Typing tool
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Typing tool
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Complete norovirus genomes
| OP162338 | GI.6 | |
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| GI.P11 |
ORF1: 1..5348
ORF2: 5332..6954
ORF3: 6954..7583
LOCUS OP162338 7586 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GI isolate RIVM-NOV-2016-0303_R02-15 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP162338
VERSION OP162338.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7586)
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JOURNAL Unpublished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 7586)
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..7586
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0303_R02-15"
/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..5348
/gene="ORF1"
CDS <1..5348
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUL90917.1"
/translation="VVATNVASNNNANNTSATSRFLSRFKGLGGGASPPNPIKIKSTE
MALGLIGKTAQEAVGASDLPPKQQRDRPPRTQEEVQYGMGWTERPVDQNVKSWEELDT
STKEEILDSHKEWFDAGGLGPCTMPSTCEQAKDDSPPGEQVRWSARDGVNLGVNRLTT
VSGPEWNLCPLPPIDLRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTVGVHSPQA
AFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLRELENEPWPYAAITNNCFEFCCQVM
NLEDTWLQRRLITSGRFHHPSQSWSQQTPEFQQDSKLELVRDAILAAVNGLVSQPFKN
FLGKLKPLNVLNILSNCDWTFMGVVEMVILLLELFGVFWNPPDVSNFIASLLPDFHLQ
GPEDLARDLVPVILGGIGLAIGFTRDKVTKVMKSAVDGLRAATQLGQYGLEIFSLLKK
YFFGGDQTERTLKGIETAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEEEKARKLS
AKNADPHVISSTNALISRIAMARSALAKAQAEMTSRMRPVVIMMCGPPGIGKTKAAEH
LAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNKLQAIADS
APLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVYCSAPEVE
QIRRVSPGDTSALKDCFKSDFSHLKMELAPQGGFDNQGNTPFGKGVMKPTTINRLLIQ
AVALTMERQDEFRLQGKMYDFDDDRVSAFTTMARDNGLGILSMASLGKKLRGVTSMDG
LKNALKGYKIGACTIKWQAKVYSLESDGNSVNIREEKNVLTQQQQSVCAASIALTRLR
AARAVAYASCIQSAITSILQIAASALVVNRAVKRMFGTRTAALSLEGPPKEHKCRVHQ
AKAAGKGPIGHDDMVDKYGLCETEEDEEVVHTEIPSATMEGKNKGKNKKGRGRKNNYN
AFSRRGLNDEEYEEYKKIREEKGGNYSIQEYLEDRQRYEEELAEVQAGGDGGIGETEM
EIRHRVFYKSKSKKHHQEERRQLGLVTGSDIRKRKPIDWTPPKSAWADDEREVDYNER
INFEAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVIPTSAKEFFGEPLASIAIHRAGE
FTLFRFSKKIRPDLTGMILEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGR
LVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVYKRANDWVVCGVHAAATKSGNTVVCA
VQASEGETTLEGGDKGHYAGHEIIKHGCGPALSTKTKFWKSSPEPLPPGVYEPAYLGG
RDPRVSGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSSLEQVMDTPVPWSY
SDACQSLDKTTSSGFPHHKKKNDDWNGTAFIRELGEQAAHANNMYEQAKSMKPMYTAA
LKDELVKPEKVYQKVKKRLLWGADLGTVIRAARAFGPFCDAIKSHTIKLPIKVGMNSI
