Typing tool
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Typing tool
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Complete norovirus genomes
| OP205569 | GII.3 | |
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| GII.P21 |
ORF1: 1..5076
ORF2: 5057..6703
ORF3: 6703..7467
LOCUS OP205569 7467 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0521_R03-24 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205569
VERSION OP205569.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7467)
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JOURNAL Unpublished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 7467)
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..7467
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0521_R03-24"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-12-02"
/note="genotype: GII.3[P21]"
gene <1..5076
/gene="ORF1"
CDS <1..5076
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV61008.1"
/translation="SAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARPKQPPPSDK
PPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLEENSTAFSV
PPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTP
LSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLNRRMIQ
RTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALASLFTRPIKDIIGKLKPLNILN
ILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPV
VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKTEL
AMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTKSASPDIV
GTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIASTL
TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTCPLTLNCDR
IENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRDFPGQ
PDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARASGLLHERL
DEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMTELKQALK
NISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLRCARIRYYV
KCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEGLEETNNEEGCPKPKNDEE
FVVSSDDIKSEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKR
NPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTH
VIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIK
RPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYK
RGNDYVVIGVHTAAARGGNTVICATQGNEGEATLEGGDNKGTYCGAPILGPGNAPKLS
TKTKFWRSSTTPLPPGTYEPAYLGGKDPRVRGGPSLQQVMRDQLKPFTEPRGKPPKPS
VLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCWNGESFTGK
LADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDLSTMIRCAR
AFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDSTQQRAVL
AAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTR
PDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGPNHEDPFET
MIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFRWMRF
SDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..966
/gene="ORF1"
/product="p48"
mat_peptide 967..2064
/gene="ORF1"
/product="NTPase"
mat_peptide 2065..2601
/gene="ORF1"
/product="p22"
mat_peptide 2602..3000
/gene="ORF1"
/product="VPg"
mat_peptide 3001..3543
/gene="ORF1"
/product="Pro"
mat_peptide 3544..5073
/gene="ORF1"
/product="RdRp"
gene 5057..6703
/gene="ORF2"
