Typing tool
|
Complete norovirus genomes
MH218624 | GII.4 Sydney | ||
---|---|---|---|
GII.P31 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218624 7560 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_153_19_02_2015, complete genome. ACCESSION MH218624 VERSION MH218624.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7560) 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 7560) 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..7560 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_153_19_02_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="19-Feb-2015" /note="genotype: GII.Pe_GII.4" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17530.1" /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGRPGIGKTHLAREL AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGC LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLRPTRPDKTEGPLVISENLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE 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..6707 /gene="ORF2" CDS 5085..6707 /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) [TAT ending at position 6705 on + strand];first in-frame stop codon exists 3' of stop position predicted by homology to reference [homology search predicted 5085..6705 revised to 5085..6707 (stop shifted 2 nt)]" /codon_start=1 /product="VP1" /protein_id="AWR17531.1" /translation="MKMASSDANPSDGSAANLVPEVTNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17532.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPERAILRDAVPARGSSSKSS NSSVATSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga 61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc 121 cctcggggcg cggcctaaac agccgccccc gaaggagata ccacccagac ccccgcgacc 181 acccacacca gaactggtca aaaagatccc tcctccccca cccaacgggg aggatgaact 241 agtggtctct tacagcgcca gagatggcgt ttccggactg cctgagctca ccactgtcag 301 gcaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag 361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca 421 ttacggcctg tacgtggaac gaggtcttgt acttggtgtg cataagccac cggcagctat 481 cagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc 541 ccagtacctc atctctccag acactcttag gaggttgcat ggagagtcat tcccctacac 601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg 661 gttaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa 721 caagaaaccc ctccccacta tggatgactc caaattaaag aaggtagcca acatattctt 781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc 841 tcttaacatc ctcaacattc tggctacatg tgattggact ttcgcaggca tagtggaatc 901 tttaatactc ttagcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact 1021 ggtccctata gtgatggggg ggataggttt ggtgttagga tttaccaaag agaaaattgg 1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg 1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga 1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa 1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga 1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg 1381 cacaatcaac gctcttctgg caagaatcgc tgccgcacgc tccctagtgc accgggcgaa 1441 agaagagctc tccagcaggc tgagacctgt cgttgtgatg atatcgggaa gaccagggat 1501 agggaaaact caccttgcca gggagctggc caagaaaatc gcggcctccc tcacagggga 1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgatcac tgggacgcat acaagggcga 1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt 1681 gcaggaactt gctgacactt gccccctcac gttaaattgt gacagaattg agaacaaagg 1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact 1801 ggattatgtc aattttgaag catgttcgag acgtattgac ttcctcgtgt acgcagaagc 1861 ccctgaggtg gagaaggcaa agcgtgactt cccaggtcaa cctgacatgt ggaagaacgc 1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa 1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat 2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc 2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga 2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac 2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta 2281 caatggtggc acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt 2341 gcaaagtgcc actgtgcaga ccaacaatga gctagccggc gccctacacc acctaaggtg 2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggcg ctgtattcca tcatccaaat 2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg 2521 gtccaagcca caggtggaag acacagaaga aatgaccaac aaagatggtt gcctaaaacc 2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga 2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga 2761 agaatacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga 2821 agaggacttt tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag 2881 gaaacaacgc aaagaagaga gggcctctct cggcctggtc acaggttctg aaatcaggaa 2941 gagaaaccca gaagacttca aacccaaggg gaagctgtgg gctgatgatg acagaagtgt 3001 tgactacaat gagaaactca actttgaggc cccaccaagc atttggtcgc ggatagtcaa 3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt 3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc aaatacacaa 3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat 3241 gattctagaa gaaggtgcgc ccgaggggac cgtggtcaca ctgctcatca agagaccaac 3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg 3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga 3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta 3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacaccgtca tatgtgccac 3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg 3601 cgcaccaatc ttgggcccag ggagcgcccc gaagctcagt accaagacta agttttggag 3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga 3721 ccccagagtc aaaggtggcc cctcattgca acaagttatg agggaccagc taaaaccatt 3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat 3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg 3901 cgcatccctt gacaaaacca cttccagcgg ccacccgcac cacatgcgga aaaacgattg 3961 ttggaatggg gagtccttta caggaaaatt ggctgatcaa gcctccaagg ccaacctaat 4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt 4081 aaagaccgat aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc 4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcgcactg 4201 tgtcacactt cctgtcagag ttggcatgaa catgaatgag gatggcccca tcatctttga 4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca 4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctccc cagaaccaca 4381 cctggcccag gtagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt 4441 tcaaatatca ataagtgagg gtcttccctc tggggtgcct tgtacctccc agtggaattc 4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga 4561 catcatacag gccaactccc tcttctcctt ctatggtgat gatgagattg tgagcacaga 4621 tataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgagaccaac 4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa aacctggatg gcctaacatt 4741 cctccggaga actgtgaccc gtgacccagc tggctggttt ggaaaattgg aacaaagttc 4801 aattcttaga caaatgtact ggaccagggg tcccaaccat gaagatccat tcgaaacaat 4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca 4921 tggcccggca ttttatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg 4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc accaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctgggc cctgatctaa 5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt tatatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttgagcccta gccaggtcac tatgttcccc catatagtag 5521 tagatgttag gcaactagaa cctgtactga ttcccttacc cgatgttagg aataattttt 5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggt gatgatgtct tcacagtttc ttgccgagtt ctcacgagac 5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagct gttcacgggc cccagcagtg cctttgttgt ccaaccacaa aacggcaggt 5881 gcacgactga tggcgtgctc ctaggcacta cccaactgtc tcctgtcaac atctgcacct 5941 tcagaggaga tgtcacccac atcacaggca gtcgcaacta tacaatgaat ttggcttctc 6001 aaaattggaa taattatgac ccaacagaag aaatcccagc ccctctagga actccagact 6061 ttgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt agtaccaccc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggattgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacact ggtagggttt 6541 tgtttgagtg taagctccat aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat tccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaacaac agaaaattgc aacaagcatc 6841 cttccaattt agcagcaatc tacaacaggc ttccttccaa catgacaaag agatgctcca 6901 agcacaaatt gaggccacca aaaagttaca acaggaaatg atgagagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacgga tgcagcccgt ggggcaatca acgcccccat 7021 gacaaaagct ctggattgga gcgggacaag gtactgggct cccgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag aaagagctat 7141 tcttagggat gctgtccctg ctcggggttc ctccagtaaa tcttctaact cttctgtcgc 7201 tacttctgtg tattcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg 7261 cgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggagtttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagagattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga 7501 gtcacgggcg taatgtgaaa agacaaaatt gattaccttt ctctttcttt agtgtctttt //