Typing tool
|
Complete norovirus genomes
MW305717 | GII.2 | ||
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GII.P16 |
ORF1: 1..5069 ORF2: 5050..6678 ORF3: 6678..7457LOCUS MW305717 7498 bp RNA linear VRL 06-JUL-2021 DEFINITION Norovirus GII isolate CMH-ST001-17 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MW305717 VERSION MW305717.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7498) AUTHORS Tohma,K., Lepore,C.J., Martinez,M., Degiuseppe,J.I., Khamrin,P., Saito,M., Mayta,H., Nwaba,A., Ford-Siltz,L.A., Galeano,M.E., Zimic,M., Stupka,J.A., Gilman,R.H., Maneekarn,N., Ushijima,H., Green,K.Y. and Parra,G.I. TITLE Genome-wide analyses of human noroviruses reveal coexistence of viral populations evolving under recombination constraints JOURNAL Unpublished REFERENCE 2 (bases 1 to 7498) AUTHORS Tohma,K., Lepore,C.J., Martinez,M., Degiuseppe,J.I., Khamrin,P., Saito,M., Mayta,H., Nwaba,A., Ford-Siltz,L.A., Galeano,M.E., Zimic,M., Stupka,J.A., Gilman,R.H., Maneekarn,N., Ushijima,H., Green,K.Y. and Parra,G.I. TITLE Direct Submission JOURNAL Submitted (23-NOV-2020) CBER/OVRR/DVP/LHV, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA COMMENT ##Assembly-Data-START## Assembly Method :: High-performance Integrated Virtual Environment (HIVE) v. 2 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7498 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="CMH-ST001-17" /isolation_source="feces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Thailand" /collection_date="11-Jan-2017" /note="genotype: GII.2[GII.P16]" gene <1..5069 /gene="ORF1" CDS <1..5069 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="QPJ59487.1" /translation="VACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDKPQK PPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVP PLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTPL SLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQR TTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNI LATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGSEDLAVELVPVV MGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELA MVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVG TINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLT GDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRI ENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQP DMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMD EFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRN VTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVK CVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFII SSKDIKEEGKKGKNKIGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR DRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPD DFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIP AGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPT GELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGN DYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKT KFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLE AAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGNPHHVRKNEFWNGEAFTGKLAD QASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFG GLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAA LEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLL TLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDK TEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIP HSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDL STWEGDRNLAPNFVNEDGVE" mat_peptide <1..965 /gene="ORF1" /product="p48" mat_peptide 966..2063 /gene="ORF1" /product="NTPase" mat_peptide 2064..2594 /gene="ORF1" /product="p22" mat_peptide 2595..2993 /gene="ORF1" /product="VPg" mat_peptide 2994..3536 /gene="ORF1" /product="Pro" mat_peptide 3537..5066 /gene="ORF1" /product="RdRp" gene 5050..6678 /gene="ORF2" CDS 5050..6678 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QPJ59488.1" /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG VISQRDKHNSPGYNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ" gene 6678..7457 /gene="ORF3" CDS 6678..7457 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QPJ59489.1" /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRTEFDFNQKLQQN SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG TRYWAPNSMRTTSYSGKFISTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA" ORIGIN 1 ccgttgcttg caacaacaac aacgacaaag aaaaatcttc aggtgaaggc ttattcacaa 61 atatgtcttc caccttaaag aaagccctcg gggctaggcc caagcagcct gccccgagag 121 acaaaccaca aaagccccca agaccaccaa ctcccgagtt ggtcaagagg ataccccctc 181 ctccacctaa tggcgaagaa gaagaagaac cagtcattag gtatgaggtt aagagtggga 241 tctccggcct gcccgagctc acaacagtcc cccaaccgga cgtggccaac acagcattca 301 gtgttccacc actgagcttg agagaaaaca gggaggccaa ggagccgcta acaggggcaa 361 tattagagat gtgggatgga gagatatacc actatggcct gtacgtggag aaaggcttag 421 tgttgggtgt gcacaaacca cctgcagcca taagcatggc aagagtggag ctgacgccgt 481 tgtcattgta ctggcgtgtg gtgtacactc cccaatacct catctcccct gaaaccctca 541 ggaggctcaa cggagaggca ttcccttaca ccgcctttga caacaactgc tatgcctttt 601 gctgctgggt gttagacctc aatgactcat ggcttagcag gaggatggta caaagaacaa 661 cgggcttctt cagaccttac caagagtgga acagaaaacc cctgcctacc atggatgact 721 ccaaaattaa gaaggtagca aatatattcc tatgttcatt gtccacatta ttcaccagac 781 ccataaaaga cctcatagga aaaattaaac cattgaacat attgaatatc ctggcaacgt 841 gtgactggac ttttgccgga atagtggagt ctctgatatt acttgctgaa ctcttcggag 901 ttttctggac acccccagat gtgtctgcta tgattgctcc cttactcggg gactacgagt 961 tgcaagggtc agaagacctc gccgttgaac tcgtacctgt ggtgatgggg gggattggtt 1021 tggtgttggg attcaccaaa gagaaaattg gcaaaatgtt gtcctcagca gcatcaacac 1081 tcagggcttg caaagatctt ggtgcctacg gcttagagat actcaaattg gtcatgaagt 1141 ggttcttccc aaagaaagag gaggccaatg agctagctat ggtgagggcc atagaggatg 1201 ctgtactaga ccttgaggca atagaaaata accacatgac aaccctgttg aaagacaaag 1261 acagcttagc aacatacatg aaaacactgg acatggagga ggagaaagcc aggaggttgt 1321 ccacaaaatc tgcatcccct gacatagttg ggacaatcaa cgccctgctg gctcgaatag 1381 cagcggccag gtcattagtc cacagggcca aggaagagct atctagcagg ataaggccag 1441 tagttgttat gatatctggc aaaccaggaa taggcaaaac tcatctggcc agggaggtgg 1501 caagaaaggt ggcatccact ctcacagggg atcaaagagt cggactcata ccacgaaacg 1561 gtgtggacca ttgggatgca tacaaaggtg agagagtcgt gctgtgggac gactatggca 1621 tgagtaaccc tattcatgat gctcttcgca tacaagaatt ggctgatacg tgtcccctta 1681 ccttaaattg tgacagaatc gaaaataagg gaaaagtttt tgacagtgaa gtcataataa 1741 ttacaacaaa ccttgccaat ccagccccac ttgattatgt caactttgag gcctgttcca 1801 ggagaattga tttcctggtg tacgctgagg caccagaagt agaaaaggca aaacgggact 1861 ttcctggtca gccagatatg tggaaggacg ccttcaagcc ggacttttca cacatcaagc 1921 tacagcttgc accccagggc