CDS 5057..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61009.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENVVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDATTRAHEAKVDTTSGRFTPKLGSLEISTESSDFDQSQP
TRFTPVGIGVDREADFQQWTLPDYAGQLTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6703..7467
/gene="ORF3"
CDS 6703..7467
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61010.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQVPKSTPSSGSSVRSNSTQITSLSS
HSTGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 tccgctgccg ctgctgccaa aagcaacaac gacaacgcaa aatcttcaag tgacggagta
61 ttatctaata tggcagtcac ttttaaacga gccctcgggg cgcggcctaa acagccgccc
121 ccgagtgaca aaccaccaaa acccccaaga ccacccacac cagagttggt taaggcaatt
181 ccccctcccc cacccaacgg ggaggacgaa ccaatcatct cttacaacgt caaagggggt
241 gtttctggtt tgcctgagct ctcaactgtc acccaactag aagagaactc cacagcattc
301 agcgttcccc ccctcagtca gagggagaac agagatgcaa aggaaccatt gactggaacc
361 atcctggaga tgtgggacgg ggaaatctac cactatggct tatacgtaga acgagggctg
421 gtgctcggtg tacacaaacc accagcagcc atcagccttg ctaaggttga gctgacccct
481 ttgtctttgt attggagacc agtgtacacc ccacagtacc tcatctcccc tgacactctc
541 agaaagttgc atggggagac gttcccttat acagcctttg ataacaactg ttatgccttc
601 tgctgttggg tgcttgactt gaacgattca tggctgaaca gaaggatgat acaaaggaca
661 acaggcttct tccgacccta ccaggattgg aacaggaaac ccctccccac gatggatgac
721 tccaaagtga aaaaggtggc caatgttgtt ctatgtgctc tcgcatcatt attcacaaga
781 ccaattaagg acattatagg gaagttaaaa cccctaaaca ttctcaacat cttagccaca
841 tgtgattgga cttttgcagg tatagtagaa tccctgatcc ttttggctga actttttgga
901 gttttctgga cacccccaga tgtgtctgcg atgatcgctc ccttactggg tgattatgaa
961 ctacagggac ccgaggacct cgctgtggaa ctcgtacccg tagtaatggg agggataggt
1021 ttggtgctgg gattcaccaa agagaaaatc ggcaaaatgc tttcttctgc tgcttcaacc
1081 ctgagggcat gtaaagatct cggtgcatac gggttggaga tcctcaaatt ggttatgaaa
1141 tggtttttcc caaagaaaga agagaaaacc gaattggcaa tggtgagatc catcgaggac
1201 gcagtgttag atcttgaagc cattgagaac aaccatatga cagctctact caaggataaa
1261 gacagccttg caacctacat gaggactctt gacatggagg aggagaaggc gagaaaactt
1321 tccaccaagt ctgcctctcc ggatattgtg ggcacgataa atgccctact gtcaaggatt
1381 gcagctgccc ggtctctagt gcacagggct aaggaggagc tgtcaagcag gccccgaccg
1441 gtcgttgtga tgatttcagg gaaaccgggt ataggaaaaa cccacctagc tagagagttg
1501 gcaaagaaga tcgcctccac actcacgggt gaccagaggg tgggtcttat cccacgtaac
1561 ggggtcgacc actgggatgc atacaaaggt gaaagagtcg ttctctggga cgactacggg
1621 atgagcagcc ctgtccacga cgccctcaga ctccaggagc tcgccgatac ctgtcctctc
1681 acactcaact gtgacaggat tgagaacaaa ggtaaagtct ttgacagtga cgtcataata
1741 ataaccacca atctagccaa cccagcacca ctggattatg tcaactttga agcttgctcg
1801 agacgcatag acttcctcgt ctatgctgat gctcctgaag ttgagaaggc taagcgggac
1861 ttcccaggcc aaccagacat gtggaaagac accttcaaac ccgacttctc acatataaaa
1921 ttggcattgg ccccgcaagg aggttttgac aagaatggta acactcctca tggaaaagga
1981 gtcatgaaga ccctcactgc cagttccctc gttgcccgag catcagggct cctccacgag
2041 agattagacg agtatgagct gcagggccca actcccacaa cattcaactt tgaccgcaac
2101 aaggtgcttg cttttaggca gcttgctgct gaaaacaagt acggtcttgt tgacacaatg
2161 agggtcgggt cacaactcaa gaatgtcaaa actatgacag aactcaagca ggccctcaag