EDGPLIYAEHSKYKYHFDADYTAWDSTQNRQIMTESFSIMCRLTASPELASVVAQDLL
APSEMDVGDYVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDVIQSMSYF
SFYGDDEIVSTDIEFDPAKLTQVLKEYGLKPTRPDKSEGPIIVRKSVDGLVFLRRTIS
RDAAGFQGRLDRASIERQIYWTRGPNHSDPFETLVPHQQRKIQLISLLGEASLHGEKF
YRKISSKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVNDDGV"
mat_peptide <1..1178
/gene="ORF1"
/product="p48"
mat_peptide 1179..2267
/gene="ORF1"
/product="NTPase"
mat_peptide 2268..2864
/gene="ORF1"
/product="p22"
mat_peptide 2865..3278
/gene="ORF1"
/product="VPg"
mat_peptide 3279..3821
/gene="ORF1"
/product="Pro"
mat_peptide 3822..5345
/gene="ORF1"
/product="RdRp"
gene 5332..6954
/gene="ORF2"
CDS 5332..6954
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUL90918.1"
/translation="MMMASKDAPTSPDGASGAGQLVPEANTAEQISMDPVAGASTAVA
TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLSQMYNG
WVGNMRVRILLAGNAFTAGKIIICCVPPGFDARILTIAQATLFPHLIADVRTLEPVEL
PLEDVRNVLFHNSSQPQPTMRLVAMLYTPLRTGGGSGGTDAFVVAGRVLTCPAPDFSF
LFLVPPSVEQKTRVFSVPNIPLKDLSNSRVPVPVQGMFMSPDVNQSVQFQNGRCQIDG
QLQGTTPVSLSQLCKIRGKTSSNARVLNLSEVDGTPFIPLESPAPVGFPDLGGCDWHV
NFTFQAQNQDPSQSVTFATNDTSFVPYLGSISPHNGGDFHAGDIIGSLGWISAPSDNS
QLNVWTIPKYGSSLPDVTHLAPAVFPPGFGEVILYFYSTFPGSGQSSQLQVPCLLPQE
FITHFCNEQAPIAGEAALLHYVDPDTGRNLGEFKLYPDGFMTCVPNSVSSGPQTLPIN
GVFVFVSWVSRFYQLKPVGTASAARRLGLRRI"
gene 6954..7583
/gene="ORF3"
CDS 6954..7583
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUL90919.1"
/translation="MAQAVIGAIAASAAGSILGAGIQAGAEAGLQAQRYQQDLQLQQN
SFKHDKEMLGYQVQASNALLAKNLNTRYALLQAGGLSSADAARAVAGAPVTRIVDWNG
TRIAAPTSSTTTLRSGGFMAVPIPLSSKTKQPVMSGQDNPNYAASSISRTASWVQSQN
SMRSVSPFHSDALRTVWVTPPGSSSTSSVQSSFYGVFNTDRLPLFANRR"
ORIGIN
1 acgtcgttgc gactaatgtt gcaagcaata ataacgctaa caacactagt gctacatctc
61 gatttttgtc gagatttaag ggtttaggtg gtggcgcgag cccccctaac cccataaaga
121 tcaaaagcac agaaatggcc ttgggtttga ttggtaagac agcccaagag gcagtaggtg
181 ccagtgacct accgcccaaa cagcaaagag atcggccccc cagaacccaa gaggaagttc
241 agtacggcat ggggtggact gaaaggcccg tggaccagaa cgttaagtca tgggaggaac
301 ttgacacctc caccaaggaa gagattttgg acagccacaa agaatggttc gacgccggcg
361 gtttgggccc gtgcaccatg ccctcaactt gtgaacaggc caaagatgat agcccacctg
421 gtgagcaagt cagatggtca gcgcgtgatg gagtcaacct tggagtgaac cgtctcacga
481 cggtgagtgg ccccgagtgg aacctctgcc ctctaccccc cattgaccta aggaatatgg
541 aaccagccag tgaacccacc attggagaca tgatagagtt ttatgaaggc cacatctacc
601 actactccat atacattggg caagggaaga cagttggtgt acattcccca caggcagcat
661 tctcagtggc tagagtaacc atccaaccta tagctgcttg gtggagggtt tgttatatac
721 cccagcccaa acatagactg agttatgacc aacttaggga attggaaaat gaaccctggc
781 catatgcagc tatcaccaac aattgttttg agttttgctg tcaagtcatg aaccttgagg
