Typing tool
|
Complete norovirus genomes
OP162339 | GI.6 | ||
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GI.P11 |
ORF1: 1..5359 ORF2: 5343..6965 ORF3: 6965..7594LOCUS OP162339 7597 bp RNA linear VRL 21-JUN-2023 DEFINITION Norovirus GI isolate RIVM-NOV-2016-0307_R02-16 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OP162339 VERSION OP162339.1 KEYWORDS . SOURCE Norovirus GI ORGANISM Norovirus GI Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7597) 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Kroneman,A. TITLE Shotgun whole genome sequencing for gastroenteritis surveillance using Norovirus as a model JOURNAL Unpublished REFERENCE 2 (bases 1 to 7597) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.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..7597 /organism="Norovirus GI" /mol_type="genomic RNA" /isolate="RIVM-NOV-2016-0307_R02-16" /isolation_source="Human feces" /host="Homo sapiens" /db_xref="taxon:122928" /country="Netherlands" /collection_date="2016-09-28" /note="genotype: GI.6[P11]" gene <1..5359 /gene="ORF1" CDS <1..5359 /gene="ORF1" /codon_start=2 /product="nonstructural polyprotein" /protein_id="UUL90920.1" /translation="ASKDVVATNVASNNNANNTSATSRFLSRFKGLGGGASPPNPIKI KSTEMALGLIGKTAQEAVGASDLPPKQQRDRPPRTQEEVQYGMGWTERPVDQNVKSWE ELDTSTKEEILDSHKEWFDAGGLGPCTMPSTCEQAKDDSPPGEQVRWSARDGVNLGVN RLTTVSGPEWNLCPLPPIDLRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTVGVH SPQAAFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLRELENEPWPYAAITNNCFEFC CQVMNLEDTWLQRRLITSGRFHHPSQSWSQQTPEFQQDSKLELVRDAILAAVNGLVSQ PFKNFLGKLKPLNVLNILSNCDWTFMGVVEMVILLLELFGVFWNPPDVSNFIASLLPD FHLQGPEDLARDLVPVILGGIGLAIGFTRDKVTKVMKSAVDGLRAATQLGQYGLEIFS LLKKYFFGGDQTERTLKGIETAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEEEKA RKLSAKNADPHVISSTNALISRIAMARSALAKAQAEMTSRMRPVVIMMCGPPGIGKTK AAEHLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNKLQA IADSAPLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVYCSA PEVEQIRRVSPGDTSALKDCFKSDFSHLKMELAPQGGFDNQGNTPFGKGVMKPTTINR LLIQAVALTMERQDEFRLQGKMYDFDDDRVSAFTTMARDNGLGILSMASLGKKLRGVT SMDGLKNALKGYKIGACTIKWQAKVYSLESDGNSVNIREEKNVLTQQQQSVCAASIAL TRLRAARAVAYASCIQSAITSILQIAASALVVNRAVKRMFGTRTAALSLEGPPKEHKC RVHQAKAAGKGPIGHDDMVDKYGLCETEEDEEVVHTEIPSATMEGKNKGKNKKGRGRK NNYNAFSRRGLNDEEYEEYKKIREEKGGNYSIQEYLEDRQRYEEELAEVQAGGDGGIG ETEMEIRHRVFYKSKSKKHHQEERRQLGLVTGSDIRKRKPIDWTPPKSAWADDEREVD YNERINFEAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVIPTSAKEFFGEPLASIAIH RAGEFTLFRFSKKIRPDLTGMILEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMR IQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVYKRANDWVVCGVHAAATKSGNT VVCAVQASEGETTLEGGDKGHYAGHEIIKHGCGPALSTKTKFWKSSPEPLPPGVYEPA YLGGRDPRVSGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSSLEQVMDTPV PWSYSDACQSLDKTTSSGFPHHKKKNDDWNGTAFIRELGEQAAHANNMYEQAKSMKPM YTAALKDELVKPEKVYQKVKKRLLWGADLGTVIRAARAFGPFCDAIKSHTIKLPIKVG MNSIEDGPLIYAEHSKYKYHFDADYTAWDSTQNRQIMTESFSIMCRLTASPELASVVA QDLLAPSEMDVGDYVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDVIQS MSYFSFYGDDEIVSTDIEFDPAKLTQVLKEYGLKPTRPDKSEGPIIVRKSVDGLVFLR RTISRDAAGFQGRLDRASIERQIYWTRGPNHSDPFETLVPHQQRKIQLISLLGEASLH GEKFYRKISSKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVNDDG V" mat_peptide <1..1189 /gene="ORF1" /product="p48" mat_peptide 1190..2278 /gene="ORF1" /product="NTPase" mat_peptide 2279..2875 /gene="ORF1" /product="p22" mat_peptide 2876..3289 /gene="ORF1" /product="VPg" mat_peptide 3290..3832 /gene="ORF1" /product="Pro" mat_peptide 3833..5356 /gene="ORF1" /product="RdRp" gene 5343..6965 /gene="ORF2" CDS 5343..6965 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UUL90921.1" /translation="MMMASKDAPTSPDGASGAGQLVPEANTAEQISMDPVAGASTAVA TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLSQMYNG WVGNMRVRILLAGNAFTAGKIIICCVPPGFDARILTIAQATLFPHLIADVRTLEPVEL PLEDVRNVLFHNSSQPQPTMRLVAMLYTPLRTGGGSGGTDAFVVAGRVLTCPAPDFSF LFLVPPSVEQKTRVFSVPNIPLKDLSNSRVPVPVQGMFMSPDVNQSVQFQNGRCQIDG QLQGTTPVSLSQLCKIRGKTSSNARVLNLSEVDGTPFIPLESPAPVGFPDLGGCDWHV NFTFQAQNQDPSQSVTFATNDTSFVPYLGSISPHNGGDFHAGDIIGSLGWISAPSDNS QLNVWTIPKYGSSLPDVTHLAPAVFPPGFGEVILYFYSTFPGSGQSSQLQVPCLLPQE FITHFCNEQAPIAGEAALLHYVDPDTGRNLGEFKLYPDGFMTCVPNSVSSGPQTLPIN GVFVFVSWVSRFYQLKPVGTASAARRLGLRRI" gene 6965..7594 /gene="ORF3" CDS 6965..7594 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UUL90922.1" /translation="MAQAVIGAIAASAAGSILGAGIQAGAEAGLQAQRYQQDLQLQQN SFKHDKEMLGYQVQASNALLAKNLNTRYALLQAGGLSSADAARAVAGAPVTRIVDWNG TRIAAPTSSTTTLRSGGFMAVPIPLSSKTKQPVMSGQDNPNYAASSISRTASWVQSQN SMRSVSPFHSDALRTVWVTPPGSSSTSSVQSSFYGVFNTDRLPLFANRR" ORIGIN 1 ggcgtcgaaa gacgtcgttg cgactaatgt tgcaagcaat aataacgcta acaacactag 61 tgctacatct cgatttttgt cgagatttaa gggtttaggt ggtggcgcga gcccccctaa 121 ccccataaag atcaaaagca cagaaatggc cttgggtttg attggtaaga cagcccaaga 181 ggcagtaggt gccagtgacc taccgcccaa acagcaaaga gatcggcccc ccagaaccca 241 agaggaagtt cagtacggca tggggtggac tgaaaggccc gtggaccaga acgttaagtc 301 atgggaggaa cttgacacct ccaccaagga agagattttg gacagccaca aagaatggtt 361 cgacgccggc ggtttgggcc cgtgcaccat gccctcaact tgtgaacagg ccaaagatga 421 tagcccacct ggtgagcaag tcagatggtc agcgcgtgat ggagtcaacc ttggagtgaa 481 ccgtctcacg acggtgagtg gccccgagtg gaacctctgc cctctacccc ccattgacct 541 aaggaatatg gaaccagcca gtgaacccac cattggagac atgatagagt tttatgaagg 601 ccacatctac cactactcca tatacattgg gcaagggaag acagttggtg tacattcccc 661 acaggcagca ttctcagtgg ctagagtaac catccaacct atagctgctt ggtggagggt 721 ttgttatata ccccagccca aacatagact