Typing tool
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Typing tool
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Complete norovirus genomes
| OP205578 | GII.3 | |
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| GII.P21 |
ORF1: 1..5100
ORF2: 5081..6727
ORF3: 6727..7491
LOCUS OP205578 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0420_R04-09 nonstructural
polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP205578
VERSION OP205578.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7491)
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JOURNAL Unpublished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 7491)
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..7491
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0420_R04-09"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-10-31"
/note="genotype: GII.3[P21]"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV61035.1"
/translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP
KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE
ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMVQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFP
KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR
CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEEANNEEGC
PKPKNDEEFVVSSDDIKSEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTSKLR
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6727
/gene="ORF2"
CDS 5081..6727
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61036.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNTFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPVLTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP
TRFTPVGIGVDHEADFQQWALPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6727..7491
/gene="ORF3"
CDS 6727..7491
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61037.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKPTPSSGSSVRSNSTQITSLSS
HSSGSSRSSGSTVISSIPTSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgctg ccaaaagcaa caacgacaac
61 gcaaaatctt caagtgacgg agtattatct aatatggctg tcacttttaa acgagccctc
121 ggggcgcggc ctaaacagcc gcccccgagt gacaaaccac caaaaccccc aaggccaccc
181 acaccagagt tggttaaggc aattccccct cccccaccca acggggagga cgaaccaatc
241 atctcttaca acgtcaaagg gggtgtttct ggtttgcctg agctctcaac tgtcacccaa
301 ctggaagaga actctacagc attcagcgtt ccccctctta gccagaggga gaacagagat
361 gcaaaggaac cattgactgg aaccatcctg gagatgtggg acggggagat ctaccattac
421 ggcttatacg tagaacgagg gttagtgctt ggtgtacaca aaccaccagc agccatcagc
481 cttgctaagg ttgagctgac ccctttgtct ttgtattgga gaccagtgta caccccacag
541 tacctcatct cccctgacac tctcagaaag ttgcatgggg agacgttccc ttatacagcc
601 tttgacaaca actgttatgc cttctgctgt tgggtgcttg acttaaacga ttcatggctg
661 aacagaagga tggtacagag gacaacaggc ttcttccgac cctaccagga ttggaacagg
721 aaacccctcc ccacgatgga tgactccaaa gtgaaaaagg tggccaatgt tgtcctatgt
781 gctctctcat cattgttcac aagaccaatt aaggacatta ttgggaaatt aaaaccccta
841 aacattctca acatcttagc cacatgtgat tggacttttg caggcatagt agaatccctg
901 atccttttgg ctgaactttt tggagttttc tggacacccc cagatgtgtc tgcgatgatc
961 gctcccttac tgggtgatta tgaactacag ggacccgagg acctcgctgt ggaactcgta
1021 cccgtagtaa tgggagggat aggtttggtg ctgggattca ccaaagagaa aatcggcaag
1081 atgctttctt ctgctgcttc aaccctgagg gcatgtaaag atctcggtgc atatgggttg
1141 gagatcctca aattgattat gaaatggttt ttcccaaaga aagaagagaa aaacgaattg
1201 gcaatggtga gatccatcga ggatgcagtg ctagatcttg aagccattga gaacaaccat
1261 atgacagctc tactcaagga taaagacagc cttgcaacct acatgaggac tcttgacatg
1321 gaagaggaga aggcgagaaa actttccacc aagtctgcct ctccggatat tgtgggcacg