841 acacatggtt gcagaggcgg ctaataacat caggtagatt ccaccatcct tcccagtctt
901 ggtcacaaca gacccctgaa tttcagcagg acagtaaact ggagctggtt agggatgcta
961 tattggccgc ggtgaatggc cttgtttcac aacccttcaa gaatttcttg ggcaagctca
1021 agcctcttaa tgtattaaac atcctatcta actgtgactg gacttttatg ggggtggtag
1081 agatggttat actacttctt gagctctttg gcgtgttctg gaacccgccc gatgtgtcta
1141 attttatagc atctctcctc cctgacttcc acctccaggg accagaagac ctggcccggg
1201 atttggtgcc agtcattctt ggtggcatag gactagccat tggatttacc agagataaag
1261 tcaccaaggt catgaagagt gctgtggatg gactccgggc cgctacacag ctggggcaat
1321 acgggttgga aatattctca ctcctcaaga agtatttctt tggtggggat cagactgaac
1381 gaaccctcaa aggcattgaa acagcagtca tagatatgga ggttttatcc tctacatcag
1441 tgacacaatt ggtgagagac aagcaggcag ctaaagctta catgaacatc ctggataatg
1501 aagaggaaaa agctaggaaa ctctctgcta agaatgctga cccccatgta atatcctcaa
1561 caaatgccct aatatcacgt atagccatgg cgcgatccgc tctggctaag gctcaggctg
1621 agatgaccag ccgaatgagg ccagttgtca tcatgatgtg tggaccccct ggaattggta
1681 agactaaagc agcggaacac ttggcaaaac gcctagctaa tgagatcagg cctggcggta
1741 aagtgggact ggtaccacgt gaggctgttg accactggga tggctaccat ggtgaggaag
1801 tgatgctatg ggatgattat ggtatgacaa agatacaaga tgactgcaac aagctccagg
1861 ctattgctga ctctgcccca ctcactctca attgtgatag gattgaaaat aaagggatgc
1921 agtttgtgtc agatgcaata gtcatcacca ccaacgctcc agggcctgcc cctgtggact
1981 ttgtcaacct tggccctgtg tgtagacggg ttgacttcct ggtctactgt tccgccccag
2041 aggtagagca gataaggaga gtcagccctg gagacacgtc ggcacttaaa gactgcttca
2101 agtcagattt ctcccacctg aagatggagt tagctcctca aggggggttt gacaaccagg
2161 ggaacacacc attcggcaag ggtgtcatga aaccaacaac catcaacagg ctcctcatac
2221 aagctgtggc tctcaccatg gagagacagg atgagttccg tctccaaggg aagatgtatg
2281 attttgatga tgatagggtg tcagccttta ccaccatggc acgcgataac ggattgggca
2341 tcctgagcat ggcgagccta ggtaagaagc tgcgcggtgt cacatcgatg gatggtctga
2401 agaatgcttt aaaagggtat aaaattggtg cgtgtacaat caagtggcag gccaaggtgt
2461 attcactaga gtcagatggc aacagtgtta acatcaggga ggagaagaat gtcttgactc
2521 aacaacagca gtcggtgtgc gctgcctcta ttgcactcac ccgtctgcgg gccgcacgcg
2581 cggtggcgta tgcgtcatgc attcaatcag ccataacctc catactacaa attgctgcct
2641 ctgccctagt ggtcaacagg gccgtgaaaa gaatgtttgg cacacgcact gctgctttgt
2701 ctctagaggg cccccccaaa gaacacaaat gcagagtcca ccaggccaaa gccgcaggaa
2761 aaggacccat tggccatgat gacatggttg ataaatatgg tctatgcgag actgaggagg
2821 atgaagaagt agtccacact gagataccat ctgccaccat ggaaggtaag aacaaaggaa
2881 agaacaagaa agggcgcggc cgaaagaaca actacaacgc cttttcccgt agggggctca
2941 atgacgaaga gtacgaggag tacaagaaaa tacgggaaga gaagggtgga aattacagca
3001 ttcaggagta cctagaggat agacaaaggt atgaagagga gcttgctgag gttcaagcag
3061 gtggagatgg aggaatcggt gaaactgaaa tggaaatccg ccacagagtg ttctacaagt
