Typing tool
|
Complete norovirus genomes
OP205561 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5082 ORF2: 5063..6685 ORF3: 6685..7491LOCUS OP205561 7491 bp RNA linear VRL 21-JUN-2023 DEFINITION Norovirus GII isolate RIVM-NOV-2018-0454_R03-16_major nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OP205561 VERSION OP205561.1 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Kroneman,A. TITLE Shotgun whole genome sequencing for gastroenteritis surveillance using Norovirus as a model JOURNAL Unpublished REFERENCE 2 (bases 1 to 7491) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.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-2018-0454_R03-16_major" /isolation_source="Human feces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="2018-11-20" /note="genotype: GII.4 Sydney[P16]" gene <1..5082 /gene="ORF1" CDS <1..5082 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="UUV60984.1" /translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR VEPQKPPRPPTPELVKRIPLPPPNGEEEQEPVIRYEVKSGISGLPELTTVPQPDAANT AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGRIKPL NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLMDTMKVGNQLKGVKTMEELK QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVERVKNTSVQTNNELAGALHHLKHARI RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSED GEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLNDEEYDEYKRIREERNGKYSIEE YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHARKNEFWNGETFT GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP TRPDKTEGPLTISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN 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="UUV60985.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD 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="UUV60986.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSIKSS NSSTATSVHSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa 61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag 121 cctgccccga gagtcgaacc acaaaagcca ccaagaccac caactcccga gttggtcaag 181 aggatacccc ttcctccacc taatggcgaa gaagaacaag aaccagtcat taggtatgag 241 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgcggcc 301 aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg 361 ctaacagggg caatattaga gatgtgggac ggagagatat accactatgg cctgtacgtg 421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg 481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc 541 cctgaaactc tcaggaggct caacggagag gcgtttcctt acaccgcctt cgacaacaac 601 tgctacgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg 661 gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgcct 721 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca 781 ttattcacca gacccataaa agacctcata ggaagaatta aaccattaaa catattgaac 841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgcc 901 gaactcttcg gagtattctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc 961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg 1021 ggagggattg gcttggtgtt gggattcacc aaagagaaaa ttggtaaaat gttgtcctca 1081 gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga gatacttaaa 1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg 1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg 1261 ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaag 1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg 1381 ctggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga gctatctagc 1441 aggataagac cagtagtcgt tatgatatct ggcaaaccag gaataggcaa aactcatctg 1501 gccagggagg tggcaagaaa ggtggcatcc actctcacag gggatcaaag agtcggactc 1561 ataccaagaa acggtgtgga ccactgggat gcatacaaag gtgagagagt cgtgctgtgg 1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat 1681 acatgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt 1741 gaagtcataa taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt 1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag 1861 gcaaaacggg attttcctgg tcagccagat atgtggaagg acgctttcaa gccggacttt 1921 tcacacatca agctacagct tgcacctcag ggcggttttg ataagaatgg caacacccca 1981 catgggaaag gagtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc 2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac cacttttaat 2101 ttcgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg 2161 atggatacca tgaaagttgg caatcaacta aaaggagtga aaaccatgga agaactcaaa 2221 caagcaatca ggaacgtgac catcaagagg tgccgaatca tctacggcgg ctccacgtat 2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa gggtcaagaa cacctctgta 2341 cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg aatcaggtac 2401 tatgttaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt 2461 gtcaccacgc gcattgcacg ccgcatgaat atacaagaac tctggtcgaa gccacaatta 2521 gatcaaaatg aatcagagac taaggaagag gcccccaagt cagaagatgg cgagttcatc 2581 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac cggccgtggc 2641 aagaaacaca ctgcattctc cagcaagggc ttgaacgatg aggagtatga cgagtacaag 2701 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac 2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag 2821 gagatcaaaa tccgtcagag gattttccgt cccaccagga aacaaagaaa ggaagagagg 