2221 aacatctcag tcaagaaatg tcagctcgtg tacggtgggg gcacatacac acttgaatct
2281 gatggcaaag gcaatgtgca tgtcgaaaag gtgaacaaca ccagtgtgca aactaacaac
2341 gagctctccg gggttttgca ccatctcagg tgtgctagaa tcaggtacta tgttaagtgt
2401 gttcaggaag ctctctactc catcttacaa attgctgggg ctgcattcat aaccacgcgc
2461 attgcaaagc gcacaaacat acaaaacctc tggtctaaac cacaagcaga aggtctagag
2521 gagactaaca acgaggaggg ttgtccaaaa cctaaaaatg atgaagaatt tgtcgtctcc
2581 tctgatgaca tcaaatctga gggtaagaaa ggaaagaaca agactggccg tggtaagaag
2641 cacacagcct tttccagcaa aggactcagt gatgaggagt acgacgagta taagagaatc
2701 agggaagaga gaaatggcaa gtattccata gaggaatacc tacaggacag agacaaatac
2761 tatgaggagg tggccatagc tagggcaact gaggaagatt tctgtgaaga agaggaggcc
2821 aagatccggc agaggatatt cagaccaaca aggaaacaac gcaaagagga aagagcttct
2881 cttggtttgg ttacaggctc tgagatcagg aagagaaacc cagatgactt caagcccaaa
2941 gggaaactat gggctgatga tgacaggagt gttgactaca atgagaaact tagttttgag
3001 gctccaccaa gtatttggtc acgaatagtc aactttggct cagggtgggg cttttgggtc
3061 tcgcccagcc tcttcataac atcaacccat gtcattcccc aaggcgcgca ggagttcttt
3121 ggagtgccca ttaaacaaat acaaattcac aagtcaggtg agttctgccg gcttaggttc
3181 ccgaaaccaa tcaggacaga tgttacaggc atgatcttgg aggaaggtgc tccagaaggc
3241 actgttgcca cacttctcat caagagacca actggggaac tcatgccctt ggcagccagg
3301 atgggcaccc acgctaccat gaaaattcag ggtcgcactg ttggtggaca gatgggcatg
3361 ttactcacag ggtctaacgc taagagcatg gacttgggca caactcctgg cgattgtggt
3421 tgtccctata tctacaagag agggaacgac tacgtggtca ttggggttca cactgccgcc
3481 gctcgtggag gaaacaccgt catctgtgca acccaaggaa acgagggtga ggccacgcta
3541 gaaggtggtg acaacaaggg aacttattgt ggggcaccaa tattaggccc tggaaatgcc
3601 cccaaactca gcaccaaaac caaattttgg aggtcctcca ccacccccct gccacccgga
3661 acctatgagc cagcttatct gggtggcaag gaccctagag taagaggtgg tccctcactg
3721 caacaggtta tgagagacca actaaaacca ttcactgagc ccagaggcaa accacccaaa
3781 ccaagtgtgc tagaagctgc caagaagact ataatcaatg tgcttgaaca aacaatagac
3841 ccacctcaaa aatggacata cgcacaagcg tgtgcatcac tagacaagac cacttccagc
3901 ggtcatcctc accacatgcg gaagaacgat tgctggaatg gggaatcttt cacaggaaaa
3961 ctggcagacc aagcatcaaa ggccaaccta atgtttgagg aaggaaagaa catgactcca
4021 gtgtacacag gagctctgaa agatgaacta gtcaagactg acaagatcta tggggtggtc
4081 aagaagaggc tcctgtgggg ttcagattta tcaaccatga tacggtgtgc acgagccttc
4141 ggtgggctaa tggacgagct caaggcccat tgcgtcacac taccagtcag ggttggtatg
4201 aacatgaatg aggatggacc cataatattt gagagacact ccagatacaa ataccattat
4261 gatgcagatt actcccgctg ggactcaaca caacaaagag cagtgctagc cgcagccctg
4321 gaaataatgg tcaaattctc accagaaccc cacctggccc aggtggttgc agaagacctt
4381 ttgtccccca gtgtgatgga tgtgggtgat ttcaggatat caatcaacga gggattaccc
4441 tctggtgttc cttgcacttc acaatggaac tccattgctc actggctcct cacactatgt
4501 gcactgtctg aagtcacaga cctgtctcct gacatcatcc aggcgaattc cctgttttcc
4561 ttttatggtg atgatgaaat agtgagcaca gacatcaaat tagacccaga gaaactgaca
4621 gcaaagctga gggaatacgg gcttaaacca actcgccctg acaaaacaga gggaccctta
4681 attatttctg aagatttgaa tggcctaacc ttcttgcgga gaacagtgac ccgcgacccg
4741 gccggatggt ttggcaaact ggaccaaagt tcaatactca ggcagatgta ctggaccaag
4801 gggccaaacc atgaagaccc ctttgaaaca atgataccac actcccaaag acccatacaa