gagttatgac caacttaggg aattggaaaa 781 tgaaccctgg ccatatgcag ctatcaccaa caattgtttt gagttttgct gtcaagtcat 841 gaaccttgag gacacatggt tgcagaggcg gctaataaca tcaggtagat tccaccatcc 901 ttcccagtct tggtcacaac agacccctga atttcagcag gacagtaaac tggagctggt 961 tagggatgct atattggccg cggtgaatgg ccttgtttca caacccttca agaatttctt 1021 gggcaagctc aagcctctta atgtattaaa catcctatct aactgtgact ggacttttat 1081 gggggtggta gagatggtta tactacttct tgagctcttt ggcgtgttct ggaacccgcc 1141 cgatgtgtct aattttatag catctctcct ccctgacttc cacctccagg gaccagaaga 1201 cctggcccgg gatttggtgc cagtcattct tggtggcata ggactagcca ttggatttac 1261 cagagataaa gtcaccaagg tcatgaagag tgctgtggat ggactccggg ccgctacaca 1321 gctggggcaa tacgggttgg aaatattctc actcctcaag aagtatttct ttggtgggga 1381 tcagactgaa cgaaccctca aaggcattga aacagcagtc atagatatgg aggttttatc 1441 ctctacatca gtgacacaat tggtgagaga caagcaggca gctaaagctt acatgaacat 1501 cctggataat gaagaggaaa aagctaggaa actctctgct aagaatgctg acccccatgt 1561 aatatcctca acaaatgccc taatatcacg tatagccatg gcgcgatccg ctctggctaa 1621 ggctcaggct gagatgacca gccgaatgag gccagttgtc atcatgatgt gtggaccccc 1681 tggaattggt aagactaaag cagcggaaca cttggcaaaa cgcctagcta atgagatcag 1741 gcctggcggt aaagtgggac tggtaccacg tgaggctgtt gaccactggg atggctacca 1801 tggtgaggaa gtgatgctat gggatgatta tggtatgaca aagatacaag atgactgcaa 1861 caagctccag gctattgctg actctgcccc actcactctc aattgtgata ggattgaaaa 1921 taaagggatg cagtttgtgt cagatgcaat agtcatcacc accaacgctc cagggcctgc 1981 ccctgtggac tttgtcaacc ttggccctgt gtgtagacgg gttgacttcc tggtctactg 2041 ttccgcccca gaggtagagc agataaggag agtcagccct ggagacacgt cggcacttaa 2101 agactgcttc aagtcagatt tctcccacct gaagatggag ttagctcctc aaggggggtt 2161 tgacaaccag gggaacacac cattcggcaa gggtgtcatg aaaccaacaa ccatcaacag 2221 gctcctcata caagctgtgg ctctcaccat ggagagacag gatgagttcc gtctccaagg 2281 gaagatgtat gattttgatg atgatagggt gtcagccttt accaccatgg cacgcgataa 2341 cggattgggc atcctgagca tggcgagcct aggtaagaag ctgcgcggtg tcacatcgat 2401 ggatggtctg aagaatgctt taaaagggta taaaattggt gcgtgtacaa tcaagtggca 2461 ggccaaggtg tattcactag agtcagatgg caacagtgtt aacatcaggg aggagaagaa 2521 tgtcttgact caacaacagc agtcggtgtg cgctgcctct attgcactca cccgtctgcg 2581 ggccgcacgc gcggtggcgt atgcgtcatg cattcaatca gccataacct ccatactaca 2641 aattgctgcc tctgccctag tggtcaacag ggccgtgaaa agaatgtttg gcacacgcac 2701 tgctgctttg tctctagagg gcccccccaa agaacacaaa tgcagagtcc accaggccaa 2761 agccgcagga aaaggaccca ttggccatga tgacatggtt gataaatatg gtctatgcga 2821 gactgaggag gatgaagaag tagtccacac tgagatacca tctgccacca tggaaggtaa 2881 gaacaaagga aagaacaaga aagggcgcgg ccgaaagaac aactacaacg ccttttcccg 2941 tagggggctc aatgacgaag agtacgagga gtacaagaaa atacgggaag agaagggtgg 3001 aaattacagc attcaggagt acctagagga tagacaaagg