Typing tool
|
Complete norovirus genomes
MH218720 | GI.2 | ||
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GI.P2 |
ORF1: 5..5371 ORF2: 5355..6995 ORF3: 6995..7630LOCUS MH218720 7710 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GI isolate NORO_79_05_07_2014, complete genome. ACCESSION MH218720 VERSION MH218720.1 KEYWORDS . SOURCE Norovirus GI ORGANISM Norovirus GI Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7710) 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 7710) 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..7710 /organism="Norovirus GI" /mol_type="genomic RNA" /isolate="NORO_79_05_07_2014" /host="Homo sapiens" /db_xref="taxon:122928" /country="United Kingdom" /collection_date="05-Jul-2014" /note="genotype: GI.P2_GI.2" gene 5..5371 /gene="ORF1" CDS 5..5371 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17820.1" /translation="MMMASKDVVATNVASNNNANNTSATSRFLSRFKGLGGGASPPSP IKIKSTEMALGLIGRTTPESTGTAGPPPKQQRDRPPRTQEEVQYGMGWSDRPIDQNVK SWEELDTTVKEEILDNHKEWFDAGGLGPCTMPPTYERVRDDSPPGEQVKWSARDGVNI GVERLTTVSGPEWNLCPLPPIDLRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTV GVHSPQAAFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLKELENEPWPYAAITNNCF EFCCQVMNLEDTWLQRRLVTSGRFHHPTQSWSQQTPEFQQDSKLELVRDAILAAVNGL VSQPFKNFLGKLKPLNVLNILSNCDWTFMGVVEMVILLLELFGVFWNPPDVSNFIASL LPDFHLQGPEDLARDLVPVILGGIGLAIGFTRDKVTKIMKSAVDGLRAATQLGQYGLE IFSLLKKYFFGGDQTERTLKGIEAAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEE EKARKLSAKNADPHVISSTNALISRISMARSALAKAQAEMTSRMRPVVIMMCGPPGIG KTKAAEHLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNK LQAIADSAPLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVY CSAPEVEQIRRVSPGDTSALKDCFKPDFSHLKMELAPQGGFDNQGNTPFGRGTMKPTT INRLLIQAVALTMERQDEFQLQGKMYDFDDDRVSAFTTMARDNGLGILSMAGLGKKLR GVTTMEGLKNALKGYKISACTIKWQAKVYSLESDGNSVNIKEERNILTQQQQSVCAAS 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" /note="predicted CDS stop by homology is invalid; there may be a valid stop in a different location due to truncation (trc) or extension (ext) (TAG|TAA|TGA) [ATA ending at position 6992 on + strand];first in-frame stop codon exists 3' of stop position predicted by homology to reference [homology search predicted 5355..6992 revised to 5355..6995 (stop shifted 3 nt)]" /codon_start=1 /product="VP1" /protein_id="AWR17818.1" /translation="MMMASKDAPQSADGASGAGQLVPEVNTADPLPMEPVAGPTTAVA TAGQVNMIDPWIVNNFVQSPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLSQMYNG WVGNMRVRILLAGNAFSAGKIIVCCVPPGFTSSSLTIAQATLFPHVIADVRTLEPIEM PLEDVRNVLYHTNDNQPTMRLVCMLYTPLRTGGGSGNSDSFVVAGRVLTAPSSDFSFL FLVPPTIEQKTRAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQ LLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMR ISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPST PPGTDIDLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPC LLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQ QLPLNGVFLFVSWVSRFYQLKPVGTASTARGRLGVRRI" gene 6995..7630 /gene="ORF3" CDS 6995..7630 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17819.1" /translation="MAQAIIGAIAASAAGSALGAGIQAGAEAALQSQRYQQDLALQRN TFEHDKDMLSYQVQASNALLAKNLNTRYSMLVAGGLSSADASRAVAGAPVTQLIDWNG TRVAAPRSSATTLRSGGFMAVPMPVQSKSKALQSSGFSNPAYDTSTVSSRTSSWVQSQ NSLRSVSPFHRQALQTVWVTPPGSTSSSSVSSTPYGVFNTDRMPLFANLRR" ORIGIN 1 gtgaatgatg atggcgtcga aagacgtcgt tgcaactaat gttgcaagca acaacaatgc 61 taacaacact agtgctacat ctcggttctt atcgagattt aagggcttag gaggcggcgc 121 aagcccccct agccctataa aaattaaaag tacagaaatg gctctggggt taattggcag 181 aacgacccca gaatcaacgg ggaccgctgg cccaccgccc aaacaacaga gagaccgacc 241 tcctagaact caggaggagg tccagtacgg tatggggtgg tctgacaggc ccattgacca 301 gaacgtcaaa tcatgggaag agcttgacac cacagttaag gaagagatcc tagacaacca 361 caaagaatgg tttgacgctg gtggtttggg tccttgcaca atgcctccaa catatgaacg 421 ggtcagggat gacagtccgc ctggtgaaca ggttaaatgg tccgcacgtg atggagtcaa 481 cattggagtg gaacgcctca caacagtgag tgggcctgag tggaatcttt gccccttacc 541 ccccattgat ttgaggaaca tggaaccagc tagtgaaccc actattggag atatgataga 601 attctacgaa ggccacatct atcattactc catatacatt gggcaaggta agacagtcgg 661 cgtccattct ccacaggcgg cattttcagt ggctagagtg accatccagc ccatagccgc 721 ttggtggaga gtttgttaca taccccaacc caagcataga ctgagttacg accaactcaa 781 ggaactagag aatgagccat ggccatacgc ggccataact aataattgtt ttgaattctg 841 ctgtcaagtc atgaaccttg aggacacgtg gttgcaaagg cgactggtca cgtcgggcag 901 attccaccac cccacccagt cgtggtcaca gcagacccct gagttccaac aagatagcaa 961 gttagagttg gttagggacg ccatattggc tgcagtgaat ggtcttgttt cgcagccctt 1021 taagaacttc ttgggtaaac tcaaacccct caatgtgctt aacatcctgt ctaactgtga 1081 ttggaccttc atgggggtgg tggaaatggt catactatta cttgaactct ttggtgtgtt 1141 ctggaacccg cctgatgtat ccaattttat agcgtccctt cttcctgatt tccatcttca 1201 gggacctgaa gacttggcac gagatctagt cccagtgatt cttggtggta taggattggc 1261 cattgggttc accagagaca aagttacaaa gatcatgaag agtgctgtgg atggtcttcg 1321 agctgctaca caactgggac agtatggatt agaaatattc tcactgctca agaagtactt 1381 ctttgggggg gaccagactg agcgcaccct caaaggcatt gaggcagcag tcatagatat 1441 ggaggtactg tcctccactt 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 gtgtggtcca cctgggattg ggaagaccaa ggctgctgag cacctagcta agcgtctagc 1741 caatgagatc agaccaggtg gtaaggtggg gttggttccc cgtgaagctg tcgaccactg 1801 ggacggctat catggtgagg aagtgatgct gtgggatgac tatggcatga caaaaataca 1861 agacgactgt aataaactcc aggccattgc tgattcggcc cccctcacat taaattgtga 1921 taggattgaa aataaaggaa tgcagttcgt ttcagatgca atagtcatca ccaccaacgc 1981 cccaggcccc gcccctgtgg actttgtcaa ccttggacca gtgtgtagac gggtcgactt 2041 tttggtgtac tgctctgccc cagaggtgga gcagatacgg agagtcagcc ctggcgacac 2101 atcagcactg aaagactgct tcaagccaga tttctcacat ttaaaaatgg agctggctcc 2161 acaaggtggg ttcgataatc aagggaacac accgtttggc aggggcacca tgaagccaac 2221 aaccattaat agactcctca