Typing tool
|
Complete norovirus genomes
OP205570 | GII.3 | ||
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GII.P16 |
ORF1: 1..5082 ORF2: 5063..6709 ORF3: 6709..7473LOCUS OP205570 7473 bp RNA linear VRL 21-JUN-2023 DEFINITION Norovirus GII isolate RIVM-NOV-2018-0352_R04-01 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OP205570 VERSION OP205570.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7473) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A. TITLE Shotgun whole genome sequencing for gastroenteritis surveillance using Norovirus as a model JOURNAL Unpublished REFERENCE 2 (bases 1 to 7473) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A. TITLE Direct Submission JOURNAL Submitted (05-AUG-2022) Center for Infectious Diseases, Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. v3.11.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7473 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="RIVM-NOV-2018-0352_R04-01" /isolation_source="Human feces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="2018-09-11" /note="genotype: GII.3[P16]" gene <1..5082 /gene="ORF1" CDS <1..5082 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="UUV61011.1" /translation="DATVAVACDNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR DKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANT AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKIGNQLKGVKTMEELK QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVERVKNISVQTNNELAGALHHLKHARI RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSED DEFVISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR KRNPDDFKPKGKLWADDNRSVDYNEKLNFEAPPSIWSRIVSFGSGWGFWVSPSLFITS THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGYPHHARKNEFWNGETFT GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA VLASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN ETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..978 /gene="ORF1" /product="p48" mat_peptide 979..2076 /gene="ORF1" /product="NTPase" mat_peptide 2077..2607 /gene="ORF1" /product="p22" mat_peptide 2608..3006 /gene="ORF1" /product="VPg" mat_peptide 3007..3549 /gene="ORF1" /product="Pro" mat_peptide 3550..5079 /gene="ORF1" /product="RdRp" gene 5063..6709 /gene="ORF2" CDS 5063..6709 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UUV61012.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNTFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPAPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDENQP TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG GRSDGILDCLVPQEWVQHFYQESAPSQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KSGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6709..7473 /gene="ORF3" CDS 6709..7473 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UUV61013.1" /translation="MAGAFIAGLAGDMLTNTVGSLVGAGANVINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gacgctaccg ttgccgttgc ttgcgacaac aacaacgaca aggaaaaatc ttcaggtgaa 61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag 121 cctgccccga gagacaaacc acaaaagccc ccaagaccac caactcccga gttggtcaag 181 aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgag 241 gttaagagcg ggatctctgg tctgcccgag ctcacaacag ttccccaacc ggacgtggcc 301 aacacagcat tcagtgttcc accactgagt ttgagagaaa acagggaggc caaagaaccg 361 ctaacagggg caatattaga gatgtgggat ggagagatat atcactatgg cctgtacgtg 421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg 481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc 541 cctgaaactc tcaggaggct taacggagag gcattccctt acaccgcttt tgataacaac 601 tgctatgcct tttgttgctg ggtgttagac ctcaacgact catggctcag caggaggatg 661 gtgcaaagaa caacgggctt ctttagacct taccaagagt ggaacagaaa acccctacct 721 accatggatg actccaaaat taagaaggta gcaaatatat tcctatgttc attgtccaca 781 ttatttacca gacccataaa agaccttata ggaaaaatta aaccattaaa catattgaat 