tatgaagagg agcttgctga 3061 ggttcaagca ggtggagatg gaggaatcgg tgaaactgaa atggaaatcc gccacagagt 3121 gttctacaag tctaagagca agaagcacca ccaggaagaa cgacgccaac tgggattagt 3181 cacaggttct gacatccgga aaagaaaacc aattgattgg acccccccta agtcagcatg 3241 ggcagatgat gagcgtgaag tggactacaa tgagaggatc aactttgagg cgccccccac 3301 cttgtggagc cgggtcacaa agtttggatc tgggtggggc ttctgggtca gtcccacagt 3361 cttcataacc acaacgcacg ttataccaac cagtgcaaaa gagttctttg gtgaacccct 3421 tgccagcata gccatccata gagccggaga attcaccctc ttcaggttct ctaagaaaat 3481 caggcccgat ctcacgggta tgattcttga ggaaggttgc ccagagggta cggtgtgctc 3541 agtattaata aaaagggact ccggtgagct actaccacta gctgtaagaa tgggcgcaat 3601 agcatcaatg cgcatacagg gtcgccttgt ccatggccag tctggtatgt tgctcactgg 3661 ggcgaatgct aaaggcatgg acctcggaac tattccaggg gattgtggag ctccctatgt 3721 ctataagaga gcaaatgact gggtggtttg tggagtgcac gctgctgcca ctaaatcagg 3781 caacacggta gtgtgcgccg tccaggctag tgaaggggaa accacacttg aggggggtga 3841 caaaggtcac tacgccggac atgagataat caagcatgga tgtgggccag ccctgtcaac 3901 caaaacaaag ttctggaaat cgtcccctga accactgccc cctggagtct atgaacctgc 3961 atacctcggt ggccgggatc caagagtgag tggtggcccc tcgctccaac aggtattacg 4021 ggatcagtta aagccatttg ctgagccacg tgggcgtatg ccggaaccag gtctcctgga 4081 ggccgcagtt gagactgtga cctcatcact ggagcaggtt atggataccc cagtgccgtg 4141 gagttacagc gatgcatgtc aatccctaga taaaactact agttctggtt ttccccatca 4201 caagaagaag aatgatgatt ggaacggcac cgccttcatt agggagttgg gagagcaggc 4261 ggcgcacgcc aataatatgt acgaacaagc taagagcatg aagcccatgt acacggcggc 4321 gcttaaggat gaattagtga aaccagaaaa agtgtaccaa aaagtgaaga agcgcttgct 4381 ttggggagca gatctaggaa cagtgatccg ggccgcacgg gcctttggcc cattctgtga 4441 tgccataaaa tcccacacaa ttaaactacc tatcaaggtt ggaatgaatt caattgagga 4501 tgggccatta atttatgcag agcattcaaa atataaatat cactttgatg cagactatac 4561 ggcttgggac tcaacacaaa ataggcaaat tatgactgaa tcattctcaa tcatgtgtcg 4621 gctaactgct tctccagaat tggcctcagt ggtggcacaa gatcttcttg caccctcaga 4681 aatggacgtt ggtgactacg tcataagagt gaaggaaggc ctcccatctg gcttcccatg 4741 cacatcacag gtcaatagca taaaccattg gttgataaca ttgtgcgccc tctctgaggt 4801 gactggcctg tcaccagatg ttatccagtc catgtcatac ttttcttttt atggtgatga 4861 tgaaatagtt tccactgaca tagaatttga cccagcaaag ctgacacaag tccttaaaga 4921 gtatggcctc aaacccaccc gccccgacaa gagtgaaggt ccaataattg tgaggaagag 4981 tgtggatggc ctggtcttct tacgtcgcac catttcccgc gacgccgcgg ggttccaggg 5041 gcgactggac cgagcatcca ttgaaaggca gatctactgg accagagggc ccaatcactc 5101 agaccccttt gaaaccttgg tgccccacca gcaaagaaaa atccagctga tatcactgtt 5161 aggtgaggcc tcattgcatg gtgagaaatt ctacaggaag atctcaagca aagtcatcca 5221 agagattaag acagggggtc ttgaaatgta tgtgccaggg tggcaagcca tgttccgctg 5281 gatgcgattc cacgaccttg gcctgtggac aggagatcgc