Typing tool
|
Complete norovirus genomes
MH218697 | GII.2 | ||
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GII.P31 |
ORF1: 5..5104 ORF2: 5085..6713 ORF3: 6713..7492LOCUS MH218697 7545 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_34-7_30_10_2015, complete genome. ACCESSION MH218697 VERSION MH218697.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7545) 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 7545) 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..7545 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_34-7_30_10_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="30-Oct-2015" /note="genotype: GII.Pe_GII.2" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17749.1" /translation="MKMASNDASAAAAANSNNDIAKSSSDGMFSNMAVTFKRALGARP KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGELFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPGVEK AKRDFPGQPDMWKDAFNPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGMMDTMRVGRQLKDVKTM SDLKQALKNIAIKKCQIVYGGSTYTLEADGKGSVRVDKVQSTTVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMVNEDGC PKLKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYEEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVAGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="ORF1" /product="p48" mat_peptide 995..2092 /gene="ORF1" /product="NTPase" mat_peptide 2093..2629 /gene="ORF1" /product="p22" mat_peptide 2630..3028 /gene="ORF1" /product="VPg" mat_peptide 3029..3571 /gene="ORF1" /product="Pro" mat_peptide 3572..5101 /gene="ORF1" /product="RdRp" gene 5085..6713 /gene="ORF2" CDS 5085..6713 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17750.1" /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG IISQRDKHNSPGHSEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ" gene 6713..7492 /gene="ORF3" CDS 6713..7492 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17751.1" /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQRLQQN SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG TRYWAPGSMRTTSYSGRFTSTAPVRQADFQHTQSRPSSGSSVSSFTTQSSRPTLTTTT GSSHNTVSSNSTRSTNLSQSTVSRATSRTGEWVRDQNKNLEPYMHGALQTAFVTPPSS RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga 61 catcgcaaaa tcttcaagtg acggtatgtt ctctaacatg gctgtcactt ttaaacgggc 121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccacgacc 181 gcccacccca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact 241 agtggtctcc tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag 301 acaaccggaa gaaaccaaca cggcgttcag tgttccccca ctcaatcaaa gggagaacag 361 ggacgccaag gaaccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca 421 ttatggcctg tacgtggaac gaggccttat actcggtgtg cacaagccac cggcagccat 481 cagccttgcc aaggtcgagc taacaccact ctctttattc tggagacctg tatacacccc 541 ccagtatctc atctctccag acactctcag gagattacat ggagagttat tcccctacac 601 tgcttttgac aacaattgct acgccttttg ttgttgggta ctagacctaa acgactcatg 661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa 721 caggaaaccc ctccccacta tggatgattc taaattaaag aaggtagcca acatattttt 781 gtgcacctta tcttcactat tcaccagacc cattaaggac ataataggaa aattgaaacc 841 tctcaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc 901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgccccc ttactaggtg attatgaact gcaagggcct gaggaccttg cagtggaact 1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaattgg 1081 aaagatgcta tcatccgccg catccacttt aagagcttgc aaagatcttg gtgcatacgg 1141 actggaaatt ttgaaattgg tcatgaagtg gttcttccca aagaaagagg aagcgaatga 1201 actggctatg gtgagatcca tcgaggatgc agtgctggac ctcgaggcaa ttgaaaacaa 1261 ccacatgacc accctgctca aagacaaaga cagcttggca acctacatga gaacccttga 1321 ccttgaggag gagaaagcca