Typing tool
|
Complete norovirus genomes
OP205565 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5082 ORF2: 5063..6685 ORF3: 6685..7491LOCUS OP205565 7491 bp RNA linear VRL 21-JUN-2023 DEFINITION Norovirus GII isolate RIVM-NOV-2018-0482_R03-20 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OP205565 VERSION OP205565.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7491) 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Kroneman,A. TITLE Shotgun whole genome sequencing for gastroenteritis surveillance using Norovirus as a model JOURNAL Unpublished REFERENCE 2 (bases 1 to 7491) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.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..7491 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="RIVM-NOV-2018-0482_R03-20" /isolation_source="Human feces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="2018-12-03" /note="genotype: GII.4 Sydney[P16]" gene <1..5082 /gene="ORF1" CDS <1..5082 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="UUV60996.1" /translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR DEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQPGVANT AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEETPKSED DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRRQRKEERATLGLVTGSEIR KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS THVIPAGVTEAFGVPIKQIQIHKSGEFCRLRFPKPIRPDVTGMILEEGAPEGTVATVL IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR PSVLEAAKQTIINVFEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN ETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPNFVNEDGVE" 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..6685 /gene="ORF2" CDS 5063..6685 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UUV60997.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6685..7491 /gene="ORF3" CDS 6685..7491 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UUV60998.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARVTTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRDLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa 61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag 121 cctgccccga gagatgaacc acaaaagccc ccaagaccac caactcccga gttggtcaag 181 aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgat 241 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc gggcgtggcc 301 aacacagcat tcagtgttcc accactgagc ttgagagaga acagggaggc caaggaaccg 361 ctaacagggg caatattaga gatgtgggac ggagagatat accactatgg cctgtacgtg 421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg 481 gagctgacgc cactgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc 541 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaacaac 601 tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg 661 gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgccc 721 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca 781 ttattcacca gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaac 841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgct 901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc 961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtgatg 1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggaaaaat gttgtcctca 1081 gcagcatcaa cactcagggc ttgcaaagat cttggcgcct atggcttaga gatactcaaa 1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg 1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg 1261 ctgaaagata aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa 1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg 1381 ctggctcgaa tagcagcagc caggtcatta gtccacaggg ccaaggaaga gctatctagc 1441 aggataagac cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg 1501 gccagggagg tggcaagaaa ggtagcatcc actctcacag gggatcaaag agtcggactc 1561 ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg 1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat 1681 acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt 1741 gaagtcataa taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt 1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag 1861 gcaaaacggg attttcctgg tcagccagat atgtggaagg acgcctttaa gtcggacttt 1921 tcacacatca agctacagct tgcacctcag ggtggctttg acaagaatgg caacacccca 1981 catgggaaag gggtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc 2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat 2101 tttgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg 2161 gtggatacca tgaaagttgg caaccaacta aaaggagtga aaaccatgga agagctcaaa 2221 caagcaatca ggaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtat 2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta 2341 cagaccaaca acgaattggc cggggccctg caccatctca aacacgcccg aatcaggtac 2401 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt 2461 gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta 2521 gatcaaaatg aatcagaggc taaggaagag acccccaagt cagaagatga cgagttcatc 2581 atatcttcca aggacatcaa ggaggaggga aagaagggca aaaacaaaac tggccgtggc 2641 aagaaacaca ctgcattctc tagcaagggc ttgagcgatg aggagtatga cgagtacaag 2701 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac 2761 aggtactatg aggagctcgc catcgccaag gccacggaag aagacttctg tgaagaggag 2821 gagatcaaaa tccgtcagag aattttccgt cccaccagga gacaaagaaa ggaagagagg 2881 gccacattag ggctggtaac aggttcagaa