Typing tool
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Typing tool
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Complete norovirus genomes
| OP205585 | GII.3 | |
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| GII.P21 |
ORF1: 1..5099
ORF2: 5080..6726
ORF3: 6726..7490
LOCUS OP205585 7490 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0522_R04-22 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205585
VERSION OP205585.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7490)
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JOURNAL Unpublished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 7490)
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..7490
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0522_R04-22"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-12-05"
/note="genotype: GII.3[P21]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61056.1"
/translation="KMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARPK
QPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLEE
NSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISL
AKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDSW
LNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGKL
KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEKTELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTK
SASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELA
KKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTCP
LTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKA
KRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARAS
GLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMT
ELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLRC
ARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEGLEETNNEEGCP
KPKNDEEFVVSSDDIKSEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT
GSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPS
LFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGT
VATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEATLEGGDNKGTYCGAPILGP
GNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVRGGPSLQQVMRDQLKPFTEPR
GKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCWN
GESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDLS
TMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLRE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGPN
HEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..989
/gene="ORF1"
/product="p48"
mat_peptide 990..2087
/gene="ORF1"
/product="NTPase"
mat_peptide 2088..2624
/gene="ORF1"
/product="p22"
mat_peptide 2625..3023
/gene="ORF1"
/product="VPg"
mat_peptide 3024..3566
/gene="ORF1"
/product="Pro"
mat_peptide 3567..5096
/gene="ORF1"
/product="RdRp"
gene 5080..6726
/gene="ORF2"
CDS 5080..6726
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61057.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENVVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDATTRAHEAKVDTTSGRFTPKLGSLEISTESSDFDQSQP
TRFTPVGIGVDREADFQQWTLPDYAGQLTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6726..7490