ggaaactctc aaccaaatct gcttcacccg atatcgtggg 1381 cacaatcaac tctctactgg caagaatcgc tgctgcacgc tctctagtgc atcgggcgaa 1441 agaagagctc tccagcaggc cgagacccgt tgttgtgatg atatcgggaa aaccagggat 1501 agggaaaact caccttgcca gggagctagc taaaaagatc gcgtcctccc tcacggggga 1561 ccagcgcgtg ggtcttatcc cgcgcaatgg tgtcgaccac tgggacgcat acaaaggtga 1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggct 1681 acaggaactt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg 1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact 1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagatgc 1861 tcctggggtg gagaaggcaa agcgcgactt cccaggccaa cctgacatgt ggaaggacgc 1921 tttcaatcct gacttctcac acataaaact gtcattagct ccacagggtg gttttgacaa 1981 gaacggcaac accccgcatg gaaaaggtgt catgaagacc ctcaccaccg gctccctcat 2041 cgcccgggca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccggc 2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttaggcagc ttgctgctga 2161 aaacaagtat gggatgatgg acacaatgag agttggaaga cagctcaagg atgtcaagac 2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aaaaagtgcc agatagtgta 2281 cggtggtagc acctacacac ttgaggccga tggcaagggt agtgtgaggg ttgacaaagt 2341 acaaagtacc actgtgcaaa ccaataatga attagccggt gccctacacc acctaaggtg 2401 cgccagaatt agatactatg ttaagtgtgt ccaggaggca ctgtattcca tcatccaaat 2461 cgctggggct gcattcgtta ccacgcgcat cgctaagcgc atgaatatac agaacctctg 2521 gtccaagcca caagtggaag acacagaaga gatggttaac gaagatggtt gcccaaaact 2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gtaagaaagg 2641 gaagaacaag tccggccgtg gcaagaaaca cacagccttc tcaagcaaag gactcagtga 2701 tgaggagtac gaggagtaca agagaatcag agaagaaagg aacggtaagt attccataga 2761 agagtacctt caggacagag acaagtacta cgaggaggtg gccattgcta gggcaaccga 2821 agaggacttc tgtgaagaag aagaggccaa aatccgacag aggattttta gaccaacaag 2881 aaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggttccg aaatcaggaa 2941 aagaaaccca gaagatttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt 3001 tgactacaat gagaaactta actttgaggc cccaccaagc atatggtcgc ggatagtcaa 3061 ctttggttca ggttggggct tctgggtgtc ccccagcctg tttataactt caacccatgt 3121 catacctcaa ggtgcaaaag agttcttcgg agtctctatc aagcaaatcc agatacacaa 3181 atcaggtgaa ttctgccgac tgagattccc aaaaccaatc agaactgatg tggcgggcat 3241 gattctagaa gaaggcgcgc ccgaagggac cgtggcaaca ctgcttatca agagaccgac 3301 tggagagctc atgcctctgg cagccagaat ggggacccac gcaaccatga agattcaggg 3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagcatgga 3421 cctaggcaca acaccaggtg actgcggctg tccctacatc tacaagagag ggaatgatta 3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac 3541 ccaggggagt gagggagaag ccacacttga aggaggtgac aataaaggaa catattgtgg 3601 tgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag 3661 gtcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga 3721 tcccagagtt aaaggtggcc cttcattgca acaagttatg agggaccagt tgaagccatt 3781 cacagaaccc agaggcaaac caccaagacc aaatgttcta gaagctgcca agaaaaccat 3841 catcaatgtt cttgagcaaa caattgaccc accccaaaaa tggtcattcg cgcaggcctg 3901 cgcatccctt gacaaaacca cctccagtgg ccacccgcac catatgcgga agaacgactg 3961 ttggaatggg gattccttca caggaaaatt ggcagaccag gcctccaagg ctaatctaat 4021 gtttgaagag ggaaagaaca tgaccccagt ctacacaggt gcactaaaag atgaattggt 4081 gaagactgat aaaatttatg gtaagatcaa gaagagactt ctgtggggct cagatctggc 4141 gaccatgata cggtgtgccc gggctttcgg aggccttatg gatgaactca aggcacactg 4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggtccca tcatctttga 4261 gaagcactcc aggtataaat atcactatga tgctgattat tcccggtggg actcaacgca 4321 acaaagggat gtgctggcag cagcactaga aattatggtc aaattctctc cagaaccaca 4381 cctggcccag gtagttgcag aagatctcct ttcccctagc gttatggatg taggtgactt 4441 