ggctttgaca agaatggcaa caccccacat gggaaaggag 1981 tgatgaagac cctcactacc ggttctctga ttgcccgtgc atcaggccta ctgcatgaga 2041 ggatggatga atttgaactc caaggtccca caatcaccac ctttaatttc gaccggaaca 2101 gaatcacggc attcagacaa ttggctgcag aaaacaagta tggattggtg gataccatga 2161 aagttggcaa tcaattaaaa ggagtgaaaa ccatggaaga actcaaacaa gcaatcagga 2221 atgtgaccat caagaggtgc cagatcatct acggtggttc cacgtatgac cttgaatctg 2281 atggcaaggg caaagttttg gtggaaaagg tcaagaacac ctctgtacag accaataacg 2341 agttggctgg ggccctgcac catctcaagc atgcccgaat caggtactat gtcaaatgtg 2401 tgcaagaagc agtctattcc atcatacaaa ttgccggcgc tgcgtttgtc accacgcgca 2461 ttgcacgccg catgaacata caagaactct ggtcgaagcc acaactagat caaaatgaat 2521 cagagactaa ggaagaggcc cccaagtcag aagatgacga gttcatcata tcttctaagg 2581 acatcaagga ggaaggaaag aagggcaaaa acaaaattgg ccgtggcaag aaacacactg 2641 cgttctccag caagggcttg agcgatgagg agtatgacga gtacaagagg ataagagaag 2701 agagaaatgg gaagtactct atagaggagt atcttcaaga cagagacagg tactatgagg 2761 agctcgccat tgccaaggcc acggaagaag acttctgtga agaggaggag atcaaaatcc 2821 gtcagagaat tttccgtccc accaggaaac aaagaaagga agagagggcc acattagggc 2881 tagtaacagg ttcagaaatc agaaaaagaa accctgatga cttcaaaccc aaagggaagc 2941 tgtgggccga tgacaacagg agtgttgact acaatgagaa actggacttt gaggcccccc 3001 caagcatatg gtctaggatt gtgagctttg gttctggctg gggcttctgg gtgtcaccaa 3061 gccttttcat aacatcaact catgtaatcc ccgcaggcat aacagaagca tttggagtcc 3121 ccatcaaaca aattcagatc cacaaatcag gcgaattttg ccgattcaga ttcccaaaac 3181 caattagacc agatgtgaca ggaatgatct tggaagaggg tgcgcctgag ggcaccgtgg 3241 caactgtgct catcaaacgc cccaccggag agctcatgcc tcttgcagcc agaatgggaa 3301 cacacgcaac catgaaaatt caaggccgca tggttggcgg acagatgggt atgttgctca 3361 ctggatcaaa tgctaaagga atggatttgg gaacaactcc tggtgactgt ggctgtcctt 3421 acatctataa aaggggcaat gactatatag tcattggggt gcacactgca gcagcccgtg 3481 gtggaaacac tgtcatctgt gccacacagg gaagtgaggg tgaggcaact cttgagggtg 3541 gagatgacaa agggacatac tgtggggcac ccattctagg ccctgggggt gcaccaaaat 3601 tgagcaccaa aaccaaattt tggaggtcat cgaacacgcc ccttccacca gggacatatg 3661 agcctgccta cctcggtggc cgtgatccgc gtgttaaggg tgggccttcc ctgcagcagg 3721 taatgagaga ccagttgaag ccattcactg aacccagggg caaacctcca agaccaagtg 3781 tattggaagc agccaaacaa accatcatca atgtcctcga acaaaccctg gaccctccac 3841 aaaaatggac gtacgcacag gcgtgtgcct cacttgacaa aaccacctcc agcgggaacc 3901 cccatcacgt ccgaaagaat gaattctgga atggtgaggc cttcactggt aaactggcag 3961 accaagcatc aaaagcaaac ctaatgtttg aggaagggaa acacatgaca ccagtgtaca 4021 cagcagcact caaggacgag ctagtcaaga ctgagaaaat ctatggaaag atcaagaaga 4081 gactgctctg gggctctgac ttgtccacca tgatccggtg cgctaggtca tttggtgggc 4141 ttatggacga gatgaaggca cactgcatat cactcccagt ccgagttggc atgaatatga 4201 atgaagatgg cccaataata tttgagaaac attccagata caaatatcac tatgatgcag 4261 actactctcg ttgggattca acacaacaga gggcagtact agcagcagcc ttggaaatca 4321 tggtcagatt ctctgcagaa ccacaattgg cacaaatagt cgctgaggat ctgctggccc 4381 ctagtgtagt agatgtagga gactttaaaa ttacaataaa tgaagggctc ccttctggtg 4441 tgccatgcac ttctcaatgg aactccatcg cacactggct gctaactctc tgtgccttgt 4501 ctgaagtcac caaattgtcc cctgacatta tacaggcaaa ttccatgttc tcattttacg 4561 gtgatgacga gattgtcagc accgacataa aattggaccc tgaacagtta accgccaaat 4621 tgaaggagta cggcctgaaa ccaacccgcc cagacaaaac cgagggaccc ctgattatca 4681 gtgaagattt gaacggtctc actttcctcc gaaggacggt