/gene="ORF3"
CDS 6726..7490
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61058.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQVPKSTPSSGSSVRSNSTQITSLSS
HSTGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 tgaagatggc gtctaacgac gcttccgctg ccgctgctgc caaaagcaac aacgacaacg
61 caaaatcttc aagtgacgga gtattatcta atatggcagt cacttttaaa cgagccctcg
121 gggcgcggcc taaacagccg cccccgagtg acaaaccacc aaaaccccca agaccaccca
181 caccagagtt ggttaaggca attccccctc ccccacccaa cggggaggac gaaccaatca
241 tctcttacaa cgtcaaaggg ggtgtttctg gtttgcctga gctctcaact gtcacccaac
301 tagaagagaa ctccacagca ttcagcgttc cccccctcag tcagagggag aacagagatg
361 caaaggaacc attgactgga accatcctgg agatgtggga cggggaaatc taccactatg
421 gcttatacgt agaacgaggg ctggtgctcg gtgtacacaa accaccagca gccatcagcc
481 ttgctaaggt tgagctgacc cctttgtctt tgtattggag accagtgtac accccacagt
541 acctcatctc ccctgacact ctcagaaagt tgcatgggga gacgttccct tatacagcct
601 ttgataacaa ctgttatgcc ttctgctgtt gggtgcttga cttgaacgat tcatggctga
661 acagaaggat gatacaaagg acaacaggct tcttccgacc ctaccaggat tggaacagga
721 aacccctccc cacgatggat gactccaaag tgaaaaaggt ggccaatgtt gttctatgtg
781 ctctctcatc attattcaca agaccaatta aggacattat agggaagtta aaacccctaa
841 acattctcaa catcttagcc acatgtgatt ggacttttgc aggtatagta gaatccctga
901 tccttttggc tgaacttttt ggagttttct ggacaccccc agatgtgtct gcgatgatcg
961 ctcccttact gggtgattat gaactacagg gacccgagga cctcgctgtg gaactcgtac
1021 ccgtagtaat gggagggata ggtttggtgc tgggattcac caaagagaaa atcggcaaaa
1081 tgctttcttc tgctgcttca accctgaggg catgtaaaga tctcggtgca tacgggttgg
1141 agatcctcaa attggttatg aaatggtttt tcccaaagaa agaagagaaa accgaattgg
1201 caatggtgag atccatcgag gacgcagtgt tagatcttga agccattgag aacaaccata
1261 tgacagctct actcaaggat aaagacagcc ttgcaaccta catgaggact cttgacatgg
1321 aggaggagaa ggcgagaaaa ctttccacca agtctgcctc tccggatatt gtgggcacga
1381 taaatgccct actgtcaagg attgcagctg cccggtctct agtgcacagg gctaaggagg
1441 agctgtcaag caggccccga ccggtcgttg tgatgatttc agggaaaccg ggtataggaa
1501 aaacccacct agctagagag ttggcaaaga agatcgcctc cacactcacg ggtgaccaga
1561 gggtgggtct tatcccacgt aacggggtcg accactggga tgcatacaaa ggtgaaagag
1621 tcgttctctg ggacgactac gggatgagca gccctgtcca cgacgccctc agactccagg
1681 agctcgccga tacctgtcct ctcacactca actgtgacag gattgagaac aaaggtaaag
1741 tctttgacag tgacgtcata ataataacca ccaatctagc caacccagca ccactggatt
1801 atgtcaactt tgaagcttgc tcgagacgca tagacttcct cgtctatgct gatgctcctg
1861 aagttgagaa ggctaagcgg gacttcccag gccaaccaga catgtggaaa gacaccttca
1921 aacccgactt ctcacatata aaattggcat tggccccgca aggaggtttt gacaagaatg
1981 gtaacactcc tcatggaaaa ggagtcatga agaccctcac tgccagttcc ctcgttgccc
2041 gagcatcagg gctcctccac gagagattag acgagtatga gctgcagggc ccaactccca
2101 caacattcaa ctttgaccgc aacaaggtgc ttgcttttag gcagcttgct gctgaaaaca
2161 agtacggtct tgttgacaca atgagggtcg ggtcacaact caagaatgtc aaaactatga
2221 cagaactcaa gcaggccctc aagaacatct cagtcaagaa atgtcagctc gtgtacggtg
2281 ggggcacata cacacttgaa tctgatggca aaggcaatgt gcatgtcgaa aaggtgaaca
2341 acaccagtgt gcaaactaac aacgagctct ccggggtttt gcaccatctc aggtgtgcta
