Typing tool
|
Complete norovirus genomes
OP689689 | GII.17 | ||
---|---|---|---|
GII.P17 |
ORF1: 5..5113 ORF2: 5094..6710 ORF3: 6710..7489LOCUS OP689689 7565 bp RNA linear VRL 25-OCT-2022 DEFINITION Norovirus GII isolate Hu/US/2022/GII.17[P17]/CA-RGDS-1164, complete genome. ACCESSION OP689689 VERSION OP689689.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7565) AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and Vinje,J. TITLE 2022 WA oyster Outbreak JOURNAL Unpublished REFERENCE 2 (bases 1 to 7565) AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and Vinje,J. TITLE Direct Submission JOURNAL Submitted (20-OCT-2022) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: Geneious v. R10; SPAdes v. 3.6 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7565 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="CA-RGDS-1164" /isolate="Hu/US/2022/GII.17[P17]/CA-RGDS-1164" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: CA" /collection_date="Apr-2022" /note="Amplicon sequencing:first 35 nt does represent primer sequence; genotype: GII.17[P17]" gene 5..5113 /gene="ORF1" CDS 5..5113 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="UYL27250.1" /translation="MKMASNDASAAVAGKNNNNDKEKSSSDSLFSNMTVTLKKALGAR SKQPPPGETKQTQRPPRPPTPELVKKIPPPPPNGEDEPKIAYKVGEGVSGLPDLTTVA QPDAQNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGLVLGVHKPPA AISLAKIELTPLSLYWRVVYTPQYLIAPETLKNLNGEAFPYTAFDNNCYAFCCWVLDL NDSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDV IGKLKPLNIMNILAICDWTFAGIVESMILLAELFGVFWTPPDVSAMIAPLLGDYEMQG PEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKW FFPKKEEASELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRSLDLEEEKARK LSSKSASPDIVGTVNALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLA RELAKKVASTLSGDQRIGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELA DTCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPD IEKAKRDFPGQPDMWKDHYRSDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLI ARASGLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLVDTLRVGNQLKSV KTLDELKQAIKNITIKKCQIVYNGCTYTMESDGRNKVVVEKVQNATVQTNNELAGALH HLRSARIRYYVKCFQEAIYSLLQIAGAAFVTTRIVRRMNISNLWSKPPVEEGDEPEDK GGCPKPRDEDDLTIDSKDIKEEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREE RNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRREERATL GLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFW VSPSLFITSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGA PEGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTT PGDCGCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAP ILGPGNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPF TEPRGKPPKPSVLESAKKTIINVLEQTIDPPEKWSYAQACASLDKTTSSGYPHHVRKN DYWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWG SDLSTMIRCARAFGGLMDELKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYS RWDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKITINEGLPSGV PCTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTA KLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWT RGPNHEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVP RQESMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..1003 /gene="ORF1" /product="p48" mat_peptide 1004..2101 /gene="ORF1" /product="NTPase" mat_peptide 2102..2638 /gene="ORF1" /product="p22" mat_peptide 2639..3037 /gene="ORF1" /product="VPg" mat_peptide 3038..3580 /gene="ORF1" /product="Pro" mat_peptide 3581..5110 /gene="ORF1" /product="RdRp" gene 5094..6710 /gene="ORF2" CDS 5094..6710 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UYL27251.1" /translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHIIVDVRTLEPIMIPLPD VRNTFFHYNNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT QLLPSGICAFRGRVTAETDNPDKWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM ASQRNVGNDAPGSTRAHEAVISTYSPRFVPKLGSVNFKSNDDDFQLQPTRFTPVGIND DGDHPFRQWELPDYSGVLTLNMNLAPPVAPNFPGEQLLLFRSSVPCSGGYNQGIIDCL IPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLVVP ANGYFRFDSWVNQFYSLAPMGTGNGRRRAQ" gene 6710..7489 /gene="ORF3" CDS 6710..7489 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UYL27252.1" /translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAISQKIDFENSKQLQSA SFQHDKEMLQEQVNATKQLQSEMIALKQGVLAAGGFSPTDAARGAIGAPMTRVLDWSG TRYWAPNSTKTTGYSGQFTSSPVHMPSPSAPQSKPAKPRSLGSSSSSSSVYSMSTQST SLTSGSSSNASSASTKLTNLSSGSSQNRTAEWVNQQRSLSPFMSGALNISHVTPPSSR ASSSGTVSTVPKGVLDSWTSAFNTRRQPLFAHLRVRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gctggcaaaa acaacaacaa 61 cgacaaggaa aaatcttcaa gtgacagctt gttttctaac atgactgtta ctcttaagaa 121 agccctcggg gcgcggtcta aacagccgcc cccgggagaa acaaaacaaa cacaaagacc 181 accaaggcca ccgacaccgg aattggtgaa gaagataccc ccaccccccc ccaatggcga 241 ggatgaacca aagatagcgt ataaggtggg agaaggtgtg tctgggctgc ccgacttaac 301 aaccgtggca caacctgacg cacagaacac agcctatagt gtccccccac tcagccagag 361 agaggtcggc gaggctaaag aaccgttgcc tggctccatt ctggaaatgt gggatggtga 421 gatctaccac tatgggctgt atgttgagcg ggggcttgta ctgggagtgc acaaaccacc 481 tgccgcaata agccttgcca aaattgaatt aacaccgctg tctctctact ggagagtggt 541 ttacactccc cagtatttga tagctccaga gacccttaag aatttaaacg gagaggcttt 601 cccatacacg gcctttgaca acaactgtta tgccttctgt tgttgggtcc tagacctcaa 661 cgactcctgg cttagcagaa gaatgatcca aagaacaact ggattcttca gaccgtatca 721 ggactggaat agaaaaccct tgccaaccat ggatgaacca aaaatcaaga aggccgcgaa 781 tgctgttctg tgtgctctct cctcactctt cactaggccc atcaaagatg tcattggaaa 841 gcttaaacca ctgaacatta tgaacatact ggcaatttgt gattggactt ttgcgggtat 901 agtggaatcc atgatccttc ttgctgagct ctttggagtg ttctggacgc ccccagatgt 961 gtctgcaatg attgctccct tactcggtga ctacgagatg caaggccccg aagacttggc 1021 cgtggaactt gtgcccgtgg taatgggagg aataggtctg gtgttaggat tcaccaagga 1081 aaagatcggc aagatgcttt catcagccgc gaccacactc agggcctgta aggatctagg 1141 atcttatggg ttggagatac tcaaactggt catgaagtgg ttcttcccca agaaggagga 1201 ggccagcgag ttagccatgg tgagggccat tgaggatgca gttctggatt tggaggcaat 1261 agaaaacaac cacatgacca ctctccttaa ggacaaagac agcctggcca catacatgag 1321 gtctcttgac ttggaagaag aaaaagcaag gaaactgtca tccaaatcgg cgtcacctga 1381 catcgtgggc acagtaaacg cattattggc gaggatagca gccgccaggt cactggtcca 1441 caaggctaag gaagagctct cgagcagaca gaggcctgtt gttgtaatga tatcaggtag 1501 gccaggtata ggaaagaccc atctggccag agagctagcc aagaaggttg cgtcaacact 1561 gtcaggcgac caaaggattg gactgatacc tagaaatggc gtcgaccatt gggacgccta 1621 caaaggagag cgggtggttc tgtgggatga ctatggcatg agcaacccta tacaggacgc 1681 actgaggctc caagaattgg ctgacacctg tcctctgacc ctaaattgtg acaggattga 1741 aaacaaagga aaagtgttcg acagtgacgc cataatcata acaaccaacc ttgcaaaccc 1801 agcaccactg gattatgtca actttgaggc ttgttccagg cgcatagact tcttggtgta 1861 tgcagacgca cctgacatcg agaaagctaa gcgtgacttc cctggccaac cagatatgtg 1921 gaaagaccat tacagatcag acttctcaca