tacaagccgt ggcccttacc atggaaaggc aggatgagtt 2281 ccagttgcag ggaaagatgt atgactttga tgatgacagg gtgtcagcgt tcaccaccat 2341 ggcacgtgac aatggcctgg gcatcttgag catggcgggt ctaggtaaga agctacgcgg 2401 tgtcacaacg atggagggct tgaagaatgc cctgaaggga tacaaaatta gtgcgtgcac 2461 aataaaatgg caggctaaag tgtactcact agagtcagat ggcaacagtg tcaacattaa 2521 agaggagagg aacatcttaa ctcaacaaca acagtcagtg tgtgctgcct ctgttgcgct 2581 cactcgcctc cgggctgcgc gtgcggtggc atacgcgtca tgcatccaat cggctataac 2641 ctctatacta caaattgctg gctcggccct agtggtcaac agagcagtga agagaatgtt 2701 tggcacgcgt actgccaccc tgtcccttga gggccccccc agagaacaca agtgcagggt 2761 ccacatggcc aaggccgcag gaaaggggcc tattggccat gatgatgtgg tagaaaagta 2821 tgggctttgc gaaactgagg aggacgaaga agtggcccac actgaaatcc cttctgccac 2881 catggagggc aagaataaag ggaagaacaa gaaaggacgt ggtcggaaga acaactacaa 2941 cgccttctcc cgcaggggac tcaatgatga agagtacgaa gagtacaaga agatacgcga 3001 ggagaaaggt ggcaattata gcatacagga gtacctagag gataggcaaa ggtatgaaga 3061 agagctagca gaggttcaag caggtggaga tggaggaatc ggggaaactg aaatggaaat 3121 ccgccacaga gtgttctaca aatctaagag tagaaagcat caccaggaag agcgacgcca 3181 gctagggctg gtaacaggtt ccgacattcg gaagagaaaa ccaatcgact ggaccccacc 3241 caagtcagca tgggcagatg atgagcgtga ggtggattac aatgagaaga tcagttttga 3301 ggcgcccccc actttatgga gcagagtgac aaagtttggg tctggatggg gtttctgggt 3361 cagctctaca gtcttcataa ccacaacgca cgtcatacca accagtgcga aggaattctt 3421 tggtgaaccc ctaaccagca tagccatcca cagggctggt gagttcactc tattcaggtt 3481 ctcaaagaaa attaggcctg acctcacagg tatgatcctt gaggagggtt gccccgaggg 3541 cacagtgtgt tcagtactaa taaaaaggga ctctggtgaa ctactgccat tggctgtaag 3601 aatgggcgca atagcatcaa tgcgtataca gggccgcctt gtccatgggc agtccggcat 3661 gttgctcacc ggggccaatg ctaagggcat ggaccttgga accatcccag gagactgtgg 3721 ggctccttat gtctataaga gagccaacga ctgggtggtc tgtggtgtac acgctgctgc 3781 caccaaatca ggcaacaccg ttgtgtgcgc cgttcaggcc agtgaaggag aaaccacgct 3841 tgaaggcggt gacaaaggtc attatgctgg acatgaaata attaagcatg gttgtggacc 3901 agccctgtca accaaaacca aattctggaa atcatccccc gaaccactac cccctggggt 3961 ctatgaaccc gcctacctcg ggggccggga ccctagggta actggcggtc cctcactcca 4021 acaggtgttg cgggaccagt taaagccatt tgctgagcca cgaggacgca tgccagagcc 4081 aggtctcttg gaggccgcag ttgagactgt gacttcatca ttagagcagg ttatggacac 4141 tcccgttcct tggagctata gtgatgcgtg ccagtccctt gataagacca ctagttctgg 4201 ttttccctac cacagaagga agaatgacga ctggaatggc accaccttta tcagggagtt 4261 aggggagcag gcagcacacg ctaataacat gtatgaacag gctaaaagta tgaaacccat 4321 gtacacggca gcacttaaag atgaactagt caaaccagag aaggtatacc aaaaagtgaa 4381 gaagcgcttg 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 aagatttgct 4681 tgcaccctca gagatggatg ttggcgacta tgtcataaga gtgaaggaag gcctcccatc 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 gtttagtctt tttgcgtcgc actatctccc gcgacgccgc 5041 aggattccag gggcgactgg accgggcatc cattgaaagg caaatctact