3121 ctaagagcaa gaagcaccac caggaagaac gacgccaact gggattagtc acaggttctg
3181 acatccggaa aagaaaacca attgattgga ccccccctaa gtcagcatgg gcagatgatg
3241 agcgtgaagt ggactacaat gagaggatca actttgaggc gccccccacc ttgtggagcc
3301 gggtcacaaa gtttggatct gggtggggct tctgggtcag tcccacagtc ttcataacca
3361 caacgcacgt tataccaacc agtgcaaaag agttctttgg tgaacccctt gccagcatag
3421 ccatccatag agccggagaa ttcaccctct tcaggttctc taagaaaatc aggcccgatc
3481 tcacgggtat gattcttgag gaaggttgcc cagagggtac ggtgtgctca gtattaataa
3541 aaagggactc cggtgagcta ctaccactag ctgtaagaat gggcgcaata gcatcaatgc
3601 gcatacaggg tcgccttgtc catggccagt ctggtatgtt gctcactggg gcgaatgcta
3661 aaggcatgga cctcggaact attccagggg attgtggagc tccctatgtc tataagagag
3721 caaatgactg ggtggtttgt ggagtgcacg ctgctgccac taaatcaggc aacacggtag
3781 tgtgcgccgt ccaggctagt gaaggggaaa ccacacttga ggggggtgac aaaggtcact
3841 acgccggaca tgagataatc aagcatggat gtgggccagc cctgtcaacc aaaacaaagt
3901 tctggaaatc gtcccctgaa ccactgcccc ctggagtcta tgaacctgca tacctcggtg
3961 gccgggatcc aagagtgagt ggtggcccct cgctccaaca ggtattacgg gatcagttaa
4021 agccatttgc tgagccacgt gggcgtatgc cggaaccagg tctcctggag gccgcagttg
4081 agactgtgac ctcatcactg gagcaggtta tggatacccc agtgccgtgg agttacagcg
4141 atgcatgtca atccctagat aaaactacta gttctggttt tccccatcac aagaagaaga
4201 atgatgattg gaacggcacc gccttcatta gggagttggg agagcaggcg gcgcacgcca
4261 ataatatgta cgaacaagct aagagcatga agcccatgta cacggcggcg cttaaggatg
4321 aattagtgaa accagaaaaa gtgtaccaaa aagtgaagaa gcgcttgctt tggggagcag
4381 atctaggaac agtgatccgg gccgcacggg cctttggccc attctgtgat gccataaaat
4441 cccacacaat taaactacct atcaaggttg gaatgaattc aattgaggat gggccattaa
4501 tttatgcaga gcattcaaaa tataaatatc actttgatgc agactatacg gcttgggact
4561 caacacaaaa taggcaaatt atgactgaat cattctcaat catgtgtcgg ctaactgctt
4621 ctccagaatt ggcctcagtg gtggcacaag atcttcttgc accctcagaa atggacgttg
4681 gtgactacgt cataagagtg aaggaaggcc tcccatctgg cttcccatgc acatcacagg
4741 tcaatagcat aaaccattgg ttgataacat tgtgcgccct ctctgaggtg actggcctgt
4801 caccagatgt tatccagtcc atgtcatact tttcttttta tggtgatgat gaaatagttt
4861 ccactgacat agaatttgac ccagcaaagc tgacacaagt ccttaaagag tatggcctca
4921 aacccacccg ccccgacaag agtgaaggtc caataattgt gaggaagagt gtggatggcc
4981 tggtcttctt acgtcgcacc atttcccgcg acgccgcggg gttccagggg cgactggacc
5041 gagcatccat tgaaaggcag atctactgga ccagagggcc caatcactca gacccctttg
5101 aaaccttggt gccccaccag caaagaaaaa tccagctgat atcactgtta ggtgaggcct
5161 cattgcatgg tgagaaattc tacaggaaga tctcaagcaa agtcatccaa gagattaaga
5221 cagggggtct tgaaatgtat gtgccagggt ggcaagccat gttccgctgg atgcgattcc
5281 acgaccttgg cctgtggaca ggagatcgca atctcctgcc cgaattcgta aatgatgatg