cattaaactt cagctggcac cacagggagg 1981 ctttgataag aatggcaaca ccccacatgg caaaggtgtg gttaagtctc tgacgattgg 2041 ttctctgatc gccagggctt ctggcttgct ccatgagaga atggatgaat tcgagctcca 2101 aggctctgac ttaccaacct tcaatttcga ccgtaacaaa gttgccgcct tcagacaatt 2161 ggcagctgaa aacaaatatg gtcttgtgga cacactgagg gtcggcaacc aactgaaaag 2221 tgtcaaaacc ctggatgagc tgaagcaggc tataaagaac atcaccatca agaagtgcca 2281 gatagtgtac aatggatgca cctacaccat ggaatctgat gggaggaaca aggttgtggt 2341 tgaaaaggtt caaaatgcaa cagtccaaac caacaatgaa cttgcaggag cactccacca 2401 cctgagatct gcaaggataa ggtattatgt caaatgtttc caagaagcta tttactctct 2461 actccaaatt gctggtgcag ccttcgtcac cacacgcatc gtgaggcgca tgaacatctc 2521 aaacctctgg tcgaagccac ccgtcgaaga gggtgacgag cctgaagaca aaggggggtg 2581 ccccaagccc agggatgaag atgacctcac tattgactct aaggacatta aagaagaagg 2641 gaagaagggc aagaacaagt ctggccgggg caagaaacac acagctttct catccaaggg 2701 cctcagtgat gaggagtacg atgagtacaa gagaatcagg gaggagagaa atggcaaata 2761 ctcaatagaa gaatacctcc aggataggga tagatactat gaagagcttg ccattgctaa 2821 ggccactgag gaagacttct gtgaagagga ggaaatcaaa attcgccaga gaatcttccg 2881 gcccaccagg aagcaacgga gagaggaaag agccacgctt gggcttgtca caggatcgga 2941 aatcagaaag aggaacccag atgactttaa gccaaaagga aaattgtggg ctgatgacaa 3001 cagaagtgtg gactacaatg agaggataga ttttgaggct cccccgagtg tttggtctag 3061 gatagtcaac tttggtacag gatggggatt ctgggtctcc ccaagtctct ttataacttc 3121 aacacatgtc ataccaaaag gaatcactga ggcctttgga gttcccatta accaaattca 3181 aattcacaaa tctggagagt tttgccgctt gcggtttcca aaaccaatca ggccagacgt 3241 gagtggaatg atcttggaag agggtgcccc tgaaggcact gttgtgtcca ttctcatcaa 3301 gagaacaaca ggggaactga tgcctctcgc agttagaatg ggaactcatg ccacaatgaa 3361 aatccaaggt agaacggtgg gtggtcaaat gggcatgctt ctcactggct caaacgctaa 3421 aagcatggac ctaggcacaa caccaggtga ctgtgggtgc ccatacatat acaaaagagg 3481 caatgacttc gtggtcattg gggtgcacac tgcagcagcc cgtggaggca acacggtcat 3541 atgtgccaca cagggaagtg aaggcgaagc caccctcgaa ggaggtgaca ataagggcac 3601 ctattgtgga gcccccatct tgggacctgg caacgcacca aaattgagca caaaaacaaa 3661 gttctggaga tcttctaacg cgccgcttcc tccaggcacc tatgaaccag cataccttgg 3721 tggaaaagac ccgcgtgtga agggaggccc atctctacaa caggttatga gagaccaact 3781 taaacctttt acagagccca gagggaagcc cccaaaacca agtgtcctag aatcagcaaa 3841 gaagaccatc attaatgtcc tggaacaaac cattgacccc cctgaaaagt ggtcatatgc 3901 ccaagcttgt gcatctctcg acaagacaac ctccagtgga tacccgcatc acgttcggaa 3961 gaatgactat tggagtggtg aatccttcac ggggaaactt gcagaccagg cctcaaaagc 4021 aaaccttatg tatgaggaag gcaaacacat gcaaccagtt tacaccgcag cactcaaaga 4081 cgagctcgtg aaaactgaca aaatttatgg caagatcaag aaaagactcc tgtggggctc 4141 tgacctatcc accatgattc ggtgcgccag ggcatttggt ggcctcatgg atgagctcaa 4201 agcaaattgt attacactcc ctatcagagt tggtatgaac atgaatgaag atggtcccat 4261 aatatttgaa aagcactcca ggtacaggta ccactatgat gctgattact cccgctggga 4321 ttccacacaa cagcgggcag tactggaagc ggcacttgaa atcatggtga gattttctgc 4381 tgagccacag ttggcacaaa tagtggcaga ggacctgcta tcaccaagtg tggttgatgt 4441 gggcgatttc aaaattacta tcaatgaagg cctaccatct ggcgtgcctt gcacttcaca 4501 atggaattct attgcccact ggttactcac cctgtgtgcc ctgtctgaag taacaggact 4561 aggccctgac atcatacaag ccaactccat gtactctttc tatggtgatg atgagattgt 4621 gagcacagac ataaaattgg acccagagaa attgactgca aaactcaaag aatatggtct 4681 taaacccacc cggcctgaca agactgaggg gccactggta attagtgagg acctgaatgg 4741 gttgactttc ctccgccgaa