Typing tool
|
Complete norovirus genomes
OR536475 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS OR536475 7543 bp RNA linear VRL 04-MAR-2024 DEFINITION Norovirus GII isolate Hu/NL/2018/GII.3[P21]/Rotterdam/I129S4_P19-d1099, complete genome. ACCESSION OR536475 VERSION OR536475.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7543) AUTHORS Izquierdo Lara,R.W., Villabruna,N., Hesselink,D.A., Schapendonk,C.M.E., Ribo Pons,S., Meier,J.I.J., Goodfellow,I., Dalm,V.A.S.H., Fraaij,P.L.A., van Kampen,J.A., Koopmans,M.P.G. and de Graaf,M. TITLE Intra-host multi-lineage evolution of human Norovirus in immunocompromised individuals: Implications for treatment JOURNAL Unpublished REFERENCE 2 (bases 1 to 7543) AUTHORS Izquierdo Lara,R.W., Villabruna,N., Hesselink,D.A., Schapendonk,C.M.E., Ribo Pons,S., Meier,J.I.J., Goodfellow,I., Dalm,V.A.S.H., Fraaij,P.L.A., van Kampen,J.A., Koopmans,M.P.G. and de Graaf,M. TITLE Direct Submission JOURNAL Submitted (11-SEP-2023) Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, Rotterdam, Zuid-Holland 3015 GD, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: Spades v. 3.15.4; BWA-MEM v. 0.7.17 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7543 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/NL/2018/GII.3[P21]/Rotterdam/I129S4_P19- d1099" /isolation_source="feaces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands: Rotterdam" /collection_date="22-Nov-2018" /note="genotype: GII.3[P21]" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="WMX17803.1" /translation="MKMASNDASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARP KQPPPRDKPPKPPRPPTPELVKSIPPPPPNGEDEPTISYNVKKGVSGLPELSTVTQPE ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLYWRPVYTPQYLISPETLKKLHGETFPYIAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVILCALASLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELEMVRAIEDAVLDLEAIENNHMTTLLKDRDSLATFMRTLDMEEEKARKLST KSASPDIVGTINSLLSRIAAARSLVHKAKEELSSRPRPVVVMISGRPGIGKTHLAREV AKKIASTLTGDQRVGLIPRNGVDHWDSYRGERIVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIMITTNLANPAPLDYVNFEACSRRIDFLVYAESPEVEK AKRDFPGQPDMWKDAFKPDCSHIKLTLAPQGGFDKNGNTPYGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISIKKCQLVYGGSTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLR SARIRYYVKCIQEALYSIVQIAGAAFITTRIARRMNIQNLWSKPQAEDLEETDNVEGC PKPKSDEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEFKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGSDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGETFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide 5..994 /gene="ORF1" /product="p48" mat_peptide 995..2092 /gene="ORF1" /product="NTPase" mat_peptide 2093..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..6731 /gene="ORF2" CDS 5085..6731 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="WMX17804.