5341 gcgtctaagg acgccccaac atcccctgat ggcgccagtg gcgccggcca gctggtaccg
5401 gaggctaata cagctgagca aatttcaatg gaccctgttg cgggtgcttc aacagcagtc
5461 gcgacagctg ggcaagttaa tatgatcgac ccatggattt tcaataactt tgtccaggca
5521 cctcaaggag aattcactat ttcccctaat aatacccccg gtgatatttt gtttgattta
5581 caactaggac cccatcttaa tccatttcta gcccacctct cacagatgta taatggttgg
5641 gtcggcaata tgcgtgtacg catactgttg gccgggaatg ccttcacagc tggaaagata
5701 atcatttgct gtgtcccccc tggttttgat gccagaatac tcacaatagc tcaagcaact
5761 ctcttcccac acttaattgc tgatgtaagg acccttgagc ctgtggagct tcctttggag
5821 gatgtgcgca atgttctctt ccacaacagt agccaaccgc agccaacaat gcggctggtt
5881 gctatgttgt acactcccct ccgcactggt ggtggttctg gaggcactga tgcctttgtg
5941 gtcgcgggta gggtgcttac gtgccccgcc cccgacttta gttttctgtt tctagtcccc
6001 ccttccgttg aacaaaagac cagagttttc agtgtcccca atatacccct gaaggatctc
6061 tcaaattccc gtgtccctgt gccagtgcag ggcatgttta tgtccccaga tgttaatcag
6121 tcagtccagt ttcagaatgg acgctgccaa attgatggcc aactccaagg caccactcca
6181 gtctcgctca gccaactctg caagattagg ggtaaaactt ctagcaatgc tagggtgctc
6241 aatttaagtg aggtagatgg cacacccttc atcccacttg aatcaccagc gccagttggt
6301 tttcccgact tgggaggttg tgactggcat gtaaatttca cttttcaggc tcaaaatcag
6361 gacccatctc aaagtgtaac ctttgcaact aatgatacca gctttgtccc ctatctaggt
6421 agtatctctc ctcacaatgg gggagatttt catgcaggtg acatcatagg tagccttggt
6481 tggatttcag ccccgtctga taattcacaa cttaatgttt ggacaatacc aaagtatgga
6541 tctagtctcc cagatgtcac tcatcttgcc cctgctgtgt tccccccagg ctttggggag
6601 gtgatcttgt acttctattc caccttccca ggttctggac aatccagcca acttcaagtc
6661 ccatgcttgt tgcctcagga gttcatcacc cacttctgca acgaacaggc tcccatcgct
6721 ggggaggctg ccctcctcca ctacgtggac cctgacacgg ggcgaaactt gggagaattt
6781 aaactttacc ctgatgggtt tatgacctgt gtccccaata gtgttagtag tggccctcaa
6841 acccttccta tcaatggagt ctttgtcttt gtttcatggg tatctagatt ctatcaactc
6901 aagcctgtgg gaacggcctc agcggctaga aggcttggat tgcggcgtat ataatggccc
6961 aagctgtcat cggtgccata gccgcatctg ccgctggtag catactaggg gcaggcatac
7021 aggctggtgc tgaggctggt ctccaggctc aacggtatca gcaggatctg cagttgcaac
7081 aaaattcttt caagcatgat aaggaaatgt taggctacca agttcaggct agtaatgctc
7141 ttttagctaa gaatcttaac actagatatg ctcttctgca ggcagggggc ctatctagcg
7201 ctgatgctgc tcgggcagtg gctggtgctc ctgtcacccg tatagtggac tggaatggca
7261 cgcgcattgc agcgcccact tcaagcacca ctacactcag atctggtggt tttatggctg
7321 tccctatacc attgtcttca aagaccaagc aaccagtgat gtctgggcag gataatccaa
7381 attatgctgc ttcttctatc tctagaactg cttcatgggt gcaatctcaa aattctatga
7441 ggtctgtttc tccttttcac agtgatgctt tgagaaccgt ttgggttaca ccacccggtt
7501 catcatcaac ctcatctgtg caatctagtt tctatggtgt ttttaataca gatagattgc
7561 ctctgttcgc aaacagaagg taataa
//