Typing tool
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Typing tool
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Complete norovirus genomes
| OP205576 | GII.3 | |
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| GII.P21 |
ORF1: 1..5081
ORF2: 5062..6708
ORF3: 6708..7466
LOCUS OP205576 7466 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0416_R04-07 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205576
VERSION OP205576.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7466)
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JOURNAL Unpublished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 7466)
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..7466
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0416_R04-07"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2017-12-04"
/note="genotype: GII.3[P21]"
gene <1..5081
/gene="ORF1"
CDS <1..5081
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61029.1"
/translation="ASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARSKQPPPRD
KPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKEGVSGLPELSTVTQLEESSTAFS
VPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELT
PLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMI
QRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGKLKPLNIL
NILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVP
VVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKNE
LAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTKSASPDI
VGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIASS
LTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCD
RIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRDFPG
QPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARASGLLHER
LDEYELQGPAPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMTELKQAL
KNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLRCARIRYY
VKCVQEALYSILQIAGAAFITTRIAKRMNIQNLWSKPQAEDLEETNNEEGCPKPKDEE
EFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEY
LQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRK
RNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITST
HVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLI
KRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIY
KRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILGPGNAPKL
STKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKP
SVLEAAKKTIINVLEQTIDPPQRWTYAQACASLDKTTSSGHPHHMRKNDCWNGETFTG
KLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDLSTMIRCA
RAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAV
LAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWNSIA
HWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPT
RPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQIYWTRGPNHEDPFE
TMIPHSQRPIQLMSLLGEAALHGPSFYSRISKLVISELKEGGMDFYVPRQEPMFRWMR
FSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..971
/gene="ORF1"
/product="p48"
mat_peptide 972..2069
/gene="ORF1"
/product="NTPase"
mat_peptide 2070..2606
/gene="ORF1"
/product="p22"
mat_peptide 2607..3005
/gene="ORF1"
/product="VPg"
mat_peptide 3006..3548
/gene="ORF1"
/product="Pro"
mat_peptide 3549..5078
/gene="ORF1"
/product="RdRp"
gene 5062..6708
/gene="ORF2"
CDS 5062..6708