2401 gaatcaggta ctatgttaag tgtgttcagg aagctctcta ctccatctta caaattgctg
2461 gggctgcatt cataaccacg cgcattgcaa agcgcacaaa catacaaaac ctctggtcta
2521 aaccacaagc agaaggtcta gaggagacta acaacgagga gggttgtcca aaacctaaaa
2581 atgatgaaga atttgtcgtc tcctctgatg acatcaaatc tgagggtaag aaaggaaaga
2641 acaagactgg ccgtggtaag aagcacacag ccttttccag caaaggactc agtgatgagg
2701 agtacgacga gtataagaga atcagggaag agagaaatgg caagtattcc atagaggaat
2761 acctacagga cagagacaaa tactatgagg aggtggccat agctagggca actgaggaag
2821 atttctgtga agaagaggag gccaagatcc ggcagaggat attcagacca acaaggaaac
2881 aacgcaaaga ggaaagagct tctcttggtt tggttacagg ctctgagatc aggaagagaa
2941 acccagatga cttcaagccc aaagggaaac tatgggctga tgatgacagg agtgttgact
3001 acaatgagaa acttagtttt gaggctccac caagtatttg gtcacgaata gtcaactttg
3061 gctcagggtg gggcttttgg gtctcgccca gcctcttcat aacatcaacc catgtcattc
3121 cccaaggcgc gcaggagttc tttggagtgc ccattaaaca aatacaaatt cacaagtcag
3181 gtgagttctg ccggcttagg ttcccgaaac caatcaggac agatgttaca ggcatgatct
3241 tggaggaagg tgctccagaa ggcactgttg ccacacttct catcaagaga ccaactgggg
3301 aactcatgcc cttggcagcc aggatgggca cccacgctac catgaaaatt cagggtcgca
3361 ctgttggtgg acagatgggc atgttactca cagggtctaa cgctaagagc atggacttgg
3421 gcacaactcc tggcgattgt ggttgtccct atatctacaa gagagggaac gactacgtgg
3481 tcattggggt tcacactgcc gccgctcgtg gaggaaacac cgtcatctgt gcaacccaag
3541 gaaacgaggg tgaggccacg ctagaaggtg gtgacaacaa gggaacttat tgtggggcac
3601 caatattagg ccctggaaat gcccccaaac tcagcaccaa aaccaaattt tggaggtcct
3661 ccaccacccc cctgccaccc ggaacctatg agccagctta tctgggtggc aaggacccta
3721 gagtaagagg tggtccctca ctgcaacagg ttatgagaga ccaactaaaa ccattcactg
3781 agcccagagg caaaccaccc aaaccaagtg tgctagaagc tgccaagaag actataatca
3841 atgtgcttga acaaacaata gacccacctc aaaaatggac atacgcacaa gcgtgtgcat
3901 cactagacaa gaccacttcc agcggtcatc ctcaccacat gcggaagaac gattgctgga
3961 atggggaatc tttcacagga aaactggcag accaagcatc aaaggccaac ctaatgtttg
4021 aggaaggaaa gaacatgact ccagtgtaca caggagctct gaaagatgaa ctagtcaaga
4081 ctgacaagat ctatggggtg gtcaagaaga ggctcctgtg gggttcagat ttatcaacca
4141 tgatacggtg tgcacgagcc ttcggtgggc taatggacga gctcaaggcc cattgcgtca
4201 cactaccagt cagggttggt atgaacatga atgaggatgg acccataata tttgagagac
4261 actccagata caaataccat tatgatgcag attactcccg ctgggactca acacaacaaa
4321 gagcagtgct agccgcagcc ctggaaataa tggtcaaatt ctcaccagaa ccccacctgg
4381 cccaggtggt tgcagaagac cttttgtccc ccagtgtgat ggatgtgggt gatttcagga
4441 tatcaatcaa cgagggatta ccctctggtg ttccttgcac ttcacaatgg aactccattg
4501 ctcactggct cctcacacta tgtgcactgt ctgaagtcac agacctgtct cctgacatca
4561 tccaggcgaa ttccctgttt tccttttatg gtgatgatga aatagtgagc acagacatca
4621 aattagaccc agagaaactg acagcaaagc tgagggaata cgggcttaaa ccaactcgcc
4681 ctgacaaaac agagggaccc ttaattattt ctgaagattt gaatggccta accttcttgc
4741 ggagaacagt gacccgcgac ccggccggat ggtttggcaa actggaccaa agttcaatac
4801 tcaggcagat gtactggacc aaggggccaa accatgaaga cccctttgaa acaatgatac
4861 cacactccca aagacccata caactgatgt cattacttgg tgaagctgca ttgcatggtc