4861 ctgatgtcat tacttggtga agctgcattg catggtccat cattctacag taaaatcagc
4921 aaattggtca tctcagaact gaaagagggt ggaatggatt tttacgtgcc cagacaagaa
4981 ccaatgttca ggtggatgag attctcagat ttgagcacgt gggagggcga tcgcaatctg
5041 gctcccagtt ttgtgaatga agatggcgtc gaatgacgcc gctccatcta atgatggtgc
5101 cgccggcctc gtcccagaga tcaataatga ggcaatggcg ctagagccag tggcgggtgc
5161 agcgatagcg gcacccctca ctggtcagca aaatataatt gatccctgga ttatgaataa
5221 ttttgtgcaa gctcctggtg gtgagtttac agtgtcccct agaaattccc ctggtgaagt
5281 ccttcttaat ttggaattgg gcccagaaat aaatccttac ttggcccatc ttgctagaat
5341 gtataatggt tatgcaggtg gatttgaagt gcaggtggtc ctagctggaa atgcgtttac
5401 agcaggaaag ataatctttg cagctattcc ccctaacttt ccagttgata atttaagtgc
5461 agcacagatt acaatgtgcc cacatgtgat tgtggatgtc agacagttgg aaccagttaa
5521 cctcccgatg cctgacgttc gcaataactt ctttcactat aatcaagggt ctgattcgag
5581 gttacgccta attgcaatgc tatatacacc tcttagagca aacaattctg gggatgatgt
5641 ttttactgtg tcttgtagag tgctaactag acctagtcct gatttctcat tcaattttct
5701 tgtgccaccc actgtggagt caaagacaaa acccttctcc ctccctatcc tgactatctc
5761 tgaaatgtct aattctaggt tcccagtgcc aattgattct ctgcatacca gtcctactga
5821 gaatgttgtt gttcagtgcc aaaatgggcg cgtcaccctt gatggtgagt tgatgggtac
5881 cacccaactc ttgcctagcc aaatctgtgc tttcaggggc gttctcacca gatcaacaag
5941 cagggccagt gaccaggccg atacagcaac tcctagattg tttaattatt attggcatat
6001 acaattggat aatctaaatg gaacccctta tgatcctgca gaagacatac caggcccctt
6061 ggggacacca gatttccgtg gcaaagtctt tggcgtggcc agccagagaa atcctgatgc
6121 cacgactagg gcacatgagg ctaaggtaga caccacatct ggccgcttca ccccaaagtt
6181 aggctcatta gagatatcca ctgaatctag tgactttgac caaagccaac caacaagatt
6241 caccccagtt ggcattgggg ttgaccgtga ggcagacttt caacaatgga ccctacccga
6301 ttacgctggt cagctcacac acaacatgaa cttagcccca gctgttgctc ccaacttccc
6361 tggtgagcag ctccttttct tccgctcaca tttgccatct tctggtgggc gatccaacgg
6421 gattctagac tgcctggtcc cccaagaatg ggtacagcac ttctaccaag agtcagcccc
6481 ctctcagtct caagtggccc tggttaggta tgttaatcct gacactggta gagtgttatt
6541 tgaggccaag ctacataaat taggtttcat gactatagct aagaatggtg attctccaat
6601 aactgttcct ccaaatggat actttaggtt tgaatcttgg gtgaacccct tttatacact
6661 tgcccccatg ggaactggga atgggcgtag aaggattcaa taatggccgg agcttttata
6721 gcaggattgg ctggtgacat gctcacaaat actgtaggat ctttagttaa tgcaggggct
6781 aatgctatta atcaaacaat tgattttgaa aataataaat atttgcaaaa tgcttctttt
6841 aatcatgata aggagatgtt gaatgcacaa attgaggcaa caaagaggtt acaggctgac
6901 atgattgcta tcaagcaagg ggtcttgacc gctggcggct tctcccctac cgatgcagcc
6961 cgtggggcaa ttaatgcccc catgacaaaa gtcctagatt ggaatggaac gagatactgg
7021 gcaccaggtg ccacctccac aacctcgatg tcgggtggct ttacacatca aactgtgcac
7081 agatccacac caaattttaa aacgaaccag gttcccaaat ccacacccag cagtgggtct
7141 tcagtgaggt caaactcaac ccaaatcact agcctgagct cacactcgac cgggtcgtct
7201 cggtccagcg ggtctacagt tatcagctca ataccatcct ctaacaggac tagagactgg
7261 gtcaaccaac aaaatttcaa tttggaacca cacatgcctg gatctcttag gacagctttt
7321 gtcactccac catctagtac agcctctagc tcaggcacag tctcgactgt gcccaaaaat
7381 gttttggact cctggacatc tgcgtttaac acgcgcagac agccgctatt cgcacacctt
7441 cgtagaaggg gggagtcaaa tgtttag
//