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61030.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKIKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLIRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESDDFDQNKP
TRFTPVGIGVDHEADFQQWTLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYINPDTGRVLFEAKLHKLGFITIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6708..7466
/gene="ORF3"
CDS 6708..7466
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61031.1"
/translation="MAGAFIAGLAGDMFTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPADAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTNQTVHRSTPNFKTNQAPKPTPSSGSSVRSNSTQITSLSS
HSSESSRSSGSIRSIPSSNRTRDWVIQQNFNLEPHMPGSLRTAFVTPPSSTASSSGTV
STVPKNVLDSWSSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 acgcttccgc tgccgctgct gcaaacagca acaacgacaa cgcaaaatct tcaagtgacg
61 gagtattatc taatatggct gtcactttta aacgagccct cggggcgcgg tctaaacagc
121 cgcccccgag ggacaaacca ccaaaacccc caagaccacc cacaccagaa ttggttaaag
181 caatcccccc tcccccaccc aacggggagg acgagccaat catttcttac aacgtcaaag
241 agggtgtttc tggtttacct gaactctcaa ctgttaccca actggaagag agctctacag
301 cattcagcgt cccccctctt agtcagaggg agaacagaga tgcaaaggaa ccattgactg
361 gaactatcct ggagatgtgg gacggggaga tttaccatta tggcttatac gtggaacgag
421 ggttggtact aggtgtacac aaaccaccag cagccatcag ccttgccaag gttgagttga
481 cccccttgtc tttgtattgg aggccagtgt acaccccaca gtacctcatt tcccccgaca
541 ctctcagaaa gttgcatggg gagacgttcc cttatacagc ctttgacaac aactgctatg
601 ccttctgctg ttgggtgctt gacttgaacg attcatggct gagcagaagg atgatacaga
661 ggacaacagg cttcttccga ccctaccagg actggaacag gaaacccctc cccacgatgg
721 atgactccaa agtgaaaaag gtggccaatg ttgttctctg tgctctctca tcattgttta
781 caagaccaat taaggacatt attgggaagt tgaaacccct aaacatcctc aacatcctag
841 ccacatgtga ttggactttt gcaggtatag tagaatccct gatccttttg gctgaactgt
901 ttggagtttt ctggacaccc ccagatgtgt ctgcaatgat cgctccctta ctgggtgatt
961 atgagctgca gggacccgag gaccttgctg tggaactcgt acccgtagta atgggaggga
1021 taggtttggt gctgggattc accaaagaga aaatcggaaa aatgctttca tctgctgctt
1081 caaccctgag ggcatgcaaa gatctcggtg catatgggtt ggagatcctc aaattggtca
1141 tgaaatggtt tttcccaaag aaagaagaga aaaatgaatt ggcaatggtg agatccatcg
1201 aggatgcagt gctagatctt gaggccattg agaacaacca tatgacagct ctactcaagg
1261 ataaagacag cctcgcaacc tacatgagga ctcttgacat ggaggaggag aaggcgagga
1321 aactttccac caagtctgcc tcaccggata ttgtgggcac gataaacgcc ctactgtcaa
1381 ggattgcagc tgcccgttct ctagtgcaca gggctaagga ggagctgtca agcaggcccc
1441 gaccggtcgt tgtgatgatt tcagggagac caggtatagg gaaaacccat ctagctaggg
1501 agttggcaaa gaagatcgcc tcctcactca caggtgacca gagggtgggt cttatcccac
1561 gcaacggggt cgatcactgg gatgcataca aaggtgaaag agtcgttctc tgggacgact
1621 acgggatgag caaccctatc cacgacgccc tcaggctcca ggaactcgcc gacacctgtc
1681 ctctcacact caactgtgac aggattgaga acaaaggcaa agtcttcgac agtgacgcca
1741 taataataac caccaatttg gccaacccag cgccactgga ctacgtcaac tttgaagcct
1801 gctcaagacg catagacttc ctcgtctatg ctgatgcccc tgaagttgaa aaggctaaac
1861 gggacttccc aggccagcca gacatgtgga aagacacctt taaacctgac ttctcacaca
1921 taaaactgac attggccccg caaggaggtt ttgacaagaa tggtaacact cctcatggga
1981 agggcgtcat gaagaccctc actgccagtt ccctcgttgc ccgagcatca ggactcctcc