841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctaat attacttgct 901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc 961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg 1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggtaaaat gttgtcctca 1081 gcagcatcaa cactcagagc ttgcaaagat cttggtgcct atggcttaga gatactcaaa 1141 ttggtcatga agtggttctt cccaaagaaa gaagaggcca atgagctagc catggtgagg 1201 gccatagagg atgctgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg 1261 ttgaaagata aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa 1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caatgccctg 1381 ctggctcgaa tagcagcggc caggtcacta gtccacaggg ctaaggaaga gctatctagc 1441 aggataaggc cagtagttgt tatgatatct ggtaaaccag gaataggcaa aactcatctg 1501 gccagggagg tggcaagaaa ggtggcatcc actctcacag gggatcaaag agtcggactc 1561 ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg 1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat 1681 acgtgtcccc tcaccttaaa ttgtgacaga attgaaaata aaggaaaagt ttttgacagt 1741 gaagtcataa taatcacaac aaaccttgcc aatccagccc cacttgatta tgtcaacttt 1801 gaggcctgtt ccaggagaat tgacttcctg gtgtacgctg aggcaccaga agtagaaaag 1861 gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt 1921 tcacacatca agttacagct tgcaccccag ggcggctttg acaagaatgg taacacccca 1981 catgggaaag gagtgatgaa gaccctcact accggttctc tgattgctcg tgcatcaggc 2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ctacaatcac caccttcaat 2101 ttcgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggactg 2161 gtggatacca tgaaaattgg caatcaatta aaaggagtta aaaccatgga agaacttaaa 2221 caagcaatca ggaatgtaac catcaagagg tgtcggatca tctacggtgg ttccacatat 2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa gggtcaagaa catctctgta 2341 cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg gatcaggtac 2401 tatgtcaaat gtgtgcaaga agcagtctat tctatcatac aaattgccgg cgctgcgttt 2461 gtcaccacgc gtatcgcacg ccgcatgaac atacaagagc tctggtcgaa gccacaatta 2521 gatcaaaatg aatcagagac taaggaagag gcccccaagt cggaagatga tgagttcgtc 2581 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaataaaac tggccgtggc 2641 aagaaacaca ctgcgttctc cagtaagggc ttgagcgatg aggagtacga cgagtacaag 2701 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac 2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag 2821 gagatcaaaa tccgtcagag aattttccgc cctaccagga aacaaagaaa ggaagagagg 2881 gccacactag ggctagtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa 2941 cccaaaggga agctgtgggc cgatgacaac agaagcgttg attataatga gaagctgaac 3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc 3061 tgggtgtcac caagcctgtt cataacatca actcatgtga tccccgcagg cataacagaa 3121 gcatttggag tccccatcaa acaaattcag atccacaaat caggcgaatt ttgccgattc 3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct 3241 gagggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca 3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg 3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac acctggtgac 3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact 3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca 3541 actcttgagg gcggagatga caaaggaaca tactgtgggg cacccattct aggccctggg 3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gcccctccca 3661 ccagggacat atgagcctgc ctacctcggc ggccgtgacc cgcgtgttaa gggtgggccc 3721 tccttgcagc aggtgatgag agaccagttg aagccgttca ctgaacccag aggcaaacct 3781 ccaaaaccaa gtgtattgga agcagccaaa caaaccatca tcaatgtcct cgaacaaacc 3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caagaccacc 3901 tccagcgggt acccccatca cgcccgaaag aatgaattct ggaatggtga gaccttcact 3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg 4021 acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa aatctatgga 4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgattcg gtgcgctagg 4141 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtccgagtt 4201 ggtatgaaca tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatac 4261 cactatgacg cagactactc tcgctgggat tcaacacaac agagggcagt actggcatca 4321 gccttggaaa ttatggtcag attctctgca gaaccacaac tggcacaaat agtcgctgag 4381 gacctgctgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg 4441 ctcccctctg gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact 4501 ctctgtgccc tgtctgaagt caccaaactt tcccctgaca ttgtacaggc aaattccatg 4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag 4621 ttaaccgcca aattgaagga gtacggcctg aaaccaaccc gcccagacaa aactgaggga 4681 cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac ggtgactcgt 4741 gacccagctg gctggtttgg aaaactggac caaagctcaa ttttgaggca gatgtactgg 4801 actagaggac caaatcacga agaccccaat gagacaatga taccccattc tcaaagaccc 4861 atacagctta tggcattgct tggtgaagcc tctcttcacg ggccctcttt ctacagtaaa 4921 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggattttta cgtgccaagg 4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc 5041 aatctggctc ccagttttgt gaatgaagat ggcgtcgaat gacgccgccc catctaatga 5101 tggtgccgcc ggcctcgtcc cagagatcaa caatgaggca atggcgctag agccagtggc 5161 gggtgcagcg atagcagcac ccctcactgg tcagcaaaat ataattgatc cctggattat 5221 gaacaacttt gtgcaagcac ctggtggtga gtttacagtg tccccaagaa attcccctgg 5281 tgaagtcctt cttaatttgg aattgggccc agagataaac ccctacttgg cccatcttgc 5341 tagaatgtac aatggttatg caggtggatt tgaagtgcag gtggtcctag ctggaaatgc 5401 gtttacagca ggaaagataa tctttgcagc catcccccct aattttccaa ttgacaattt 5461 aagtgcagca cagatcacaa tgtgcccaca tgtaatcgtg gacgtcagac agttggaacc 5521 agtcaacctc ccgatgcctg acgttcgcaa taccttcttt cattataatc aagggtctga 5581 ttcgaggtta cgcctaattg caatgctata cacacctctt agggcaaaca attctgggga 5641 tgatgttttt actgtgtctt gtagagtgct aactagacct agtcctgatt tctcgttcaa 5701 tttccttgtg cctcccactg tggagtcaaa gacaaaaccc ttttccctcc ccatcttgac 5761 tatctctgaa atgtccaact ctaggttccc agcaccaata gattccctac acaccagtcc 5821 tactgagaat attgttgttc agtgccaaaa tgggcgcgtc acccttgatg gtgagctgat 5881 gggcaccacc caactcttgc ccagccaaat ctgtgctttc aggggcgttc ttaccagatc 5941 aacaagcaga gccagtgacc aggccgatac agcaacccct agattattta attactattg 6001 gcatatacaa ttggataatc taaatggaac cccttatgat cctgcagaag acataccagg 6061 ccccctaggg acaccagatt tccgtggcaa agtctttggc gtggccagcc agagaaatcc 6121 tgataccacg actagagcac atgaagcaaa gatagacacc acatccggcc gtttcacccc 6181 aaagctaggc tcattagaga tatccactga atctagtgat tttgatgaaa accaaccaac 6241 aagattcacc ccagttggca ttggagttga ccatgaggca gactttcaac aatggaccct 6301 acccgactat gctggtcagt tcacacataa catgaacttg gccccagctg ttgctcccaa 6361 tttccctggt gaacagctcc ttttcttccg ctcacatttg ccatcttctg gtgggcgatc 6421 tgacgggatt ctagactgcc tggttcccca agaatgggta cagcacttct accaagagtc 6481 agccccctct cagactcaag tggccctggt taggtatgtt aatcctgaca ctggcagagt 6541 gttatttgag gccaagctac acaaattagg tttcatgact atagccaaga gtggtgattc 6601 cccaataact gtccccccaa atggatactt taggtttgaa tcttgggtga acccctttta 6661 cacacttgcc cccatgggaa ctgggaatgg gcgtagaagg attcaataat ggctggagct 6721 tttatagcag gattggctgg tgacatgctc acaaatactg taggatcttt agttggtgca 6781 ggagctaatg ttatcaatca aacaattgat tttgaaaata ataaatattt gcaaaatgct 6841 tcttttaatc atgataagga gatgttgaat gcacaaattg aggcaacaaa gaagttacag 6901 gctgacatga ttgctatcaa acaaggggtt ttgaccgctg gcggcttctc ccctactgat 6961 gcagcccgtg gggcaattaa tgcccccatg acaaaagtcc tagattggaa tggaacgaga 7021 tactgggcac caggtgccac ctccacaacc tcgatgtcgg gtggctttac acaccaaact 7081 gtgcacagat ccacaccaaa ttttaaaacg aaccaggccc ccaaatccac acctagtagt 7141 ggttcttcag tgaggtcaaa ctcaacccaa atcactagcc tgagctcaca ctcgtccggg 7201 tcgtctcgat ccagcgggtc tacagtcatc agctcaatac catcctctaa caggactagg 7261 gactgggtca accaacaaaa ttttaatttg gaaccacaca tgcctggatc tcttaggaca 7321 gcttttgtca ctccaccatc tagtacagcc tctagctcag gcacagtctc aactgtgccc 7381 aaaaatgttt tggactcctg gacatctgcg tttaacacgc gcagacagcc gctattcgca 7441 caccttcgca gaagggggga gtcaaatgtt tag //