Typing tool
|
Complete norovirus genomes
MH218617 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MH218617 7570 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_147_05_01_2015, complete genome. ACCESSION MH218617 VERSION MH218617.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7570) 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 7570) 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..7570 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_147_05_01_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="05-Jan-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="AWR17509.1" /translation="MKMASNDASAAAVANSNNDTAKTSSDGVLSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE ETNTAFSVPPLNQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKIELTPLSLYWRPVYTPQYLISPDSLKKLAGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDSSKIKKVADIFLCTLSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIATSLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDKIQSAAVQTNNELTGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVITSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP 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="AWR17510.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSHNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17511.1" /translation="MAGAVFAGLASDVLSSGLGSLINAGAGAINQTIEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIESTKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTVTSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa acttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc 181 acctactcca gaactggtta agaacatccc ccctcccccg cccaacgggg aagatgaaat 241 agtggtctct tatagtgtca aaaatggtgt ctccggcttg cctgaccttt ctaccgtcag 301 gcaaccggaa gaaaccaaca cagccttcag tgtccctccg ctcaatcaga gggagaataa 361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctatca 421 ttatggcctg tatgtggagc gaggccttgt actaggtgtg cacaaaccgc cagctgccat 481 cagccttgct aagattgagc tgacaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccag acagtctcaa gaaattggcc ggagagacgt tcccctacac 601 agcctttgat aacaactgtt atgccttttg ctgctgggtt ctggacctga atgactcgtg 661 gctgagcaga agaatgatcc agagaacaac tggtttcttc aggccctacc aggactggaa 721 caggaaaccc ctccccacta tggatagctc caaaataaag aaggtagctg acatatttct 781 gtgtaccctg tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc 841 tcttaacatc ctcaacatct tggcctcatg tgattggacc tttgcgggca tagtggagtc 901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct 1021 tgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg 1081 gaaaatgttg tcatctgctg cgtccacttt gagagcttgc aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttag tcatgaaatg gttcttccca aagaaggagg aggcaaatga 1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa 1261 tcacatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga 1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg 1381 tacagtcaac gccctcctgg cgagaatcgc cgccgcacgt tctctggtgc atcgagcgaa 1441 ggaggagctt tccagcagac caagacctgt ggtgctgatg atatcaggca ggccaggaat 1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcaacctccc ttacagggga 1561 tcagcgtgtg ggcctcgtcc cacgcaatgg tgtcgaccat tgggatgcgt acaaggggga 1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaacaaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact 1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt atgcagaggc 1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttct gatttctcac acataaaact aacactggcc ccacagggtg gtttcgataa 1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctcccttat 2041 tgcccgggca tcagggctac tccatgagag gttggatgaa tttgaactgc agggcccagc 2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga 2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac 2221 catgccagaa ctcaagcaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta 2281 tagtggctgc acttacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaaaat 2341 ccaaagcgcc gccgtgcaga ccaacaatga gctgactggt gccctgcacc acttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt tcaggaagcc ctgtattcca tcatccaaat 2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcga atgaacatac aagacctgtg 2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggatgggt gcccaaaacc 2581 caaggatgat gaggagttcg tcattacatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagcattc tcaagcaaag gtctcagtga 2701 tgaagagtat gatgaataca agaggattag agaagaaagg aatggcaagt actctataga 2761 agagtacctt caggacagag acaaatacta tgaggaggtg gccattgcca gggcgactga 2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaggaaa gagtctctct tggtctggtc acaggctctg aaattaggaa 2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggaatgt 3001 ggactacaat gagaaactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa 3061 ctttggctca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt 3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa 3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggtat 3241 gatcttggaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca agaggcccac 3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg 3361 acgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga 3421 cctgggtaca acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta 3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac 3541 ccaagggagt gaaggggagg ctacacttga gggtggtgac aacaagggga catactgtgg 3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaaaacca aattctggag 3661 gtcgtccaca gcatcacttc cacctggcac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agagaacagt tgaagccatt 3781 cacagagccc aggggcaagc caccaaaacc aagtgtacta gaagctgcca agaagaccat 3841 cattaatgtc cttgagcaaa caattgatcc accagagaaa tggtcgttcg cacaagcttg 3901 cgcgtccctc gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtatgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttggt 4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggatctggc 4141 aaccatgatt cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg 4201 tgtcacactc cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca 4321 acagagagcc gtgctggcag cagctctgga aatcatggtt aaattctccc cagaaccaca 4381 tttggctcag gtagtcgcgg aagaccttct ctcccccagc gtggtggacg tgggcgactt 4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga 4561 caccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaga aattgacagc aaaactcaga gaatatgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgc catctctgaa gacctggatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat 4861 gattccacac tcccaaaggc ccatacaatt gatgtcccta ctaggggagg ccgctctcca 4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg 4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa 5341 acccctacct atcccattta gccagaatgt acaatggtta tgcaggtggc tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac catgttcccc catatagtgg 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 atcattataa ccaatcaaat gactccacca ttaagctgat agcaatgttg tatacaccac 5641 ttagggctaa taatgctggg gacgatgttt tcacagtttc ttgccgagtt ctcacaaggc 5701 catcccccga ttttgatttc atatttttgg tgccccccac agttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacgactga tggcgtgctt ctaggcacca cccaactgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcacccat atcacaggca gtcacaacta cacaatgaat ttggcttctc 6001 taaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagact 6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg 6121 gccacaaagc cacagtgtac actgggagtg ccgattttgc tccaaaactg ggtagagttc 6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga acctcaacag tgggtgcttc 6301 ctagttactc aggcagaaat attcataatg tgcatctggc ccccgctgta gcccccactt 6361 ttccaggtga gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgcttg ctcccccagg aatgggtgca gcacttctac caagaggcag 6481 ccccagcaca atctgatgtg gccctgctga gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg caagcttcat aaatcaggct atgttacagt ggctcacact ggccaacacg 6601 atctggttat cccccccaat ggttatttta ggtttgattc ttgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagctgt 6721 ctttgctgga ttggcatctg atgtcctcag ctctggactt ggttccctta tcaatgctgg 6781 ggccggggcc atcaaccaaa caattgagtt tgaaaataac agaaaattgc aacaagcatc 6841 attccaattt agcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agcacaaatt gagtctacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcca ggaccacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcttctaact cttctactgt 7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg 7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gattattctt cctttttctt tagtgtcttt 7561 taaaaaaaaa //