagaggtgga acagatacgg agagtcagcc ctggcgacac 2101 atcagcactg aaagactgct tcaagccaga tttctcacat ttaaaaatgg agctggcccc 2161 acaaggtggg tttgataatc aagggaacac accgtttggc aggggcgcca tgaagccaac 2221 aaccattaat agactcctca tacaagccgt ggccctcacc atggaaaggc aggatgagtt 2281 ccagttgcag gggaagatgt atgactttga tgatgacagg gtgtcagcgt tcaccaccat 2341 ggcacgtgac aatggcctgg gcatcttgag catggcgggt ctgggtaaga agttacgcgg 2401 tgtcacaacg atggagggct tgaagaatgc cctgaaggga tacaaaatta gtgcgtgcac 2461 aataaaatgg caggctaaag tgtactcact agagtcagat ggcaatggtg tcaacattaa 2521 agaggagagg aacatcttaa cccaacaaca acagtcagtg tgtgctgcct ctgtcgcgct 2581 cactcgcctc cgggctgcgc gtgcggtggc atacgcgtca tgcatccaat cggctataac 2641 ttccatacta caaattgctg gctcagccct agtggttaac agagcagtga agagaatgtt 2701 tggcacgcgc actgccaccc tgtcccttga gggccccccc agagaacaca aatgcagggt 2761 ccacatggcc aaggctgcag gaaaggggcc tattggccat gatgatgtgg tagaaaagta 2821 tgggctttgt gaaactgagg aggacgaaga agtggcccac actgaaatcc cttctgccac 2881 catggagggc aagaataaag ggaagaacaa gaaaggacgt ggtcggaaga acaactataa 2941 cgccttctcc cgcaggggac tcaatgatga agagtacgaa gagtacaaga agatacgcga 3001 ggagaaaggt ggcaattata gcatacagga gtacctagag gataggcaaa ggtatgaaga 3061 agaactagca gaggttcaag caggtggaga tggaggaatc ggggaaactg aaatggagat 3121 ccgccacaga gtgttctaca aatccaagag tagaaagcat caccaggaag agcgacgcca 3181 gctagggctg gtgacaggat ccgacattcg gaagagaaaa ccaatcgact ggaccccacc 3241 caagtcagca tgggcagatg atgagcgtga agtggactac aatgagaaga tcagttttga 3301 ggcgcccccc actttatgga gcagagtgac aaagtttggg tctggatggg gtttctgggt 3361 tagctctaca gtcttcataa ccacaacgca cgtcatacca accagtgcga aggaattctt 3421 tggtgaaccc ctaaccagca tagccatcca cagggctggt gagttcactc tattcaggtt 3481 ctcaaagaaa attaggcctg acctcacagg tatgatcctt gaggagggtt gccccgaggg 3541 cacagtgtgt tcagtactga taaaaaggga ctctggtgaa ctactgccat tggctgtaag 3601 aatgggcgca atagcatcaa tgcgtataca gggccgcctt gtccatgggc agtccggcat 3661 gttgctcacc ggggctaatg ctaagggcat ggaccttgga accatcccag gagactgtgg 3721 ggctccttat gtctataaga gagccaacga ctgggtggtc tgtggtgtac acgctgctgc 3781 caccaaatca ggcaacaccg ttgtgtgcgc tgttcaggcc agtgaaggag aaaccacgct 3841 tgaaggcggt gacaaaggtc actatgctgg acatgaaata attaagcatg gttgtggacc 3901 agccctgtca accaaaacca aattctggaa atcatccccc gaaccactac cccctggggt 3961 ctatgaaccc gcctacctcg ggggccggga ccctagggta actggcggtc cctcactcca 4021 acaggtgttg cgggaccaat taaagccatt tgctgagcca cgaggacgca tgccagagcc 4081 aggtctcttg gaggccgcag ttgagactgt gacttcatca ttagagcagg ttatggacac 4141 tcccgttcct tggagctata gtgatgcgtg ccagtccctt gataagacca ccagttctgg 4201 ttttccctac cacagaagga agaatgacga ctggaatggc accaccttta tcagggagtt 4261 aggggagcag gcagcacacg ccaataacat gtatgaacag gctaaaagta tgaaacccat 4321 gtacacggca gcgcttaaag atgaactagt caaaccagag aaggtatacc aaaaagtgaa 4381 gaagcgctta ttatgggggg cagacttggg cacggtggtt cgggccgcgc gggcttttgg 4441 tccattctgt gatgctataa aatcccacac aatcaaattg cccattaaag ttggaatgaa 4501 ttcaattgag gatgggccac tgatctatgc agaacattca aagtataagt accattttga 4561 tgcagattac acagcttggg attcaactca aaatagacaa atcatgacag agtcattctc 4621 aatcatgtgt cggctaactg catcacctga actagcttca gtggtggctc aggatttgct 4681 tgcaccctca gagatggatg ttggcgacta tgtcataaga gtgaaggaag gtctcccatc 4741 tggttttcca tgtacatcac aggttaatag tataaaccat tggttaataa ctctgtgtgc 4801 cctttctgaa gtaactggtc tgtcgccaga tgtcatccag tccatgtcat atttctcttt 4861 ctatggtgat gatgaaatag tgtcaactga catagaattt gatccagcaa