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAALAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLSLELGPEINPYLAHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAIPPNFPTDNLSAAQITMCPHVIVDVRQLEPVNLPLPD IRNNFFHYNQRSESRVRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFAFNFLVPP TVESKTKPFSLPVLTISEMSNSRFPVPIDSLHTSPTDAVVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVIAGSTSRASDQADTATPRSFNNRWHIQLDNLNGTPYDPSEDIPGP LGTPDFRGRVFGVASQRNPDATTRAHEAKIDTASPRFTPKLGSLEILTESDDFDQNQP TRFTPVGIGVDQETDFQQWTLPNYAGQVTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYINPDTGRVLFEAKLHKLGFITIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="WMX17805.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKHLQNA SFNHDKEMLNAQIEATKKLQASMIAIKEGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRHWAPGATSTTSLSGGFTNQTVHRPTPNFKTNQTPRLAPSNGSSVRSNSTQITSLSS HSSGSSRSSGSTVVSSIPSSNRTRDWVTQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgcaaaca gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtact atctaatatg gccgtcactt tcaaacgagc 121 cctcggggcg cggcctaaac agccgccccc gagggataaa ccaccaaaac ccccaagacc 181 ccccacacca gaattggtta aatcaatccc ccctccccca cccaacgggg aggacgaacc 241 aaccatttct tacaacgtca aaaagggtgt ttctggtttg cctgagctct caaccgtcac 301 ccaaccggaa gagaactcta cagcatttag cgttccccct cttagtcaga gggagaacag 361 agatgcaaag gaaccattga ctggaactat cctggagatg tgggatgggg agatctacca 421 ttatggctta tatgtggaac gggggttagt actaggtgtg cacaaaccac cagcagccat 481 cagccttgcc aaggttgagc tgaccccctt gtccttgtat tggagaccag tgtacacccc 541 acagtacctc atttcccctg aaactctcaa aaagttgcat ggggaaacgt tcccttatat 601 agcctttgac aacaactgtt acgccttctg ctgttgggtg cttgacttga acgattcatg 661 gctgagcaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggactggaa 721 taggaagccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atgttatcct 781 ctgtgctctc gcatcattgt ttacaagacc aattaaggac attattggga agttgaaacc 841 cctaaacatc cttaacatcc tagccacatg tgattggact tttgcgggca tagtagaatc 901 cctgatcctc ttggctgaac tgtttggagt cttctggaca cccccagatg tgtctgcaat 961 gatcgctcct ttactgggtg attatgagct gcagggaccc gaggaccttg ctgtggagct 1021 cgtacccgta gtaatgggag gggtaggtct ggtgctggga ttcaccaaag agaaaatcgg 1081 caaaatgctt tcatctgctg cttcaacctt gagggcatgc aaagatctcg gtgcatatgg 1141 gttggagatc ctcaaattgg tcatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 attggaaatg gtgagagcca tcgaggatgc agtgctagat cttgaggcca ttgagaacaa 1261 ccatatgaca actctactca aggatagaga cagccttgca accttcatga gaactcttga 1321 catggaggag gagaaggcga ggaaactctc caccaagtct gcctcgccgg atattgtggg 1381 cacgataaac tccctactgt caaggattgc agctgcccgg tctctagtgc acaaggctaa 1441 ggaggagctg tcaagcaggc cccgaccggt cgttgtgatg atctcaggga gaccaggtat 1501 agggaaaacc catctagcta gagaggtggc aaagaagatc gcctccacac tcacaggtga 1561 tcagagggtg ggtcttatcc cacgcaatgg ggtcgatcac tgggattcat acagaggtga 1621 aagaatcgtt ctctgggacg actatggaat gagcaacccc atccacgacg ccctcagact 1681 ccaggagctc gctgacacct gtcctctcac actcaactgc gacaggattg agaacaaagg 1741 caaggttttt gacagtgacg tcataatgat aaccaccaac ttggcaaacc cagcgccact 1801 ggactacgtc aactttgaag cgtgctcaag acgcatagac ttcctcgttt atgctgaatc 1861 ccctgaagtt gagaaggcta aacgggactt cccaggccaa ccagacatgt ggaaagatgc 1921 cttcaaacct gactgctcac acataaaatt aacattggcc ccacaagggg gttttgacaa 1981 aaatggtaac actccttatg ggaagggtgt catgaagacc ctcactgcca gttccctcgt 2041 tgcccgagca tcagggctcc tccatgagag gttagacgaa tatgagctgc aggggccaac 