Typing tool
|
Complete norovirus genomes
MH218665 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218665 7554 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_207_07_12_2015, complete genome. ACCESSION MH218665 VERSION MH218665.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7554) 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 7554) 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..7554 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_207_07_12_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="07-Dec-2015" /note="genotype: GII.P4_GII.4" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17653.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELIKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCTLSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSEDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPRPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE 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="AWR17654.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGLL TQTTRTDGSTRGHKATVLTGSADFAPKLGRVQFGTDTNNDFDTNQNTKFTPVGVIQDG GTTHQNEPLQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17655.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNKNLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDSVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRSRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac aacctccccc gagggaaaaa ccacaaagac ccccacgacc 181 acctactcca gaactgatta aaaatgttcc ccccccccca cccaacggag aggatgaaat 241 agtggtttct tatagtgtca aagatggtgt ctccggcttg cctgaccttt ccaccgtcag 301 gcaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag 361 agatgccaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt gctaggcgtg cacaaaccgc cagctgctat 481 cagcctcgct aaggttgagt tagcaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccgg acactctcaa gaaattgtcc ggagaaacgt tcccctacac 601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg 661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa 721 taggaaacct cttcccacta tggatgactc caaaataaag aaggtggcta acatatttct 781 gtgtactctg tcctcactat tcaccaggcc cataaaagat ataataggga agataaggcc 841 tcttaacatc ctcaatatct tagcttcatg tgattggacc tttgcaggca tagtggagtc 901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttactcggtg actacgagct acaagggcct gaggaccttg cagtggagct 1021 cgtccccgtg gtgatggggg gaattggttt ggtgctaggt ttcaccaaag agaagattgg 1081 gaaaatgttg tcatcagctg cgtccacctt aagagcttgc aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga 1201 gctggctata gtgaggtcca tcgaggatgc agtcctggac ctcgaagcaa ttgaaaacaa 1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga 1321 ccttgaagag gagaaagcca ggaagctctc aaccaagtct gcctcacccg acatcgtggg 1381 cacaattaac gccctcctgg cgagaatcgc tgccgcacgt tcactggtgc atcgagcgaa 1441 ggaggaactt tccagcagac caagaccagt ggtgttgatg atatcaggca ggccaggaat 1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc tcacaggaga 1561 ccaacgtgtt ggactcattc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga 1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ttggccaacc cagcaccact 1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt atgcagaagc 1861 ccctgatgtc gaaaaggcga agcgcgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagtcct gacttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa 1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat 2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactgc agggcccagc 2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc tcgctgctga 2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac 2221 catgccagaa ctcaaacaag cacttaagaa tgtatcaatc aagaagtgtc aaatagtgta 2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgataggat 2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat 2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg 2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc 2581 taaggatgat gaggagtttg tcatttcatc cgaagacatc aaaactgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga 2701 tgaagagtat gatgagtaca agaggatcag agaagaaagg aatggcaagt actctataga 2761 agagtatctt caggacaggg acaaatatta tgaggaggtg gccattgcca gagcgactga 2821 ggaagacttc tgtgaggagg aggaagccaa gatccgacaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaggaaa gagtctccct cggcttggtc acaggttctg aaattaggaa 2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gccgacgatg acaggagtgt 3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atttggtcaa gaatagtcaa 3061 ctttggttca ggctggggat tctgggtctc ccccagcttg ttcataacat caacccatgt 3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtgcacaa 3181 gtcaggcgag ttctgtcgct tgagattccc tagaccaatc agaactgatg tgacgggcat 3241 gatcttggaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac 3301 tggggaactt atgcctctag cagctaggat ggggacccat gcgaccatga agatccaagg 3361 gcgcactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga 3421 cctgggtact acaccaggtg attgtggttg cccctacatc tacaagagag gtaatgacta 3481 tgtggttatc ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac 3541 ccaggggagt gaaggtgagg ctacacttga gggtggcgac aacaagggga catactgtgg 3601 tgcaccaatc ttaggcccag ggagtgcccc aacacttagc accaagacca aattctggag 3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctaccttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacaat tgaagccatt 3781 cacagagccc aggggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat 3841 cattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg 3901 cgcgtctctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcctccaagg ccaacctgat 4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt 4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctttggggct cagacctggc 4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg 4201 tgttacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattct aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca 4321 acagagagcc gtgttggcag cagctctaga aatcatggta aaattctccc cagaaccaca 4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggatg tgggcgactt 4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacgaacc tgtctcccga 4561 taccatacag gctaattctc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac 4681 ccgtcctgac aaaactgaag gacccctcgt catctctgaa gacctgaatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttc ggaaaactag agcagagttc 4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat 4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttttacagta aaatcagcaa attggtcatt gcagagctaa aagaaggtgg 4981 aatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttaa 5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttgagcccta gtcaggtcac tatgtttccc catatagtag 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataacttct 5581 atcattataa tcaatcaaat gactccacca ttaaattgat agcaatgttg tatacaccac 5641 ttagagctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgaggc 5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct aggactaaac 5761 cattctctgt tccagtccta actgttgagg agatgaccaa ttcaaggttc cccattcctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggtaggt 5881 gtacgactga tggcgtactc ctaggcacca cccaattgtc tcctgtcaat atctgcacct 5941 tcagagggga cgtcacccac attgcgggta ctcataacta cacaatgaat ttggcttctc 6001 aaaattggaa taattatgac ccaacagaag agattccagc ccctctagga actccagatt 6061 ttgtggggaa gattcaaggc ttgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gccacaaagc tacggtgctc actgggagcg ccgactttgc tccaaaactg ggcagagttc 6181 aatttggaac tgacacaaac aatgattttg ataccaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt ggcaccaccc accaaaatga acccctacag tgggtgctcc 6301 caagttattc aggcagaaat actcctaatg ttcatctggc ccccgctgta gcccccactt 6361 ttccgggtga gcaacttctc ttctttagat ccaccatgcc cggatgtagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg taaacttcat aaatcaggct atgtaacagt ggctcacact ggccaacatg 6601 atttggttat cccccccaat ggctatttta ggtttgactc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgc agtataatgg ctggagcttt 6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggtc attaaccaaa aagttgattt tgaaaacaac aaaaatttgc aacaagcatc 6841 cttccaattt agcagcaatt tacaacaggc ttcctttcaa catgacaaag aaatgctcca 6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaaatta agcaggcaat 6961 gctcctggag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag atactgggct cccgatgcta ggactacaac 7081 atacaatgca ggccgctttt caacccctca accatcgggg gcactgccag gaagagctaa 7141 tcttagggac tctgtccctg ctcggggctc ctccagtaaa tcctctaact cttctactgc 7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg 7261 taccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag 7321 taggaatttg tctcctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta gtcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt tttt //