1381 ataaatgccc tactgtcaag gattgcagct gcccggtctc tagtgcacag ggctaaggag
1441 gagctgtcaa gcaggccccg accggtcgtt gtaatgattt cagggaaacc gggtatagga
1501 aaaacccatc tagctagaga gttggcaaag aagatcgcct ccacactcac gggtgaccag
1561 agggtgggtc ttatcccacg taacggggtc gaccactggg atgcttacaa aggtgaaaga
1621 gtcgttctct gggacgacta cgggatgagc agccctgtcc acgacgccct cagactccag
1681 gagctcgctg atacctgtcc tctcacactc aactgtgaca ggattgagaa caaaggtaaa
1741 gtctttgaca gtgacgtcat aataataacc accaatttag ccaacccagc accactggat
1801 tatgtcaact ttgaagcttg ctcgagacgc atagacttcc tcgtctatgc tgacgctcct
1861 gaagttgaga aggctaagcg ggacttccca ggccaaccag acatgtggaa agacaccttc
1921 aaacccgact tctcacatat aaaattggca ttggccccgc aaggaggttt tgacaagaat
1981 ggtaacactc ctcatgggaa gggagtcatg aagaccctca ccgccagttc cctcgttgcc
2041 cgagcatcag ggctcctcca cgagagatta gacgagtatg agctgcaggg cccaactccc
2101 acaacattca acttcgaccg caacaaggtg cttgctttta ggcagcttgc tgctgaaaac
2161 aagtacggtc ttgttgacac aatgagggtc gggtcacaac tcaaaaatgt caaaactatg
2221 acagaactca aacaggccct caagaacatc tcagtcaaga aatgtcagct tgtgtacggt
2281 gggggcacat acacacttga atctgatggc aaaggcaatg tgcatgtcga aaaggtgaac
2341 aacaccagtg tacaaactaa caacgagctc tccggggttt tgcatcatct caggtgtgct
2401 agaatcaggt actatgttaa gtgtgttcag gaggctctct actccatatt gcaaattgcc
2461 ggggccgcat tcataaccac gcgcattgca aagcgcacaa acatacaaaa cctctggtct
2521 aaaccacaag cagaagatct agaggaggct aacaacgagg aaggttgtcc aaaacctaaa
2581 aatgatgaag aattcgtcgt ctcctctgat gacatcaaat ctgagggtaa gaaaggaaag
2641 aacaagactg gccgtggtaa gaagcacaca gccttttcca gcaaaggact cagtgatgag
2701 gagtacgatg agtataagag aatcagggaa gagagaaatg gtaagtactc catagaggaa
2761 tatctacagg acagggacaa atactatgag gaggtggcca tagccagggc aactgaggaa
2821 gatttctgtg aagaagagga ggccaagatc cggcagagga tattcagacc aacaaggaaa
2881 caacgcaaag aggaaagagc ttctcttggt ttggttacag gctctgagat caggaagaga
2941 aacccagatg acttcaagcc caaagggaaa ctatgggctg atgatgacag gagtgttgac
3001 tacaatgaga aacttagttt cgaggcacca ccaagcattt ggtcacgaat agtcaacttt
3061 ggctcagggt ggggcttttg ggtctcgccc agcctcttca taacatcaac ccatgtcatt
3121 ccccaaggcg cgcaggagtt ctttggagtg cccatcaaac aaatacaaat tcacaagtca
3181 ggtgagttct gccggcttag gttcccgaaa ccaatcagga cagatgtcac aggcatgatc
3241 ttggaggaag gtgctccaga aggcactgtt gccacacttc tcatcaagag accaactggg
3301 gaactcatgc ccttggcagc caggatgggc acccacgcta ccatgaaaat tcagggtcgc
3361 actgttggtg gacagatggg catgctactt acagggtcta acgctaagag catggatttg
3421 ggcacaactc ctggcgattg tggttgtccc tatatctaca agagagggaa cgactacgtg
3481 gtcattggag ttcacactgc cgccgctcgt gggggaaaca ccgtcatctg tgcaacccaa
3541 ggaaacgagg gtgaggccat gctagagggt ggtgacaaca agggaactta ttgtggggca
3601 ccaatattag gccctggaaa tgcccccaaa ctcagcacca aaacaaaatt ttggaggtct
3661 tccaccaccc ccctgccacc cggaacctat gagccagctt atctgggtgg caaggaccct
3721 agagtgaaag gtggtccctc actgcaacag gttatgagag accaactaaa accattcact
3781 gagcccaggg gcaaaccacc caaaccaagt gtgctagaag ctgccaagaa gactataatc
3841 aatgtgcttg aacaaacaat agatccacct caaaaatgga catacgcaca agcgtgtgca
3901 tcactagaca agaccacttc cagcggtcac cctcaccaca tgcggaagaa cgactgctgg
3961 aatggggaat ctttcacagg aaaactggca gaccaagcat caaaggccaa cctaatgttt
4021 gaggaaggaa agaacatgac tccagtgtac acaggagctc tgaaagatga gctagtcaag
4081 actgacaaga tctatggggt agtcaagaag aggctcctgt ggggttcaga cctatcaacc
4141 atgatacggt gtgcacgagc cttcggtggg ctaatggacg agctcaaggc ccattgcgtc
4201 acactaccag tcagagttgg tatgaacatg aatgaggatg gacccataat atttgagaaa
4261 cactctagat ataaatacca ctatgatgca gattactccc gctgggactc aacacaacaa
4321 agagcagtgc tagccgcagc cctggaaata atggtcaaat tctcaccaga accccacctg
4381 gcccaggtgg ttgcagaaga cctcttgtct cccagtgtga tggacgtggg tgatttcagg