atcagaaaaa gaaaccccga tgacttcaaa 2941 cccaaaggga agctgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac 3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc 3061 tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg cgtaacagaa 3121 gcatttggag tccccatcaa acaaattcag atccacaaat caggtgaatt ttgccgactc 3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct 3241 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca 3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg 3361 ggtatgttgc tcactggatc aaatgctaaa ggtatggatt tgggaacaac tcctggtgac 3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact 3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacgc agggaagtga gggcgaggcg 3541 actcttgagg gtggagatga caaaggaaca tactgtgggg cacccatttt aggccctggg 3601 ggtgcaccaa aattgagcac caaaaccaaa ttctggaggt catcgaacac gccccttcca 3661 ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc 3721 tctttgcagc aggtgatgag agaccagttg aagccattca ctgaacccag gggcaaacct 3781 ccaagaccaa gtgtattgga agcagccaaa caaaccatta tcaatgtttt cgaacaaacc 3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc 3901 tccagcggac atcctcacca cgtccgaaag aatgaattct ggaatggtga gaccttcact 3961 ggtaaattgg cagaccaagc gtcaaaagca aacctaatgt ttgaggaagg gaaacacatg 4021 acaccagtgt atacagcagc actcaaggac gagctagtta agactgagaa aatctatgga 4081 aaaatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg 4141 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtacgagtt 4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat 4261 cactatgatg cagactactc tcgttgggat tcaacacaac aaagggcagt actagcagca 4321 gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag 4381 gatctactgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg 4441 ctcccatctg gtgtgccatg cacttcccaa tggaactcca tcgcacactg gctgctaact 4501 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc aaattccatg 4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag 4621 ttgaccgcca agttgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgaggga 4681 cccctgatca tcagtgaaga tctgaacgga ctcactttcc tccgaaggac ggtgactcgt 4741 gacccagctg gctggtttgg aaaactggac cagagttcaa ttttgaggca gatgtactgg 4801 actagaggac caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc 4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaga 4921 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg 4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc 5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg 5101 gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg agcccgttgt 5161 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag 5221 aaataatttt gtacaagccc ctggtgggga gttcacagtg tcccctagaa acgctccagg 5281 tgaaatacta tggagcgcgc ccctaggccc tgatctaaat ccctacctat cccatttggc 5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc 5401 gttcaccgcc gggaagatta tatttgcagc agtcccacca aattttccaa ctgaaggctt 5461 aagtcccagc caggtcacta tgttccccca tataatagta gatgttagac aattagaacc 5521 tgtgctgatt cccttacccg atgttaggaa taatttctat cattacaatc agtcaaatga 5581 ttccactatt aagttgatag caatgttgta cacaccactt agggctaata atgctggaga 5641 tgatgttttc acagtttcgt gccgagttct cacgaggcca tcccccgatt ttgatttcat 5701 atttttagtg ccccccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac 5761 tgttgaggag atgaccaatt caaggttccc catccctttg gaaaagttgt tcacaggccc 5821 cagtagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct 5881 aggcaccacc caactttctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat 5941 cacaggtagt cgcaactaca cgatgaattt ggcttcccaa aattggaaca actatgaccc 6001 gacagaagaa atcccagccc ctctagggac tccagatttt gtagggaaga ttcaaggcat 6061 gctcacccaa accacaagga cagacggttc aacacgcggc cacaaagcaa cagtgtacac 6121 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacagacca 6181 tgattttgaa gctaatcaaa acacaaaatt taccccagtc ggtgtcatcc aagatggtag 6241 caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaatac 6301 tcacaatgta catctggccc ctgctgtagc ccccaccttt ccgggtgagc aacttctctt 6361 tttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgcctgct 6421 cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat ccgatgtggc 6481 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcataa 6541 atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc cccccaatgg 6601 ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg 6661 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat 6721 gtccttggct ctggacttgg ttcccttatc aatgctgggg ctggggccat caaccaaaaa 6781 gttgaatttg aaaataacag aaaattgcaa caagcatcct tccaatttag cagcaatctg 6841 caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga ggccactaaa 6901 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcttagaggg tgggttctct 6961 gagacagatg cagcccgcgg ggcaatcaat gcccccatga caaaagtttt ggattggagc 7021 gggacaaggt actgggctcc agatgctagg gttacaacat acaatgcagg ccacttttcc 7081 acccctcaac catcgagggc actgccagga agagctaatc ttagggatgc tgtccctgct 7141 cggggaccct ccaacaaatc ttctaactct tctactgcta cctctgtgta ctcaaatcaa 7201 actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagtctcccg 7261 tcaactgcaa ggactaggag ctgggttgag gatcaaaata gggatttgtc tcctttcatg 7321 aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc tagccaaggc 7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt taacacgcgc 7441 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta a //