2881 gccacattag ggctggtgac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa 2941 cccaaaggga agctgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac 3001 ttcgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc 3061 tgggtatcac caagcctgtt cataacatca acccatgtaa tccccgcagg cataacagaa 3121 gcatttggag tccccatcaa acaaattcag atccacaaat caggtgaatt ttgccgattc 3181 aggttcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct 3241 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca 3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg 3361 ggcatgttgc tcaccggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac 3421 tgtggctgcc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact 3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca 3541 actcttgagg gtggagatga caaaggaaca tactgtgggg cacccattct aggccctggg 3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca 3661 ccagggacat atgagcctgc ctaccttggt ggccgcgatc cgcgtgttaa gggtgggccc 3721 tccttacagc aggtaatgag agaccagttg aagccattca ctgaacccag gggcaaacct 3781 ccaagaccaa gtgtgttgga agcagccaaa caaactatta tcaatgttct cgaacaaacc 3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc 3901 tccagcgggc atccccatca cgcccgaaag aatgaattct ggaatggtga gaccttcact 3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg 4021 acaccagtgt acacagcagc actcaaggac gagctagtca agactgagaa aatctatgga 4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg 4141 tcatttggtg ggctcatgga cgagatgaag gcgcactgca tatcactccc agtgcgagtt 4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacactccag atacaaatac 4261 cactatgatg cagactactc tcgttgggat tcaacacaac agagggcagt actagcagca 4321 gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag 4381 gatctgctgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg 4441 ctcccatctg gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact 4501 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc aaattccatg 4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgagcag 4621 ttaaccgcca agttgaagga gtacggcctg aagccaaccc gcccagacaa gaccgaggga 4681 cccctgacca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac ggtgactcgt 4741 gacccagctg gctggtttgg aaaactggac caaagttcaa ttttgaggca gatgtactgg 4801 actagaggac caaaccatga agaccccaat gagacaatga taccccattc tcaaagaccc 4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaga 4921 atcagcaaat 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 gtttacagta tcccctagaa acgctccagg 5281 tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctgt cccatttggc 5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc 5401 gttcaccgcc gggaagatta tatttgcagc agtcccacca aattttccaa ctgaaggctt 5461 aagtcctagc caggtcacta tgttccccca tatagtagta gatgttagac aattagaacc 5521 tgtgctaatt cccttacccg atgttaggaa taatttctat cattacaatc agtcaaatga 5581 ctccactatt aagttgatag caatgttgta tacaccactt agggctaata atgctgggga 5641 tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt ttgatttcat 5701 atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac 5761 tgttgaggag atgaccaatt caagattccc catccctttg gaaaagttgt tcacaggccc 5821 cagcagtgcc tttgttgttc aaccacaaaa cggcagatgc acaactgatg gcgtgctcct 5881 aggcaccacc caactttctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat 5941 cacaggtagt cgcaactata caatgaattt ggcttctcaa aattggaaca actatgaccc 6001 aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga ttcaaggcat 6061 gctcacccaa accacaagga cagatggttc aacacgcggc cacaaagcta cagtgtacac 6121 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacagacca 6181 tgattttgaa gctaaccaaa acacaaagtt caccccagtc ggtgtcatcc aagatggtag 6241 caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaatac 6301 tcacaatgta catttggccc ccgctgtagc ccccaccttt ccgggtgagc aacttctctt 6361 ctttagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgtctgct 6421 cccccaggaa tgggtgcagt acttctacca agaagcagcc ccagcacaat ctgatgtggc 6481 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcacaa 6541 atcaggctat gttacagtgg ctcatactgg ccaacatgat ttggttatcc cccccaatgg 6601 ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg 6661 aacggggcgt agacgtgtgg tataatggct ggagctttct ttgctggatt ggcatctgat 6721 gtccttggct ctggacttgg ttccctcatc aatgctgggg ctggggccat caaccaaaaa 6781 gttgagtttg aaaataacag gaaattgcaa caagcatcct tccaatttag cagcaatttg 6841 caacaggctt cttttcaaca tgataaagag atgctccaag cacaaattga ggccaccaaa 6901 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcctagaggg tgggttctct 6961 gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt ggactggagc 7021 gggacaaggt actgggctcc agatgctaga attacaacat acaatgcagg ccacttttcc 7081 acccctcaac catcgagggc actgccagga agagctaatc ttagggatgc tgtccctgct 7141 cggggaccct ccattaaatc ttctaactct tctactgcta cctctgtgca ctcaaatcaa 7201 accatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagcctcccg 7261 tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggaatttgtc acctttcatg 7321 aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc tagccaaggc 7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caacacgcgc 7441 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta a //