aatctcctgc ccgaattcgt 5341 aaatgatgat ggcgtctaag gacgccccaa catcccctga tggcgccagt ggcgccggcc 5401 agctggtacc ggaggctaat acagctgagc aaatttcaat ggaccctgtt gcgggtgctt 5461 caacagcagt cgcgacagct gggcaagtta atatgatcga cccatggatt ttcaataact 5521 ttgtccaggc acctcaagga gaattcacta tttcccctaa taataccccc ggtgatattt 5581 tgtttgattt acaactagga ccccatctta atccatttct agcccacctc tcacagatgt 5641 ataatggttg ggtcggcaat atgcgtgtac gcatactgtt ggccgggaat gccttcacag 5701 ctggaaagat aatcatttgc tgtgtccccc ctggttttga tgccagaata ctcacaatag 5761 ctcaagcaac tctcttccca cacttaattg ctgatgtaag gacccttgag cctgtggagc 5821 ttcctttgga ggatgtgcgc aatgttctct tccacaacag tagccaaccg cagccaacaa 5881 tgcggctggt tgctatgttg tacactcccc tccgcactgg tggtggttct ggaggcactg 5941 atgcctttgt ggtcgcgggt agggtgctta cgtgccccgc ccccgacttt agttttctgt 6001 ttctagtccc cccttccgtt gaacaaaaga ccagagtttt cagtgtcccc aatatacccc 6061 tgaaggatct ctcaaattcc cgtgtccctg tgccagtgca gggcatgttt atgtccccag 6121 atgttaatca gtcagtccag tttcagaatg gacgctgcca aattgatggc caactccaag 6181 gcaccactcc agtctcgctc agccaactct gcaagattag gggtaaaact tctagcaatg 6241 ctagggtgct caatttaagt gaggtagatg gcacaccctt catcccactt gaatcaccag 6301 cgccagttgg ttttcccgac ttgggaggtt gtgactggca tgtaaatttc acttttcagg 6361 ctcaaaatca ggacccatct caaagtgtaa cctttgcaac taatgatacc agctttgtcc 6421 cctatctagg tagtatctct cctcacaatg ggggagattt tcatgcaggt gacatcatag 6481 gtagccttgg ttggatttca gccccgtctg ataattcaca acttaatgtt tggacaatac 6541 caaagtatgg atctagtctc ccagatgtca ctcatcttgc ccctgctgtg ttccccccag 6601 gctttgggga ggtgatcttg tacttctatt ccaccttccc aggttctgga caatccagcc 6661 aacttcaagt cccatgcttg ttgcctcagg agttcatcac ccacttctgc aacgaacagg 6721 ctcccatcgc tggggaggct gccctcctcc actacgtgga ccctgacacg gggcgaaact 6781 tgggagaatt taaactttac cctgatgggt ttatgacctg tgtccccaat agtgttagta 6841 gtggccctca aacccttcct atcaatggag tctttgtctt tgtttcatgg gtatctagat 6901 tctatcaact caagcctgtg ggaacggcct cagcggctag aaggcttgga ttgcggcgta 6961 tataatggcc caagctgtca tcggtgccat agccgcatct gccgctggta gcatactagg 7021 ggcaggcata caggctggtg ctgaggctgg tctccaggct caacggtatc agcaggatct 7081 gcagttgcaa caaaattctt tcaagcatga taaggaaatg ttaggctacc aagttcaggc 7141 tagtaatgct cttttagcta agaatcttaa cactagatat gctcttctgc aggcaggggg 7201 cctatctagc gctgatgctg ctcgggcagt ggctggtgct cctgtcaccc gtatagtgga 7261 ctggaatggc acgcgcattg cagcgcccac ttcaagcacc actacactca gatctggtgg 7321 ttttatggct gtccctatac cattgtcttc aaagaccaag caaccagtga tgtctgggca 7381 ggataatcca aattatgctg cttcttctat ctctagaact gcttcatggg tgcaatctca 7441 aaattctatg aggtctgttt ctccttttca cagtgatgct ttgagaaccg tttgggttac 7501 accacccggt tcatcatcaa cctcatctgt gcaatctagt ttctatggtg tttttaatac 7561 agatagattg cctctgttcg caaacagaag gtaataa //