ggactagagg 5101 acccaaccac tcagaccctt ttgagaccct ggtgccacat caacaaagga aggtccaact 5161 aatatcatta ttgggtgagg cctcactgca tggtgaaaag ttttacagga agatttcaag 5221 taaagtcatc caggagatta aaacaggggg ccttgaaatg tatgtgccag gatggcaagc 5281 catgttccgt tggatgcggt tccatgacct tggtttgtgg acaggagatc gcaatctcct 5341 gcccgaattt gtaaatgatg atggcgtcta aggacgcccc tcaaagcgct gatggcgcaa 5401 gcggcgcagg tcaactggtg ccggaggtta atacagctga ccccttaccc atggaacctg 5461 tggctgggcc aacaacagcc gtagccactg ctgggcaagt taatatgatt 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 agctcaggcc acattgtttc cccatgtaat tgctgatgtg agaacccttg 5821 agccaataga aatgcccctc gaggatgtac gcaatgtcct ctatcacacc aatgataatc 5881 aaccaacaat gcggttggtg tgtatgctat acacgccgct ccgcactggt ggggggtctg 5941 gtaattctga ttcctttgta gttgctggca gggttctcac agcccctagt agcgacttta 6001 gtttcttgtt ccttgtcccg cctaccatag agcagaagac tcgggctttc actgtgccta 6061 atatcccctt gcaaaccttg tccaattcta ggtttccttc cctcatccag gggatgattc 6121 tgtcccccga tgcatctcaa gtggtccaat tccaaaatgg gcgctgcctt atagatggtc 6181 aactcctagg cactacaccc gctacatcag gacagctgtt cagagtaaga ggaaagataa 6241 atcagggagc ccgcacactt aacctcacag aggtggatgg taaaccattc atggcatttg 6301 attcccctgc acctgtgggg ttccccgatt ttggaaaatg tgattggcat atgagaatca 6361 gcaaaacccc aaacaacaca agttcaggtg accccatgcg cagtgtcagc gtgcaaacca 6421 atgtgcaggg ttttgtgcca cacctgggaa gtatacaatt tgatgaagtg tttaaccatc 6481 ccacaggtga ctacattggc accattgaat ggatttccca gccatctaca ccccctggaa 6541 cagatattga tctgtgggag atccccgatt atggatcatc cctttcccaa gcagctaatc 6601 tggccccccc agtattcccc cctggatttg gtgaggccct tgtgtacttt gtttctgctt 6661 tcccgggccc caataaccgc tcagccccga atgatgtacc ctgtcttctc cctcaagagt 6721 acataaccca ctttgtcagt gaacaagccc caacgatggg tgacgcagcc ttactgcatt 6781 atgtcgaccc tgataccaac aggaaccttg gggagttcaa gctataccct ggaggttacc 6841 tcacctgtgt accaaatggg gtaggtgccg ggcctcaaca gcttcctctt aatggtgttt 6901 ttctctttgt ttcttgggtg tctcgttttt atcagcttaa gcctgtggga acagccagta 6961 cggcaagagg taggcttgga gtgcgccgta tataatggcc caagccatca taggagcaat 7021 tgccgcgtca gctgcaggct cagcattggg tgcgggcatc caggctggtg ccgaggctgc 7081 gcttcagagt caaagatacc aacaagactt agccctgcaa aggaatactt ttgaacatga 7141 caaggatatg ctttcctacc aggtccaggc aagtaatgca cttttggcaa agaatctcaa 7201 tacccgctat tctatgcttg ttgcaggggg tctttctagt gctgatgctt ctcgggctgt 7261 tgctggggcc cctgtaacac aattgattga ttggaacggc actcgggttg ccgcccccag 7321 atcaagtgca acaactctga ggtctggtgg tttcatggca gtccccatgc ctgttcaatc 7381 caaatctaag gccctgcaat cctctgggtt ttctaatcct gcttatgaca cgtccacagt 7441 ttcttctagg acttcttctt gggtgcagtc acagaattcc ctgcgaagtg tgtcaccctt 7501 tcataggcag gcccttcaaa ctgtatgggt tactccacct gggtctactt cctcttcttc 7561 tgtttcctca acaccttatg gtgtttttaa tacggatagg atgccgctat tcgcaaattt 7621 gcggcgttaa tgttgtaata taatgcagca gtgggcacta tattcaattt ggtttaatta 7681 gtgaataatt tggccattga ttagtgttaa //