Typing tool
|
Complete norovirus genomes
MT738527 | GII.2 | ||
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GII.P16 |
ORF1: 5..5104 ORF2: 5085..6713 ORF3: 6713..7492LOCUS MT738527 7550 bp RNA linear VRL 14-JUL-2020 DEFINITION Norovirus GII isolate Hu/US/2019/GII.2[P16]/CA-RGDS-1097, complete genome. ACCESSION MT738527 VERSION MT738527.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7550) AUTHORS Pan,C.-Y., Huynh,T., Padilla,T., Montmayeur,A.M., Chhabra,P., Barclay,L., Vinje,J. and Morales,C. TITLE Direct Submission JOURNAL Submitted (08-JUL-2020) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.6; Geneious v. R10 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7550 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/US/2019/GII.2[P16]/CA-RGDS-1097" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: California" /collection_date="Sep-2019" /note="genotype: GII.2[P16]" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QLF80458.1" /translation="MKMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP KQPAPRDKTQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNVLNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMLSGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVSIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide 5..1000 /gene="ORF1" /product="p48" mat_peptide 1001..2098 /gene="ORF1" /product="NTPase" mat_peptide 2099..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" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QLF80459.1" /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG IISQRDKHNDPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT PVGFNDIEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP VVVPANGYFRFDSWVNQFYTLAPMGTGNGRRRVQ" gene 6713..7492 /gene="ORF3" CDS 6713..7492 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QLF80460.1" /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gcttgcaaca acaacaacga 61 caaagaaaaa tcttcaggtg aaggcttatt tacaaatatg tcttccacct taaagaaagc 121 cctcggggct aggcccaaac agcctgcccc gagagacaaa acacaaaagc ccccaagacc 181 accaactccc gagttggtca agaggatacc ccctcctcca cccaacggcg aagaagaaga 241 agagccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac 301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga 361 aaacagggag gccaaggagc cgctaacagg ggcaatacta gagatgtggg atggagagat 421 ataccactat ggtctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc 481 agccataagc atggcaagag tggagctgac gccgttgtca ttgtactggc gtgtggtgta 541 cactccccaa tacctcatct cccctgaaac cctcaggagg ctcaacggag aggcattccc 601 ttacaccgcc tttgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga 661 ctcatggctt agcaggagga tggtacaaag aacaacgggc ttcttcagac cttaccaaga 721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa attaagaagg tagcaaatat 781 attcctatgt tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat 841 taaaccattg aacgtactga atatcctggc aacgtgtgac tggacttttg ccggaatagt 901 ggagtctctg atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc 961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt 1021 tgaactcgta cctgtggtaa tgggggggat tggtttggtg ttgggattca ccaaagagaa 1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc 1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc 1201 caatgagcta gctatggtga gggccataga ggatgctgta ctagaccttg aggcaataga 1261 aaataaccac atgacaaccc tgttgaaaga taaagacagc ttagcaacat acatgaaaac 1321 actggacatg gaggaggaga aagccaggag gttgtccaca aaatctgcat cccctgacat 1381 agttgggaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag 1441 ggccaaggaa gagctatcta gtaggataag gccagtagtt gttatgctat ctggcaagcc 1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac 1561 aggggatcaa agagtcggac tcataccacg aaacggtgtg gaccattggg atgcatacaa 1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccctattc atgatgctct 1681 tcgcatacaa gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa 1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaatccagc 1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgacttcc tggtgtacgc 1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa 1921 ggatgccttc aagccggact tttcacacat caagctacag cttgcacccc agggcggctt 1981 tgacaagaat ggcaacaccc cacacgggaa aggagtgatg aagaccctca ctaccggttc 2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg 2101 ccccacaatc accaccttca atttcgaccg aaacagaatc acggcattca gacaattggc 2161 tgcagaaaac aagtatggat tggtggatac catgaaagtt ggcaatcaat taaaaggagt 2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccagat 2281 catctacggt ggttccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga 2341 aaaggtcaag aacacctctg tacagaccaa taacgagttg gctggggccc tgcaccatct 2401 caaacatgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat 2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga 2521 actctggtcg aagccacaac tagatcaaaa tgaatcagag actaaggaag aggcccccaa 2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg 2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaaag gcttgagcga 2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga 2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga 2821 agaagacttc tgtgaagagg aggagattaa aatccgtcag agaattttcc gtcccaccag 2881 gaaacaaaga aaggaagaga gggccacatt agggctagta acaggttcag aaatcagaaa 2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acaggagtgt 