2041 acgagagact agacgagtat gagctgcagg gaccagctcc cacaacattc aactttgacc
2101 gcaacaaggt gcttgctttt aggcaacttg ctgctgaaaa caagtacggt cttgtcgaca
2161 caatgagggt cgggtcacag ctcaagaatg tcaaaaccat gacagaactc aagcaagccc
2221 tcaaaaacat ctcagtaaaa aaatgtcagc ttgtgtatgg tgggggcacg tacacacttg
2281 aatctgatgg caaaggtaat gtgcatgtcg agaaggtgaa caacaccagt gtgcaaacta
2341 acaacgagct ctccggggct ttacaccatc tcaggtgtgc cagaatcagg tactatgtta
2401 agtgtgtcca ggaagctctc tactccatct tgcaaattgc cggggccgca ttcatcacca
2461 cgcgcattgc aaagcgcatg aacatacaaa acctttggtc caaaccacaa gcagaagacc
2521 tggaggagac taacaacgag gagggttgtc caaaacctaa agatgaagag gagtttgtta
2581 tctcctctga tgacatcaaa actgagggca agaaaggaaa gaacaagact ggccgtggca
2641 agaagcacac agccttttcc agcaaaggac tcagtgatga ggagtacgat gagtataaga
2701 gaatcaggga agagagaaat ggcaagtact ccatagagga atacctacag gacagagaca
2761 aatactatga ggaggtggcc atagccaggg caactgagga agacttctgt gaagaagagg
2821 aggcaaaaat ccggcaaagg atatttaggc caacaaggaa acaacgcaaa gaggaaagag
2881 cctctcttgg tttggttaca ggttctgaga ttaggaagag aaacccagat gacttcaagc
2941 ccaaaggaaa attatgggcc gatgatgaca ggagtgttga ctacaatgag aaacttagtt
3001 tcgaggctcc accaagcatt tggtcacgaa tagtcaactt tggctcgggg tggggctttt
3061 gggtctcgcc cagcctcttc ataacatcaa cccatgtcat tccccaaggc gcacaggagt
3121 tctttggagt gcccatcaaa cagatacaaa ttcacaagtc gggtgagttc tgccggctta
3181 gattcccaaa accaatcagg acagatgtca caggcatgat cttggaagaa ggtgctccag
3241 aaggcactgt tgctacactt ctcatcaaga gaccaactgg ggaactcatg cccttggcag
3301 ccagaatggg cacccacgcg accatgaaaa ttcagggtcg cactgttggt ggacagatgg
3361 gcatgctact cacagggtct aacgctaaga gcatggactt gggtacaacc cctggcgatt
3421 gtggttgtcc ctacatctac aagagaggga acgactacgt agtcattggg gttcacactg
3481 ccgccgctcg tggaggaaac accgtcatct gtgcaaccca aggaaacgag ggtgaggcca
3541 tgctagaagg tggtgacaac aagggaactt attgtggggc accaatatta ggccctggaa
3601 atgcccccaa actcagcacc aaaaccaaat tctggaggtc ctccaccacc cccctgccac
3661 ccggaactta tgagccagct tatctgggtg gcaaggaccc tagagtgaaa ggtggcccct
3721 cactgcaaca ggttatgaga gaccaactaa aaccattcac tgagcctaga ggcaagccac
3781 ctaaaccaag tgtgctagaa gccgccaaga agactataat caatgtgctt gaacaaacaa
3841 tagacccacc tcaaagatgg acatacgcac aggcgtgtgc atcactagat aagaccactt
3901 ccagcggcca ccctcaccac atgcggaaga acgattgctg gaatggggag actttcacag
3961 gaaaactggc agaccaagca tcaaaggcta acctaatgtt tgaggaagga aagaacatga
4021 ccccagtgta cacaggagct ctgaaagatg agctagtcaa gactgataag atctatggga
4081 caattaagaa gagactccta tggggttcag acctatcaac catgatacgg tgtgcacgag
4141 ccttcggtgg gctaatggac gaactcaagg cccattgtgt cacactacca gtcagggttg
4201 gtatgaacat gaatgaggat ggacccataa tatttgagaa acattccaga tacaaatacc
4261 attatgatgc agattactcc cgctgggact caacacaaca aagagcagtt ctagctgcag
4321 ccctggaaat aatggtcaaa ttctcaccag aaccccatct ggcccaagtg gttgcagagg
4381 acctcttgtc ccccagtgtg atggatgtgg gtgatttcaa gatatcaatt aacgagggat
4441 taccctctgg tgttccctgc acctcacaat ggaactccat tgcccactgg ctcctcacac
4501 tatgtgcact gtctgaagtc acagacctgt cccctgacat catccaggca aattccctgt
4561 tctcctttta tggtgatgat gaaatagtga gcacagacat taaactggac ccagagaaat
4621 taacagcaaa attgaaggag tacgggctaa aaccaacccg ccctgacaaa acggaaggac
4681 ccttaattat ctctgaagat ttggatggcc tgaccttctt acggagaacg gtgacccgtg