cagtcacccg cgatccagcg ggttggtttg gaaagttgga 4801 ccaaaactcc atcctcaggc agctgtactg gacaagggga cccaaccatg aagatcccag 4861 tgagactatg ataccacacg cacagagacc tgtgcagctc atggcactgc taggagagtc 4921 ctccctacat ggaccctcat tttacagcaa agttagcaag ctggtcatat ctgaacttaa 4981 agagggggga atggattttt atgtgcccag acaagagtca atgttcagat ggatgagatt 5041 ctcagatcta agcacatggg agggcgatcg caatctggct cccagttttg tgaatgaaga 5101 tggcgtcgaa tgacgccgct ccatctaatg atggtgctgc tggtctcgta ccagagggca 5161 ataacgagac ccttccccta gaaccagttg cgggcgcagc tatagccgca cccgttactg 5221 gccaaaataa tataattgac ccctggatta gaacaaattt tgtgcaagca ccaaatggag 5281 agttcacagt gtcacctaga aactctcctg gagaaatttt gctaaaccta gagttgggcc 5341 ctgatttgaa cccttatttg gctcatttgt caaggatgta caatgggtat gctggtggag 5401 ttgaagttca ggttctcctg gcagggaacg cgttcactgc cgggaagatc ctcttcgccg 5461 ctgtcccgcc aaatttccca gtggaattct taagcccagc ccagattaca atgctcccac 5521 atataatagt agatgttagg actcttgaac caattatgat cccattacct gatgttagga 5581 acacattctt ccactataat aaccagccca acagccgcat gagattagtg gctatgctct 5641 atacccccct tagatctaat ggttcaggtg atgatgtttt cactgtttct tgcagggttt 5701 tgactaggcc tactcctgat tttgagttca cttatctagt gccaccctct gttgaatcta 5761 agactaagcc cttttcttta cccattctaa ccctttctga gctcacaaat tcgaggttcc 5821 cggtccccat tgattcgctt ttcaccgccc agaataatgt gttgcaggtg cagtgtcaaa 5881 atggcaggtg cacacttgac ggtgagctac aaggcacaac ccagttgctc ccatctggca 5941 tctgtgcgtt cagaggacgg gtgacagcag aaactgacaa tcctgacaag tggcacatgc 6001 aactgcaaaa cctcaatggc acaacatatg acccaactga tgatgtgcca gccccactgg 6061 gtacacctga cttcaagggc gtcgtgtttg ggatggcaag ccaaagaaat gtgggcaacg 6121 atgcgcccgg ctcaaccagg gcccatgagg cggtgatttc aacctacagc cccagatttg 6181 ttcccaaatt aggctctgtc aattttaaaa gtaatgacga tgatttccaa ttgcagccaa 6241 caagattcac accagtgggc attaatgatg atggcgacca cccgttcaga caatgggaac 6301 tgccagacta ttcaggggtg cttaccttga atatgaacct tgcccccccg gttgctccaa 6361 atttccctgg tgaacaatta ttactcttca gatcttccgt gccatgttca ggaggttaca 6421 accaaggtat tatagattgt cttatccccc aagaatggat ccaacacttc taccaggaat 6481 cagcaccttc tcagtcagac gtggccctga tcaggtacgt caaccccgac acgggtcgca 6541 cactgtttga ggcaaaactg cacagatctg gctatatcac tgtggctcac tctggagact 6601 atcctcttgt tgttccggct aatggatact ttagatttga ctcttgggta aatcagtttt 6661 actcactcgc cccaatggga actgggaatg ggcgaaggag ggctcagtaa tggctggagc 6721 cttcattgca ggattggcgg gtgacatgct cacgtcatcc gtgggctccc tggtgaacgc 6781 aggggcaaac gccatcagcc aaaagataga ctttgaaaac agcaagcaac tccagtctgc 6841 ttcttttcaa catgataaag agatgctcca agaacaggtg aatgcaacca agcagctgca 6901 atctgagatg atagccctaa aacagggggt tttggccgca ggcggctttt cccccactga 6961 tgcagcgagg ggggccatcg gtgcacccat gacaagggtg cttgactggt ctggcactcg 7021 atactgggct cccaattcta caaagacaac tggttattcg gggcaattca cctcctcacc 7081 tgtgcacatg cccagcccga gcgctccaca atcaaaaccc gcaaagccca ggtctctagg 7141 ttcttcttct tcttctagta gtgtttatag tatgtctacc caatcaactt ctctaacatc 7201 tggctcttct agtaatgctt cttctgcttc tactaaactg acaaatctaa gctctggctc 7261 ctctcaaaac agaacagcag agtgggtgaa ccaacagaga agtctcagcc ctttcatgag 7321 tggcgcactc aatatctcac atgtcacgcc accttcaagt agggcctcca gttctgggac 7381 ggtctcaacc gtgcccaagg gagttttgga ctcctggaca tctgcattca acacacgcag 7441 acagccgctc ttcgcacacc tcagagtgag gggggagtca cgtgtttagt gaaaagaaac 7501 aattggctat aatatgattt ctttaaaaat ttaaatttgg ctaatttgta tcttttaaaa 7561 aaaaa //