gactcgtgac ccagctggct 4741 ggtttggaaa actggatcaa agctcaattt tgaggcagat gtactggact agaggaccaa 4801 atcatgaaga ccccaatgag acaatgatac cccattctca aagacccata cagcttatgg 4861 cactgcttgg tgaagcctct cttcacggac cctctttcta cagtaaaatc agtaaattgg 4921 tcataactga actcaaagaa ggtgggatgg acttttacgt gccaaggcag gaacccatgt 4981 tcaggtggat gaggttttct gacttgagca cgtgggaggg cgatcgcaat ctggctccca 5041 attttgtgaa tgaagatggc gtcgaatgac gccgccccat ctactgatgg tgcagccggc 5101 ctcgtgccag aaagtaacaa tgaggtcatg gctcttgaac ccgtggctgg tgccgccttg 5161 gcagccccgg tcaccggtca aacaaatatt atagaccctt ggattagagc aaattttgtc 5221 caggccccca atggtgaatt tacagtctct ccccgaaatg cccctggtga agtgctactg 5281 aatctagagt tgggtccaga attaaatcct tatctggcac atttagcaag aatgtacaat 5341 gggtatgccg gtgggatgga ggtgcaggtc atgttggctg ggaacgcgtt cacagccggc 5401 aagttggtct tcgccgccgt gccaccccac ttcccggttg aaaacctcag cccacagcaa 5461 attaccatgt tccctcatgt gatcatagat gtgagaacct tggaacctgt tttattacca 5521 ctccctgatg ttaggaataa cttcttccat tataaccaga aagatgatcc caagatgaga 5581 attgtggcta tgctttatac ccccctcagg tctaatggtt caggtgatga tgtgtttaca 5641 gtctcctgta gagtgttgac tagaccttcc cctgactttg acttcacata cctggtgcca 5701 ccaacagtgg agtctaaaac aaagccattc accctcccaa tcctcacact tggggaactt 5761 tccaattcta ggttcccagt gtccatagac cagatgtaca ccagccctaa tgaaattata 5821 tcagtgcagt gtcaaaatgg taggtgcaca ctggacgggg agctccaagg gacaacacaa 5881 ctccaagtca gtggcatttg tgctttcaaa ggtgaagtga ccgcccactt gcatgacaat 5941 gatcacctat ataatgtcac catcacaaac ttgaatgggt ccccttttga tccctccgag 6001 gatatccctg cccctctggg tgtgcctgac ttccagggaa gggtttttgg tgtcatctcc 6061 caaagagata aacacaatag tcctgggtat aatgaaccag caaacagggg acacgacgct 6121 gtggtcccta cttacacagc acagtacact ccaaagcttg gacaaattca aattggcaca 6181 tggcaaactg acgaccttac agtcaaccaa ccagtcaaat tcaccccagt tggactcaat 6241 gacactgaac actttaacca atgggtggtc cctaggtatg ctggtgccct aaacctcaat 6301 acaaaccttg ccccttctgt tgctccagta tttccaggag agcgcctgct cttcttcaga 6361 tcatacattc ccctcaaggg cggttatgga aacccagcca ttgattgcct actaccacaa 6421 gagtgggtgc aacacttcta tcaggaagca gccccttcaa tgagtgaggt ggccctcgtc 6481 agatacatca acccggacac tggtcgggca ctgtttgagg ccaagctcca cagagctggt 6541 ttcatgacag tctcgagcaa caccagtgcc ccggtggttg tacctgccaa cgggtacttc 6601 agatttgatt cttgggtgaa ccaattttat tctctcgccc ccatgggaac tgggaatggg 6661 cgtagaaggg ttcaataatg gctggagctt ttgtagctgg tcttgcaggg gatgtgctca 6721 gcaatgggct tagttcatta atcaatgcag gtgctaatgc aataaatcag aggacagaat 6781 ttgattttaa tcagaaattg cagcaaaatt cttttaatca tgataaggag atgttgcagg 6841 ctcagattca ggcaactaag cagctgcagg cagacatgat ggctataaaa caaggggtct 6901 tgaccgctgg cggcttttcc cctgctgatg cagccagagg tgctgtgaac gcgcccatga 6961 cacaggcgct ggattggaat ggcacaaggt attgggcacc aaactccatg aggaccacat 7021 cttattctgg aaaattcata tcaaccgccc cagtgaggca ggctgacttc cagcacaccc 7081 aaagccggcc ttcgagtggc tcctctgtgt cttcctttgc cactcagtct tcaaggccaa 7141 ctctgaccac aaccactggt tcctcacatg gcacagcctc atcaaattca actcgcagca 7201 caagcctctc ccaatcaacg gtctccagag ctacatctag gactggtgag tgggttagag 7261 atcaaaatag aaatttggaa ccctacatgc atggtgcctt acagacagcc tttgtcaccc 7321 caccttccag cagggcatct gacgggacag tctcaaccgt ccctaaaggt gttttggact 7381 cctggacacc tgcgtttaac acccgcaggc agccgctctt tgcacacctc cgtaagaggg 7441 gggagtcaca agcttagtga aaaggtgaaa atttatttag gatgaattga ttttacct //