2101 tcccacgaca ttcaacttcg accgcaacaa ggttctcgct tttaggcaac ttgctgctga 2161 aaacaagtac ggccttgttg acacaatgag ggtcggatca cagctcaaga atgtcaaaac 2221 catgacagaa ctcaagcagg ctctcaagaa catctcaatc aagaaatgcc agcttgtata 2281 tggtgggagc acgtacacac ttgaatctga tggtaaaggt aatgtgcatg tcgagaaggt 2341 gaacaacacc agtgtgcaaa ctaacaatga gctctccggg gctttgcacc acctcaggag 2401 tgccagaatc aggtactatg ttaagtgtat ccaggaagct ctctactcca tcgtgcaaat 2461 tgccggggct gcattcatta ccacgcgcat tgcaaggcgc atgaacatac aaaacctttg 2521 gtccaaacca caagcagaag atttggagga gactgacaac gtggagggtt gtccaaaacc 2581 taaaagtgat gaagaatttg tcatctcctc tgacgacatc aaagccgagg gcaagaaagg 2641 taagaacaag actggccgtg gcaagaagca cacagccttt tccagcaaag ggcttagtga 2701 tgaggagtac gatgagttca aaaggatcag ggaagagaga aatggcaaat actccataga 2761 ggaataccta caggatagag acaaatacta tgaggaggtg gccatagcta gggcaactga 2821 ggaagacttc tgtgaagaag aagaggcaaa aatccggcaa aggatattta gaccaacaag 2881 gaaacagcgc aaagaagaaa gggcctctct cggtttggtt acaggttctg agattaggaa 2941 gagaaaccca gacgacttca aacccaaagg gaaactgtgg gccgatgatg acaggagtgt 3001 tgactacaat gagaaactta gtttcgaagc tccaccaagc atttggtcac gaatagtcaa 3061 ctttggctcg gggtggggtt tttgggtctc gcctagcctc ttcataacat caacccatgt 3121 catcccccaa ggcgcacagg aattctttgg ggtgtccatc aaacaaattc aaattcacaa 3181 gtcgggtgag ttctgccggc ttagattccc aaaaccaatc aggacagatg tcacaggcat 3241 gattttggag gaaggtgctc cagaaggcac tgttgccact cttctcatca agaggccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gcgaccatga gaattcaggg 3361 acgcactgtt ggtgggcaga tgggcatgct actcacaggg tctaacgcta agagcatgga 3421 cttgggcaca actcccggcg attgtggttg tccctacatc tacaagagag ggaacgacta 3481 cgttgtcatt ggggttcaca cagccgccgc tcgtggagga aacaccgtca tctgtgcaac 3541 ccaaggaagc gagggtgagg ctgtgctaga aggtagtgac aacaagggaa cttattgtgg 3601 agcaccaata ttgggacctg gaaatgcccc caaactcagc accaaaacca aattctggag 3661 gtcttccacc acccccctgc cacctggaac ctatgaacca gcctatctgg gtggcaagga 3721 ccctagagtg aagggtggcc cctcactgca acaggttatg agggatcagc taaaaccgtt 3781 cactgagccc agaggcaagc caccaaaacc aagtgtgcta gaagctgcca aaaagactat 3841 aatcaatgta cttgagcaaa caatagaccc acctcaaaaa tggacatacg cacaggcgtg 3901 tgcatcatta gataagacca cctccagcgg ccaccctcac cacatgcgga agaacgactg 3961 ctggaatggg gagaccttca caggaaaact ggcagaccaa gcatcaaagg ctaacctaat 4021 gtttgaggaa ggaaagaaca tgaccccagt gtacacaggg gctctaaaag atgagctagt 4081 taagactgat aagatctatg ggacaatcaa gaagagactc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tggattgatg gacgaactca aggcccactg 4201 tgtcacacta ccagtcagag ttggcatgaa catgaatgag gatggaccca taatatttga 4261 gaaacattcc agatataaat atcattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagca gtactggctg cagccctgga aataatggtc aaattctcac cagaacccca 4381 tctggctcag gtggttgcag aggacctctt gtcccccagt gtgatggatg tgggtgattt 4441 caggatatca attaacgagg gattgccctc tggtgttccc tgcacctcac aatggaactc 4501 cattgcccac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 cattaaactg gatccagaga aattaacaac aaaattgaag gaatacggac taaaaccaac 4681 ccgtcctgac aaaacagaag gacccttgat tatctctgaa gatttggatg gcctaacatt 4741 cttacggaga acggtaaccc gtgatccggc cgggtggttt ggcaaactgg atcaaagctc 