3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag 3061 ctttggctct ggctggggct tctgggtgtc accaagcctt ttcataacat caactcatgt 3121 aatccccgca ggcataacag aagcatttgg ggtctccatc aaacaaattc agatccacaa 3181 atcaggcgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat 3241 gatcttggaa gaaggtgcgc ctgagggcac cgtggcaact gtgctcatca aacgccccac 3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg 3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga 3421 cttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta 3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacactgtca tctgtgccac 3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg 3601 ggcacccatt ctgggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag 3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gcggccgtga 3721 tccgcgtgtt aagggtgggc cttccctgca gcaggtgatg agagaccagt tgaagccatt 3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat 3841 catcaatgtc ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcttg 3901 tgcctcactt gacaaaacca cctccagcgg gcacccccat cacgtccgaa agaatgaatt 3961 ctggaacggt gagaccttca ctggtaaact ggcagaccaa gcatcaaaag caaacctaat 4021 gtttgaggaa gggaaacaca tgacaccagt gtacacagca gctctcaagg acgagctagt 4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc 4141 caccatgatc cggtgcgcta ggtcgtttgg tgggcttatg gacgagatga aggcacactg 4201 catatcactc ccagtccgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga 4261 gaaacattcc agatacaaat atcactatga tgcagactac tctcgttggg attcaacaca 4321 acagagggca gttctagcag ctgccttgga aatcatggtc agattctctg cagaaccaca 4381 attggcacaa atagtcgctg aggatctgct ggcccctagt gtagtagatg taggagactt 4441 taaaattaca ataaatgaag ggctcccttc tggtgtgcca tgcacttctc aatggaactc 4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga 4561 cattatacag gcaaattcca tgttctcatt ttacggtgat gacgagatcg tcagtaccga 4621 cataaaattg gaccctgaac agttaaccgc caaattgaag gagtacggcc tgaaaccaac 4681 ccgcccagac aaaaccgagg gacccctgat tatcagtgaa gatttgaacg gtctcacttt 4741 cctccgaagg acggtgactc gtgacccggc tggctggttt ggaaaactgg accaaagctc 4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat 4861 gataccccat tcccaaagac ccatacagct catggcactg cttggtgaag cctctcttca 4921 cggaccctct ttctacagta aaatcagtaa attggtcata actgaactca aagaaggtgg 4981 gatggatttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctact gatggtgcag ccggcctcgt gccagaaagt aacaatgagg 5161 tcatggctct tgaacccgtg gctggtgccg ccttggcagc cccggtcacc ggtcaaacaa 5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccctaatggt gaatttacag 5281 tctctccccg aaatgcccct ggtgaagtgc tactgaatct agagttgggt ccagaattaa 5341 atccttatct ggcacattta gcaagaatgt acaatgggta tgccggtggg atggaggtgc 5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtcttcgcc gccgtgccac 5461 cccacttccc ggttgaaaac cttagcccac agcaaatcac catgttccct catgtgatca 5521 tagatgtgag aaccttggaa cctgttttat taccactccc tgatgttagg aataacttct 5581 tccattataa ccagaaagat gatcccaaga tgagaattgt ggctatgctt tatacccccc 5641 tcaggtctaa tggttcaggt gatgatgtgt ttacagtctc ctgtagagtg ttgactagac 5701 cttcccctga ctttgacttc acatacctgg tgccaccaac agtggagtct aaaacaaagc 5761 cattcaccct cccaatcctc acacttgggg aactttccaa ttctaggttc ccagtgtcca 5821 tagaccagat gtacaccagc cccaatgaaa ttatatcagt gcagtgtcaa aatggtaggt 5881 gcacactgga cggggagctc caagggacaa cacaactcca agtcagtggc atttgtgctt 5941 tcaaaggtga ggtgaccgcc cacttgcatg acaatgatca cctatataat gtcaccatca 6001 caaacttgaa tgggtcccct tttgatccct ccgaggatat ccctgcccct ttgggtgtgc 6061 ctgacttcca gggaagggtt tttggtatca tctcccaaag agataaacac aatgatcctg 6121 ggcataatga accagcaaac aggggacacg acgctgtggt ccctacttac acagcacagt 6181 acactccaaa acttggacaa attcaaattg gcacatggca aacagacgac cttacagtca 6241 accaaccagt caaattcacc ccagttggat tcaatgacat tgaacacttt aaccaatggg 6301 tggtccctag gtatgctggt gccctaaacc tcaatacaaa ccttgcccct tctgttgctc 6361 cagtatttcc aggagagcgc ctgctcttct tcagatcata cattcccctc aagggcggtt 6421 atggaaaccc agccattgat tgcctactac cacaagagtg ggtgcaacac ttctatcagg 6481 aagcagcccc ttcaatgagt gaggtggccc tcgtcagata catcaacccg gacactggtc 6541 gggcactgtt tgaggccaag ctccacagag ctggtttcat gacggtctcg agcaacacca 6601 gtgccccggt ggttgtgcct gccaacgggt acttcagatt tgattcttgg gtgaaccaat 6661 tttatactct cgcccccatg ggaactggga atgggcgtag aagggttcaa taatggctgg 6721 agctttcgta gctggtcttg caggggacgt gctcagcaat gggcttagtt cattaatcaa 6781 tgcaggtgct aatgcaataa atcagagggc agaattcgat tttaatcaaa aattgcagca 6841 aaattctttt aatcatgata aggagatgtt gcaggctcag attcaggcaa ctaagcagct 6901 gcaggcagac atgatggcta taaaacaagg ggtcttgacc gctggcggct tttcccctgc 6961 tgatgcagcc agaggtgctg taaacgcgcc catgacacag gcgctggatt ggaatggcac 7021 aaggtattgg gcaccaaact ccatgaggac cacatcttat tctggaaaat tcacatcaac 7081 cgccccagtg aggcaggctg acttccagca cacccaaagc cggccttcga gtggctcctc 7141 tgtgtcttcc tttgccactc agtcttcaag gccaactctg accacaacca ctggttcctc 7201 acatggcaca gcctcatcaa attcaactcg cagcacaagc ctctcccaat caacggtctc 7261 cagagctaca tctaggactg gtgagtgggt tagagatcaa aatagaaatt tggaacccta 7321 catgcatggt gccttacaga cagcctttgt caccccacct tccagcaggg catctgacgg 7381 gacagtctca accgtcccta aaggtgtttt ggactcctgg acacctgcgt ttaacacccg 7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacaagctt agtgaaaagg 7501 tgaaaattta tttaggatta attgatttta ccttttaaaa aaaaaaaaaa //