aactgacaca 4921 agtcctcaga gagtatggac ttaaacccac ccgccccgac aaaagcgagg gcccaataat 4981 tgtgaggaag agtgtggatg gtttggtctt tctgcgtcgc actatctccc gcgacgccgc 5041 aggattccag gggcgactgg accgggcatc cattgaaaga caaatctact ggactagagg 5101 acccaatcat tcagaccctt ttgagaccct ggtgccacac caacaaagga aggtccaact 5161 aatatcatta ttgggtgagg cctcactgca tggtgaaaag ttttacagga agatttcaag 5221 taaagtcatc caggaaatta aaacaggggg ccttgaaatg tatgtgccag gatggcaagc 5281 catgtttcgt tggatgcggt tccatgacct tggtttgtgg acaggagatc gcaatctcct 5341 gcccgaattt gtaaatgatg atggcgtcta aggacgcccc tcaaagcgct gatggcgcaa 5401 gcggcgcagg tcaactggtg ccggaggtta atacagctga ccccttaccc atggaacctg 5461 tggctgggcc aacaacagcc gtagccactg ctgggcaagt taacatgatt gatccctgga 5521 ttgttaataa ttttgtccag tcacctcaag gtgagttcac aatctctcct aacaataccc 5581 ccggtgatat tttgtttgat ttacaattag gtccacatct aaaccctttc ttgtcacatt 5641 tgtcccaaat gtataatggc tgggttggga acatgagagt cagaattctc cttgctggga 5701 atgcattctc agctggaaag attatagttt gttgtgtccc ccctggcttt acatcttctt 5761 ctctcaccat agctcaggct acattgtttc cccatgtgat tgctgatgtg aggacccttg 5821 agccaataga aatgcccctc gaggatgtac gcaacgtcct ctatcacacc aatgataatc 5881 aaccaacaat gcggctggtg tgtatgctat acacgccgct ccgcactggt ggggggtctg 5941 gtagttctga ttcctttgta gttgctggca gggttctcac agcccctagt agcgacttca 6001 gtttcttgtt ccttgtcccg cctaccatag aacagaagac tcgggctttc actgtgccta 6061 atatcccctt gcaaaccttg tccaattcta ggttcccttc cctcatccag gggatgattc 6121 tgtcccccga tgcatctcaa gtggtccaat tccaaaatgg gcgttgcctt atagatggtc 6181 aactcttagg cactacaccc gctacatcag gacagctgtt cagagtaaga ggaaagataa 6241 atcagggagc ccgcacactt aacctcacag aggtggatgg taaaccattc atggcatttg 6301 attcccctgc acctgtgggg ttccccgatt ttggaaaatg tgattggcac atgagaatca 6361 gcaaaacccc gaacaacaca agttcaggtg accccatgcg cagtgtcagc gtgcaaacca 6421 atgtgcaggg ttttgtgcca cacctgggaa gtatacaatt tgatgaagtg tttaatcatc 6481 ccacaggtga ctacattggc accattgaat ggatttccca gccatctaca ccccctggaa 6541 cagatattaa tctgtgggag atccccgatt atggatcgtc cctttcccaa gcagctaatc 6601 tggccccccc agtattcccc cctggatttg gtgaggccct tgtatacttt gtttctgctt 6661 tcccgggccc caataaccgc tcagccccga atgatgtacc ctgtcttctc cctcaagagt 6721 acataaccca ctttgtcagt gaacaagccc caacgatggg tgacgcagct ttactgcatt 6781 atgtcgaccc tgataccaac aggaaccttg gggagttcaa gctataccct ggaggttacc 6841 tcacctgtgt accaaatggg gtaggtgccg gtcctcaaca gctccctctc aatggtgttt 6901 ttctctttgt ttcttgggtg tctcgttttt accagcttaa gcctgtggga acagccagta 6961 cggcaagagg taggcttgga gtacgccgta tataatggcc caagccatca taggagcaat 7021 tgccgcgtca gctgcaggct cagcattggg tgcgggcatc caggctggtg ccgaggctgc 7081 gcttcagagt caaagatacc aacaagactt agccctgcaa aggaatactt ttgaacatga 7141 taaggatatg ctttcctacc aggtccaggc aagtaatgca cttttggcaa agaatctcaa 7201 tacccgctat tctatgcttg ttgcaggggg tctttctagt gctgatgctt ctcgggctgt 7261 tgctggggcc cctgtaacac aattgattga ttggaacggc actcgggttg ccgcccccag 7321 gtcaagtgca acaactctga ggtctggtgg ttttatggca gtccccatgc ctgttcaacc 7381 caaatctaag gccttgcaat cctctgggtt ttccaatcct gcttatgaca cgtccacagt 7441 ttcttctagg acttcttctt gggtgcagtc acagaattcc ctgcgaagtg tatcaccctt 7501 tcataggcag gcccttcaaa ctgtatgggt tactccacct gggtctactt cctcttcttc 7561 tgtttcctca acaccttatg gtgtttttaa tacggatagg atgccgctat tcgcaaattt 7621 gcggcgttaa tgttgtaata taatgcagca gtgggcacta tattcaattt ggtttaatta 7681 gtgaataatt tggctattga ttagtgttaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa //