Typing tool
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Typing tool
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Complete norovirus genomes
| OP205556 | GII.3 | |
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| GII.P16 |
ORF1: 1..5081
ORF2: 5062..6708
ORF3: 6708..7472
LOCUS OP205556 7472 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0395_R03-11 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205556
VERSION OP205556.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7472)
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JOURNAL Unpublished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 7472)
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..7472
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0395_R03-11"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-10-11"
/note="genotype: GII.3[P16]"
gene <1..5081
/gene="ORF1"
CDS <1..5081
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60969.1"
/translation="ATVAVACDNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRD
KPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTA
FSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVE
LTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLN
ILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVA
STLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLN
CDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKIGNQLKGVKTMEELKQ
AIRNVTIKRCRIIYGGSTYDLESDGKGKVLVERVKNISVQTNNELAGALHHLKHARIR
YYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDD
EFVISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEY
LQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRK
RNPDDFKPKGKLWADDNRSVDYNEKLNFEAPPSIWSRIVSFGSGWGFWVSPSLFITST
HVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLI
KRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIY
KRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKL
STKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKP
SVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGYPHHARKNEFWNGETFTG
KLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCA
RSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAV
LASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIT
HWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPT
RPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNE
TMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMR
FSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..977
/gene="ORF1"
/product="p48"
mat_peptide 978..2075
/gene="ORF1"
/product="NTPase"
mat_peptide 2076..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="UUV60970.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPAPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDENQP
TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KSGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6708..7472
/gene="ORF3"
CDS 6708..7472
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60971.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVGAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESSV"
ORIGIN
1 acgctaccgt tgccgttgct tgcgacaaca acaacgacaa ggaaaaatct tcaggtgaag
61 gcttattcac aaatatgtct tccaccttaa agaaagccct cggggctagg cccaaacagc
121 ctgccccgag agacaaacca caaaagcccc caagaccacc aactcccgag ttggtcaaga
181 ggataccccc tcctccacct aatggcgaag aagaagaaga accagtcatt aggtatgagg
241 ttaagagtgg gatctctggt ctgcccgagc tcacaacagt ccctcaaccg gacgtggcca
301 acacagcatt cagtgttcca ccactgagtt tgagagaaaa cagggaggcc aaagaaccgc
361 taacaggggc aatattagag atgtgggatg gagagatata tcactatggc ctgtacgtgg
421 agaaaggctt agtgttgggt gtgcacaaac cacctgcagc cataagcatg gcaagagtgg
481 agctgacgcc gctgtcattg tactggcgtg tggtgtacac tccccaatac ctcatctccc
541 ctgaaactct caggaggctt aacggagagg cattccctta caccgctttt gataacaact
601 gctatgcctt ttgttgctgg gtgttagacc tcaacgactc atggctcagc aggaggatgg
661 tgcagagaac aacgggcttc tttagacctt accaagagtg gaacagaaaa cccctaccta
721 ccatggatga ctccaaaatt aagaaggtag caaatatatt cctatgttca ttgtccacat
781 tatttaccag acccataaaa gacctcatag gaaaaattaa accattaaac atattgaata
841 tcctggcaac gtgtgactgg acgtttgccg gaatagtgga gtctctaata ttacttgctg
901 aactcttcgg agttttctgg acacccccag atgtgtctgc tatgatcgct cccctactcg
961 gggactacga gttgcaaggg ccagaagacc tcgccgttga actcgtacct gtggtaatgg
1021 gagggattgg tttggtgttg ggattcacca aagagaaaat tggcaaaatg ttgtcctcag
1081 cagcatcaac actcagagct tgcaaagatc ttggtgccta tggcttagag atactcaaat
1141 tggtcatgaa gtggttcttc ccaaagaaag aagaggccaa tgagctagcc atggtgaggg
1201 ccatagagga tgctgtacta gatcttgagg caatagaaaa taaccacatg acaaccctgt
1261 tgaaagataa agacagctta gcaacataca tgaaaacact ggacatggag gaggagaaag
1321 ccagaagatt gtccacaaaa tctgcatccc ctgacatagt tgggacaatc aatgccctgc
1381 tggctcgaat agcagcggcc aggtcactag tccacagggc taaggaagag ctatctagca
1441 ggataaggcc agtagttgtt atgatatctg gtaaaccagg aataggcaaa actcatctgg
1501 ccagggaggt ggcaagaaag gtggcatcca ctctcacagg ggatcaaaga gtcggactca
1561 taccaagaaa cggtgtggac cattgggatg catacaaagg tgagagagtc gtgctgtggg
1621 acgactatgg catgagtaac cccattcatg atgctcttcg catacaagaa ttggctgata
1681 cgtgtcccct caccttaaat tgtgacagaa ttgaaaataa aggaaaagtt tttgacagtg
1741 aagtcataat aatcacaaca aaccttgcca atccagcccc acttgattat gtcaactttg
1801 aggcctgttc caggagaatt gacttcctgg tgtacgctga ggcaccagaa gtagaaaagg
1861 caaaacggga ctttcctggt cagccagata tgtggaagga cgccttcaag tcggactttt
1921 cacacatcaa gttacagctt gcaccccagg gcggctttga caagaatggt aacaccccac
1981 atgggaaagg agtgatgaag accctcacta ccggttctct gattgcccgt gcatcaggcc
2041 tactgcatga gaggatggat gaatttgaac tccaaggtcc tacaatcacc accttcaatt
2101 tcgaccggaa cagaatcaca gcatttagac aattggctgc agaaaacaag tatggactgg
2161 tggataccat gaaaattggc aatcaattaa aaggagtgaa aaccatggaa gaacttaaac
2221 aagcaatcag gaatgtaacc atcaagaggt gccggatcat ctacggtggt tccacatatg
2281 accttgaatc tgatggcaag ggcaaagttt tggtggaaag ggtcaagaac atctctgtac
2341 agaccaacaa cgagttggcc ggggccctgc accatctcaa acacgcccgg atcaggtact
2401 atgtcaaatg tgtgcaagaa gcagtctatt ctatcataca aattgccggc gctgcatttg
2461 tcaccacgcg catcgcacgc cgcatgaaca tacaagagct ctggtcgaag ccacagttag
2521 atcaaaatga atcagagact aaggaagagg cccccaagtc ggaagatgat gagttcgtca
2581 tatcttctaa ggacatcaag gaggaaggaa agaagggcaa aaataaaact ggccgtggca
2641 agaaacacac tgcgttctcc agtaagggct tgagcgatga ggagtacgac gagtacaaga
2701 ggataagaga agagagaaat gggaagtact ctatagagga gtatcttcaa gacagagaca
2761 ggtactatga ggagctcgcc attgccaagg ccacggaaga agacttctgt gaagaggagg
2821 agatcaaaat ccgtcagaga attttccgcc ctaccaggaa acaaagaaag gaagagaggg
2881 ccacactagg gctagtaaca ggttcagaaa tcagaaaaag aaaccctgat gacttcaaac
2941 ccaaagggaa gctgtgggcc gatgacaaca gaagcgttga ttataatgag aaactgaact
3001 ttgaggcccc cccaagcata tggtctagga ttgtgagctt tggttctggc tggggcttct
3061 gggtgtcacc aagcctgttc ataacatcaa ctcatgtgat ccccgcaggc ataacagaag
3121 catttggagt ccccatcaaa caaattcaga tccacaaatc aggcgaattt tgccgattca
3181 gattcccaaa accaattaga ccagatgtga caggaatgat cttggaagaa ggtgcgcctg
3241 agggcaccgt ggcaactgtg ctcatcaaac gccccaccgg agagctcatg cctcttgcag
3301 ccagaatggg aacacacgca accatgaaaa ttcaaggccg catggttggc ggacagatgg
3361 gtatgttgct cactggatca aatgctaaag gaatggattt gggaacaaca cctggtgact
3421 gtggctgtcc ttacatctat aaaaggggca atgactatat agtcattggg gtgcacactg
3481 cagcagcccg tggtggaaac accgtcatct gtgccacaca gggaagtgag ggtgaggcaa
3541 ctcttgaggg cggagatgac aaaggaacat actgtggggc acccattcta ggccctgggg
3601 gtgcaccaaa attgagcacc aaaaccaaat tttggaggtc atcgaacacg cccctcccac
3661 cagggacata tgagcctgcc tacctcggcg gccgtgaccc gcgtgttaag ggtgggccct
3721 ccttgcagca ggtgatgaga gaccagttga agccattcac tgaacccaga ggcaaacctc
3781 caaaaccaag tgtattggaa gcagccaaac aaaccatcat caatgtcctc gaacaaaccc
3841 tggaccctcc acaaaaatgg acatacgcac aggcgtgtgc ctcacttgac aagaccacct
3901 ccagcgggta cccccatcac gcccgaaaga atgaattctg gaatggtgag accttcactg
3961 gtaaattggc agaccaagca tcaaaagcaa acctaatgtt tgaggaaggg aaacacatga
4021 caccagtgta tacagcagca ctcaaggacg agctagtcaa gactgagaaa atctatggaa
4081 agatcaagaa gagactgctc tggggctctg acttgtccac catgattcgg tgcgctaggt
4141 catttggtgg gctcatggac gagatgaagg cacactgcat atcactccca gtccgagttg
4201 gtatgaacat gaatgaagat ggcccaataa tatttgagaa acattccaga tacaaatacc
4261 actatgatgc agactactct cgctgggatt caacacaaca gagggcagta ctggcatcag
4321 ccttggaaat tatggtcaga ttctctgcag aaccacaact ggcacaaata gtcgctgagg
4381 acctgctggc ccctagtgta gtagatgtag gagactttaa aatcacaata aatgaagggc
4441 tcccctctgg tgtgccatgc acttctcaat ggaactccat cacacactgg ctgctaactc
4501 tctgtgccct gtctgaagtc accaaacttt cccctgacat tgtacaggca aattccatgt
4561 tctcatttta cggtgatgac gagattgtca gcaccgacat aaaattggac cctgaacagt
4621 taaccgccaa attgaaggag tacggcctga aaccaacccg cccagacaaa actgagggac
4681 ccctgatcat cagtgaagat ttgaacggac tcactttcct ccgaaggacg gtgactcgtg
4741 acccagctgg ctggtttgga aaactggacc aaagctcaat tttgaggcag atgtactgga
4801 ctagaggacc aaatcacgaa gaccccaatg agacaatgat accccattct caaagaccca
4861 tacagcttat ggcattgctt ggtgaagcct ctcttcacgg gccctctttc tacagtaaaa
4921 tcagtaaatt ggtcataact gaactcaaag aaggtgggat ggatttttac gtgccaaggc
4981 aggaacccat gttcaggtgg atgaggtttt ctgacttgag cacgtgggag ggcgatcgca
5041 atctggctcc cagttttgtg aatgaagatg gcgtcgaatg acgccgcccc atctaatgat
5101 ggtgccgccg gcctcgttcc agagatcaac aatgaggcaa tggcgctaga gccagtggcg
5161 ggtgcagcga tagcagcacc cctcactggt cagcaaaata taattgatcc ctggattatg
5221 aacaactttg tgcaagcacc tggtggtgag tttacagtgt ccccaagaaa ttcccctggt
5281 gaagtccttc ttaatttgga attgggccca gagataaacc cctacttggc ccatcttgct
5341 agaatgtaca atggttatgc aggtggattt gaagtgcagg tggtcctagc tggaaatgcg
5401 tttacagcag gaaagataat ctttgcagcc atccccccta attttccaat tgacaattta
5461 agtgcagcac agatcacaat gtgcccacat gtaatcgtgg acgtcagaca gttggaacca
5521 gtcaacctcc cgatgcctga cgttcgcaat aacttctttc attataatca agggtctgat
5581 tcgaggttac gcctaattgc aatgctatac acacctctta gggcaaacaa ttctggggat
5641 gatgttttta ctgtgtcttg tagagtgtta actagaccta gtcctgattt ctcgttcaat
5701 ttccttgtgc ctcccactgt ggagtcaaag acaaaaccct tttccctccc catcttgact
5761 atctctgaaa tgtccaactc taggttccca gcaccaatag attccctaca caccagtcct
5821 actgagaata ttgttgttca gtgccaaaat gggcgcgtca cccttgatgg tgagctgatg
5881 ggcaccaccc aactcttgcc cagccaaatc tgtgctttca ggggcgttct taccagatca
5941 acaagcagag ccagtgacca ggccgataca gcaaccccca gattatttaa ttactattgg
6001 catatacaat tggataatct aaatggaacc ccttatgatc ctgcagaaga cataccaggc
6061 cccctaggga caccagattt ccgtggcaaa gtctttggcg tggccagcca gagaaatcct
6121 gacaccacga ctagagcaca tgaagcaaag atagacacca catccggccg tttcacccca
6181 aagctaggct cattagagat atccactgaa tctagtgatt ttgatgaaaa ccaaccaaca
6241 agattcaccc cagttggcat tggagttgac catgaggcag actttcaaca atggacccta
6301 cccgactatg ctggtcagtt cacacacaac atgaacttgg ccccagctgt tgctcccaac
6361 ttccctggtg aacagctcct tttcttccgc tcacatttgc catcttctgg tgggcgatct
6421 aacgggattc tagactgcct ggttccccaa gaatgggtac agcacttcta ccaagagtca
6481 gccccctctc agactcaagt ggccctggtt aggtatgtta atcctgacac tggcagagtg
6541 ttatttgagg ccaagctaca caaattaggt ttcatgacta tagccaagag tggtgattcc
6601 ccaataactg tccccccaaa tggatacttt aggtttgaat cttgggtgaa ccccttttac
6661 acacttgccc ccatgggaac tgggaatggg cgtagaagga ttcaataatg gctggagctt
6721 ttatagcagg attggctggt gacatgctca caaatactgt aggatcttta gttggtgcag
6781 gagctaatgc tatcaatcaa acaattgatt ttgaaaataa taaatatttg caaaatgctt
6841 cttttaacca tgataaggag atgttgaatg cacaaattga ggcaacaaag aagttacagg
6901 ctgacatgat tgctatcaaa caaggggttt tgaccgctgg cggcttctcc cctactgatg
6961 cagcccgtgg ggcaattaat gcccccatga caaaagtcct agattggaat ggaacgagat
7021 actgggcacc aggtgccacc tccacaacct cgatgtcggg tggctttaca caccaaactg
7081 tgcacagatc cacaccaaat tttaaaacga atcaggcccc caaatccaca cctagtagtg
7141 gttcttcagt gaggtcaaac tcaacccaaa tcactagcct gagctcacac tcgtccgggt
7201 cgtctcgatc cagcgggtct acagtcatca gctcaatacc atcctctaac aggactaggg
7261 actgggtcaa ccaacaaaat tttaatttgg aaccacacat gcctggatct cttaggacag
7321 cttttgtcac tccaccatct agtacagcct ctagctcagg cacagtctca actgtgccca
7381 aaaatgtttt ggactcctgg acatctgcgt ttaacacgcg cagacagccg ctattcgcac
7441 accttcgcag aaggggggag tcaagtgttt ag
//