tcaaatatca ataagtgagg ggctcccctc cggggtacct tgtacctccc agtggaattc 4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga 4561 catcattcag gccaattccc ttttctcctt ctatggtgat gatgagattg tgagcacaga 4621 cataaagttg gatccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac 4681 ccgccccgat aaaactgaag gaccccttgt tatctctgaa gatctggatg gcctaacatt 4741 ccttcggagg actgtgaccc gtgacccagc tggctggttt ggaaaactgg aacaaagctc 4801 aattctcagg caaatgtact ggaccagggg gcccaaccat gaagacccat ctgaaacaat 4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca 4921 cggcccgaca ttttatagca aaattagcaa attagtcatt gcagagctga aggaaggtgg 4981 catggacttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tttcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctact gatggtgcag ccggcctcgt gccagaaagt aacaatgagg 5161 tcatggctct tgaacccgtg gctggtgccg ccttggcagc cccagtcacc ggacaaacaa 5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccctaatggt gaatttacag 5281 tttctccccg taatgcccct ggtgaagtgt tattgaatct agagttgggt ccagagttaa 5341 atccttatct ggcacattta gcaagaatgt acaacgggta tgccggtggg atggaggtgc 5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtctttgcc gccgtaccac 5461 ctcacttccc ggttgaaaac cttagtccac agcaaattac catgtttccc catgtgatta 5521 tagatgtgag aactttggaa cctgttttat taccactccc tgatgttaga aataatttct 5581 tccattacaa tcagaaggat gatcctaaga tgagaattgt ggctatgctt tatactcccc 5641 ttaggtctaa tggctcaggt gatgacgtgt ttacagtctc atgcagggtg ttgactagac 5701 cctcccctga ttttgatttc acatatttgg tgccaccaac agtggagtct aagactaaac 5761 cattcaccct cccaatcctc acgcttgggg agctctccaa ttctagattt ccagtgtcca 5821 tagaccagat gtataccagc cccaatgaag ttatatcagt gcaatgtcaa aatggtaggt 5881 gcacactgga tggggaactc caaggaacaa cacaactcca agtcagtggc atttgtgcct 5941 tcaagggaga ggtgaccgcc catttgcatg acaatgacca tctatataat gtcaccatca 6001 caaacttgaa cgggtcccct tttgacccct ccgaggacat ccctgcccct ctgggcgtac 6061 ctgattttca gggaagggtc tttggtatca tctcccaaag agacaaacac aatagccctg 6121 gacatagtga accagcaaac aggggacacg acgctgtggt ccctacttac acagcacagt 6181 acaccccaaa attgggtcaa attcaaattg gcacatggca gaccgatgat cttacagtca 6241 accaaccagt caaattcacc ccagttggac ttaatgacac tgaacatttt aaccaatggg 6301 tggtccccag atatgctggt gctctaaacc tcaacacaaa tcttgcccct tctgttgctc 6361 cagtttttcc aggggagcgc ctgctctttt ttagatcata tatccccctc aagggtggtt 6421 atggaaatcc agctattgat tgtctgctac cacaagagtg ggtgcaacat ttctatcagg 6481 aagcagctcc ttcaatgagt gaggtggccc ttgtcagata catcaacccg gacactggtc 6541 gagcactgtt tgaggccaag ctccacagag ctggtttcat gacggtctcg agcaacacca 6601 gtgccccggt ggttgtgcct gccaacggat acttcagatt tgattcttgg gtgaaccaat 6661 tctattctct cgcccccatg ggaactggaa atgggcgtag aagggttcaa taatggctgg 6721 agcttttgta gctggtcttg caggggacgt gctcagcaat gggctcagtt cactaattaa 6781 tgcaggtgct aatgcaataa atcagagggc agaatttgat tttaatcaga gattacaaca 6841 aaattctttc aatcatgata aggagatgtt acaggctcag attcaggcaa ctaagcagct 6901 gcaggcagac atgatggcta taaagcaggg agtcttgacc gctggcggct tctcccccgc 6961 tgatgcagcc agaggtgctg tgaatgcacc catgacacag gcgctggatt ggaacggcac 7021 aaggtattgg gcaccaggct ccatgaggac cacatcttac tctggaagat tcacatcaac 7081 tgccccagtg aggcaggccg acttccaaca cacccagagc cggccttcga gtggctcttc 7141 tgtgtcctcc tttactactc agtcttcaag gccaactctg actacaacca ctgggtcctc 7201 acataacacg gtttcatcaa attcaactcg cagcacaaac ctctcccaat caacggtttc 7261 tagggctaca tctaggacag gtgagtgggt tagagatcaa aataaaaatt tggaacctta 7321 catgcatggt gccttgcaga cagcctttgt caccccacct tccagcaggg cgtctgatgg 7381 gacagtctca accgtcccaa aaggtgtttt ggactcctgg acacctgcgt tcaacacccg 7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacaagcct agtgaaaagg 7501 taaatttatt tagaatgaat tgattttatc ttttaaaaaa aaaaa //