4921 catcattcta cagtaaaatc agcaaattgg tcatctcaga actgaaagag ggtggaatgg
4981 atttttacgt gcccagacaa gaaccaatgt tcaggtggat gagattctca gatttgagca
5041 cgtgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgaatgac
5101 gccgctccat ctaatgatgg tgccgccggc ctcgtcccag agatcaataa tgaggcaatg
5161 gcgctagagc cagtggcggg tgcagcgata gcggcacccc tcactggtca gcaaaatata
5221 attgatccct ggattatgaa taattttgtg caagctcctg gtggtgagtt tacagtgtcc
5281 cctagaaatt cccctggtga agtccttctt aatttggaat tgggcccaga aataaatcct
5341 tacttggccc atcttgctag aatgtataat ggttatgcag gtggatttga agtgcaggtg
5401 gtcctagctg gaaatgcgtt tacagcagga aagataatct ttgcagctat tccccctaac
5461 tttccagttg ataatttaag tgcagcacag attacaatgt gcccacatgt gattgtggat
5521 gtcagacagt tggaaccagt taacctcccg atgcctgacg ttcgcaataa cttctttcac
5581 tataatcaag ggtctgattc gaggttacgc ctaattgcaa tgctatatac acctcttaga
5641 gcaaacaatt ctggggatga tgtttttact gtgtcttgta gagtgctaac tagacctagt
5701 cctgatttct cattcaattt tcttgtgcca cccactgtgg agtcaaagac aaaacccttc
5761 tccctcccta tcctgactat ctctgaaatg tctaattcta ggttcccagt gccaattgat
5821 tctctgcata ccagtcctac tgagaatgtt gttgttcagt gccaaaatgg gcgcgtcacc
5881 cttgatggtg agttgatggg taccacccaa ctcttgccta gccaaatctg tgctttcagg
5941 ggcgttctca ccagatcaac aagcagggcc agtgaccagg ccgatacagc aactcctaga
6001 ttgtttaatt attattggca tatacaattg gataatctaa atggaacccc ttatgatcct
6061 gcagaagaca taccaggccc cttggggaca ccagatttcc gtggcaaagt ctttggcgtg
6121 gccagccaga gaaatcctga tgccacgact agggcacatg aggctaaggt agacaccaca
6181 tctggccgct tcaccccaaa gttaggctca ttagagatat ccactgaatc tagtgacttt
6241 gaccaaagcc aaccaacaag attcacccca gttggcattg gggttgaccg tgaggcagac
6301 tttcaacaat ggaccctacc cgattacgct ggtcagctca cacacaacat gaacttagcc
6361 ccagctgttg ctcccaactt ccctggtgag cagctccttt tcttccgctc acatttgcca
6421 tcttctggtg ggcgatccaa cgggattcta gactgcctgg tcccccaaga atgggtacag
6481 cacttctacc aagagtcagc cccctctcag tctcaagtgg ccctggttag gtatgttaat
6541 cctgacactg gtagagtgtt atttgaggcc aagctacata aattaggttt catgactata
6601 gctaagaatg gtgattctcc aataactgtt cctccaaatg gatactttag gtttgaatct
6661 tgggtgaacc ccttttatac acttgccccc atgggaactg ggaatgggcg tagaaggatt
6721 caataatggc cggagctttt atagcaggat tggctggtga catgctcaca aatactgtag
6781 gatctttagt taatgcaggg gctaatgcta ttaatcaaac aattgatttt gaaaataata
6841 aatatttgca aaatgcttct tttaatcatg ataaggagat gttgaatgca caaattgagg
6901 caacaaagag gttacaggct gacatgattg ctatcaagca aggggtcttg accgctggcg
6961 gcttctcccc taccgatgca gcccgtgggg caattaatgc ccccatgaca aaagtcctag
7021 attggaatgg aacgagatac tgggcaccag gtgccacctc cacaacctcg atgtcgggtg
7081 gctttacaca tcaaactgtg cacagatcca caccaaattt taaaacgaac caggttccca
7141 aatccacacc cagcagtggg tcttcagtga ggtcaaactc aacccaaatc actagcctga
7201 gctcacactc gaccgggtcg tctcggtcca gcgggtctac agttatcagc tcaataccat
7261 cctctaacag gactagagac tgggtcaacc aacaaaattt caatttggaa ccacacatgc
7321 ctggatctct taggacagct tttgtcactc caccatctag tacagcctct agctcaggca
7381 cagtctcgac tgtgcccaaa aatgttttgg actcctggac atctgcgttt aacacgcgca
7441 gacagccgct attcgcacac cttcgtagaa ggggggagtc aaatgtttag
//