4441 atatcaatca acgagggatt accctctggt gttccttgca cttcacaatg gaactccatt
4501 gctcactggc tcctcacact atgtgcactg tctgaagtca cagacctgtc ccctgacatc
4561 atccaggcga attccctgtt ttccttctat ggtgatgatg aaatagtgag cacagacatc
4621 aaattagacc cagagaaact aacatcaaag ctgagggaat acgggcttaa accaactcgc
4681 cctgacaaaa cagagggacc cttaattatc tctgaagatt tgaacggcct aaccttcctg
4741 cggagaacag tgacccgcga cccggccgga tggtttggca aactggacca aagttcaata
4801 ctcaggcaga tgtattggac taaggggcca aaccatgaag acccttttga aacaatgata
4861 ccacactccc aaagacccat acaactgatg tcattacttg gtgaagctgc attgcatggt
4921 ccgtcattct acagtaaaat cagcaaattg gtcatctcag aactgaaaga gggtggaatg
4981 gatttttacg tgcccagaca agaaccaatg ttcaggtgga tgagattctc agatttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga
5101 cgccgctcca tctaatgatg gtgccgccgg cctcgtccca gagatcaaca atgaggcaat
5161 ggcgctggag ccagtggcgg gtgcagcaat agcagcaccc ctcactggtc agcaaaatat
5221 aattgatccc tggattatga ataattttgt gcaagctcct ggtggtgagt tcacagtgtc
5281 ccccagaaat tcccctggtg aagtccttct taatttggaa ctgggcccag aaataaatcc
5341 ctacttggcc catcttgcta gaatgtataa tggttatgca ggtggatttg aagtgcaggt
5401 ggtcctagct ggaaatgcgt ttacagcagg aaagataatc tttgcagcta ttccccccaa
5461 ctttccagtt gataatttaa gtgcagcaca aatcacaatg tgcccacatg tgattgtgga
5521 tgtcagacag ctggaaccag tcaacctccc gatgcctgac gttcgcaata ccttctttca
5581 ctataaccaa gggtctgatt cgaggttacg cctaattgca atgctataca cacctcttag
5641 agcaaacaat tctggggatg atgtttttac tgtgtcttgt agagtgctaa ctagacctag
5701 tcctgatttc tcattcaatt tccttgtgcc acctactgtg gagtcaaaga caaaaccctt
5761 ctccctccct gtcctgacta tctctgagat gtctaattct agattcccag taccaattga
5821 ttctctgcac accagtccta ctgagaatat tgttgttcag tgccaaaatg ggcgcgtcac
5881 ccttgatggt gagttgatgg gcaccaccca acttttgcct agccaaatct gtgctttcag
5941 gggcgttctc accagatcaa caagcagggc cagtgaccag gccgatacag caactcctag
6001 attgtttaat tattattggc atatacaatt ggataatcta aatggaaccc cttatgaccc
6061 tgcagaagat ataccaggtc ccctagggac accagatttc cgtggcaaag tctttggcgt
6121 ggccagccag agaaatcctg acaccacgac tagggcacat gaagcaaaga tagacaccac
6181 atctggccgc ttcaccccaa agttgggctc attagagata tccactgaat ctagtgattt
6241 tgaccaaaac caaccaacaa ggttcacccc agttggcatt ggggttgacc atgaggcaga
6301 ctttcaacaa tgggccctac ctgattacgc tggtcagttc acacacaaca tgaacttagc
6361 tccagctgtt gctcccaact tccctggtga gcagctcctt ttcttccgct cacatttgcc
6421 atcttctggt gggcgatcca acgggattct agactgcctg gtcccccaag aatgggtaca
6481 gcacttctac caagagtcag ccccctctca gtctcaagtg gccctggtta ggtatgttaa
6541 tcctgatact ggtagagtgt tatttgaggc taagttacac aaattaggtt tcatgactat
6601 agctaagaat ggtgattctc caataactgt ccctccaaat ggatacttta ggtttgaatc
6661 ttgggtgaac cccttttaca cacttgcccc catgggaact gggaatgggc gtagaaggat
6721 tcaataatgg ctggagcttt tatagcagga ttggctggtg atatgctcac aaatactgta
6781 ggatctttag ttaatgcagg ggctaatgct attaatcaaa caattgattt tgaaaataat
6841 aaatatttgc aaaatgcttc ttttaatcat gataaggaga tgttgaatgc acaaattgaa
6901 gcaacaaaga agttacaggc tgacatgatt gctatcaagc aaggggtctt gactgctggc
6961 ggcttctccc ctactgatgc agcccgtggg gcaattaatg cccccatgac aaaggtccta
7021 gattggaatg gaacgagata ctgggcacca ggtgccacct ccacaacctc gatgtcgggt
7081 ggctttacac atcaaactgt gcatagatcc acaccaaatt ttaaaacgaa ccaggctccc
7141 aaacctacac ccagcagtgg gtcttcagtg aggtcaaact caacccaaat cactagcctg
7201 agctcacact cgtccgggtc gtctcgatcc agcgggtcta cagttatcag ctcaatacca
7261 acctctaaca ggactaggga ctgggtcaac caacaaaatt ttaatttgga accgcacatg
7321 cctggatctc ttaggacagc ttttgtcact ccaccatcta gtacagcctc tagctcaggc
7381 acagtctcaa ctgtgcccaa aaatgttttg gactcctgga catctgcgtt taacacgcgc
7441 agacagccgc tattcgcaca ccttcgcaga aggggggagt caaatgttta g
//