4801 aatactcagg cagatgtact ggaccagggg accaaaccat gaggatccct ttgaaacaat 4861 gataccacac tcccaaagac ccatacaact gatgtcatta ttgggtgaag ctgcattgca 4921 tggtccgtca ttttacagta aaatcagcaa attagtcatc tcagaattga aagagggtgg 4981 aatggatttt tacgtgccca ggcaagaacc aatgttcaga tggatgagat tttcagactt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agaaccagtg gcgggtgcag cgttggcagc acccctcact ggccagcaaa 5221 atataattga tccctggatt atgaataatt ttgtacaagc acctggtggt gagtttacag 5281 tgtcccctag aaattctcct ggtgaagttc ttcttagttt ggaattgggt ccagaaataa 5341 acccctattt ggcccatctt gctagaatgt ataatggtta tgcaggtgga tttgaagtgc 5401 aggtgatcct agctgggaat gcgttcacag caggaaagat aatctttgca gctattcccc 5461 ctaatttccc aaccgacaat ctaagtgcag cacagatcac aatgtgtcca catgtgatcg 5521 tggatgtcag acagctggaa ccagtcaact taccgttgcc tgacattcgc aataatttct 5581 ttcattacaa tcaaaggtct gaatcgagag tgcgcttaat tgcaatgttg tatacacctc 5641 ttagggcaaa taattctggg gatgatgttt ttactgtgtc ttgcagagtg ttaactagac 5701 ctagtcctga ctttgcattt aatttccttg tgccacctac tgtggagtca aagacaaaac 5761 ccttttccct ccctgttctg actatctctg aaatgtccaa ttcgaggttc ccagtaccaa 5821 ttgattccct gcacaccagc cctactgatg ctgttgttgt ccagtgtcag aatgggcgcg 5881 tcacccttga tggtgagttg atgggcacca cccaactctt acctagtcaa atctgtgctt 5941 tcaggggcgt gatcgccgga tcaacaagca gggccagtga ccaggccgac acagcaaccc 6001 ctaggtcgtt caataatcgt tggcacatac aattggataa tctaaatgga actccttatg 6061 acccttcaga agacatacca ggccccttgg ggacaccaga tttccggggc agagtctttg 6121 gcgtggccag ccagagaaac cctgatgcta caactagagc acatgaagca aagatagaca 6181 cagcatctcc ccgtttcacc ccgaaattag gttcattaga aattctcact gaatccgatg 6241 attttgacca aaaccaacca acaagattca ccccagttgg cattggggtc gaccaggaga 6301 cagactttca acaatggact cttcccaact atgctggcca ggtcacccac aacatgaact 6361 tagccccagc tgttgctccc aacttccctg gcgagcaact ccttttcttc cgctcacagt 6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggtcccc caagaatggg 6481 tacagcactt ctaccaagaa tcagccccct cccaatctca agtagccctg gttaggtata 6541 tcaatcctga cactggtaga gtgttatttg aggccaaatt gcacaaattg ggtttcataa 6601 ctatagccaa aaatggtgac tctccaataa cagtccctcc caatggatac tttaggtttg 6661 aatcttgggt gaaccccttt tatacacttg cccccatggg aacagggaat gggcgtagaa 6721 ggattcaata atggctgggg cttttatagc aggattggct ggtgacatgc tcacaaatac 6781 tgtagggtct ttagttaatg caggggctaa tgccattaat caaacaattg attttgaaaa 6841 taataaacat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaaat 6901 tgaggcaaca aagaaattac aggccagcat gattgctatc aaagaagggg ttttgaccgc 6961 tggcggcttc tcccctactg atgcggcccg cggggcaatc aatgccccca tgacaaaagt 7021 cctagattgg aatggcacga gacactgggc accaggtgcc acctccacaa cctcattgtc 7081 gggtggcttt acaaatcaaa ctgtgcatag accaacacca aattttaaaa cgaaccagac 7141 ccccagactc gcacccagta atgggtcttc agtaaggtca aattcaaccc aaatcactag 7201 cttgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagttg tcagctcaat 7261 accatcctct aacaggacta gggattgggt cacccaacaa aattttaatt tggaaccaca 7321 catgcctggg tctcttagga cagcttttgt cactccacca tctagcacag cctctagctc 7381 aggcacagtc tcaactgtac ctaaaaatgt tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa 7501 agattattat aaatttgatt taaattagat ttaatttgga atc //