4741 acccggccgg gtggtttggc aaactggacc aaagttcaat actcaggcag atatactgga
4801 ccaggggacc aaaccatgag gaccccttcg aaacaatgat accacactcc caaagaccca
4861 tacaactgat gtcattactg ggtgaagctg cgttgcatgg tccatcattt tacagtagaa
4921 tcagcaaact agttatttca gaattgaaag agggtggaat ggatttttac gtgcccagac
4981 aagaaccaat gtttaggtgg atgagattct cagatttgag cacgtgggag ggcgatcgca
5041 atctggctcc cagttttgtg aatgaagatg gcgtcgaatg acgccgctcc atctaatgat
5101 ggtgccgccg gcctcgtccc agagatcaac aatgaggcaa tggcgctaga gcctgtggcg
5161 ggtgcagcga tagcggctcc cctcaccggt cagcaaaata taattgatcc ctggattatg
5221 aataattttg tacaagcacc tggtggtgag tttacagtat cccctagaaa ttcccctggt
5281 gaagttcttc ttaatttgga attgggtcca gaaataaatc cctatttggc ccatcttgct
5341 agaatgtata atggttatgc aggtggattt gaagtgcagg tggtcctagc tggaaatgcg
5401 tttacagcag gaaagataat ctttgcagct attcccccca attttccaat tgacaatcta
5461 agtgcagcac agatcacaat gtgtccacat gtgatcgtgg acgtcagaca gctggaacca
5521 gtcaacctcc cgatgcctga cgttcgcaat aacttctttc attacaatca agggtctgat
5581 tcgagattgc gcctaattgc aatgctatat acacctctta gggcaaataa ttctggggat
5641 gatgttttta ctgtgtcttg cagagtgtta actagaccta gtcctgattt ctcattcaat
5701 tttcttgtgc cacctactgt ggagtcaaag ataaaaccct tttccctccc tattctgact
5761 atctctgaaa tgtccaactc gaggttccca gtaccaattg attctctgca caccagtcct
5821 actgagaata ttgttgtcca gtgtcagaat gggcgcgtca cccttgatgg tgagttgatg
5881 ggcactaccc aactcttacc tagtcaaatc tgtgctttca ggggcgtgct catcagatca
5941 acaagtaggg ccagtgatca ggccgacaca gcaaccccta gattgtttaa ttattattgg
6001 catatacaat tggataatct aaatggaact ccttatgacc ctgcagagga tataccaggc
6061 cccttgggga caccagattt taggggcaaa gtctttggcg tagccagcca gagaaatcct
6121 gatgctacaa ctagggcaca tgaagcaaag atagacacaa catctggccg tttcacccca
6181 aagttgggct cattagagat ttccactgaa tctgatgatt ttgaccaaaa caaaccaaca
6241 agattcaccc cagttggcat tggggtcgac catgaagcag attttcaaca atggaccctc
6301 cccgactact ctggccagtt cacccacaac atgaacttgg ctccagctgt tgcccccaac
6361 ttccctggtg agcaactcct tttcttccgc tcacagttgc catcttctgg tgggcgatcc
6421 aatgggattc tagactgcct agtcccccaa gaatgggtac agcacttcta ccaagaatca
6481 gccccctccc aatctcaagt ggccctggtt aggtatatca accctgacac tggtagagtg
6541 ttatttgagg ccaagctgca caaattgggt ttcataacta tagccaagaa tggtgactct
6601 ccaataactg tccctccaaa tggatacttt agatttgaat cttgggtgaa ccccttttac
6661 acacttgccc ccatgggaac agggaatggg cgtagaagga ttcaataatg gctggggctt
6721 ttatagcagg attggctggt gacatgttca caaacactgt gggatcttta gttaatgcag
6781 gggctaatgc cattaatcaa acaatagatt ttgaaaataa taaatatttg caaaatgctt
6841 cttttaatca tgataaggaa atgttgaatg cacaaattga ggcaacaaag aggttacagg
6901 ctgacatgat tgccatcaaa caaggggttt tgaccgctgg cggcttctcc cctgctgatg
6961 cagcccgcgg ggcaattaac gcccccatga caaaagtcct agattggaat ggaacgagat
7021 actgggcacc aggtgccacc tccacaacct cgatgtcggg tggcttcaca aaccaaactg
7081 tgcacaggtc cacaccaaat tttaaaacga atcaggctcc caaacccaca cccagcagtg
7141 ggtcttcagt gaggtcaaat tcaacccaaa tcactagcct gagctcgcac tcgtccgagt
7201 cgtctcgatc cagcgggtct atcagatcaa taccatcttc taacaggact agggactggg
7261 tcattcaaca aaattttaat ttggaaccac atatgcctgg atctcttagg acagcttttg
7321 tcactccacc atctagcaca gcctctagct caggcacagt ctcaaccgtg cctaaaaatg
7381 ttttggactc ctggtcatct gcgtttaata cgcgcagaca gccgctattc gcacaccttc
7441 gcagaagggg ggagtcaaat gtttag
//