Typing tool
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Typing tool
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Complete norovirus genomes
| OR536487 | GII.3 | |
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| GII.P21 |
ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS OR536487 7547 bp RNA linear VRL 04-MAR-2024
DEFINITION Norovirus GII isolate
Hu/NL/2020/GII.3[P21]/Rotterdam/I129S18_P19-d1533, complete genome.
ACCESSION OR536487
VERSION OR536487.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7547)
AUTHORS Izquierdo Lara,R.W., Villabruna,N., Hesselink,D.A.,
Schapendonk,C.M.E., Ribo Pons,S., Meier,J.I.J., Goodfellow,I.,
Dalm,V.A.S.H., Fraaij,P.L.A., van Kampen,J.A., Koopmans,M.P.G. and
de Graaf,M.
TITLE Intra-host multi-lineage evolution of human Norovirus in
immunocompromised individuals: Implications for treatment
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7547)
AUTHORS Izquierdo Lara,R.W., Villabruna,N., Hesselink,D.A.,
Schapendonk,C.M.E., Ribo Pons,S., Meier,J.I.J., Goodfellow,I.,
Dalm,V.A.S.H., Fraaij,P.L.A., van Kampen,J.A., Koopmans,M.P.G. and
de Graaf,M.
TITLE Direct Submission
JOURNAL Submitted (11-SEP-2023) Viroscience, Erasmus Medical Center, Dr.
Molewaterplein 40, Rotterdam, Zuid-Holland 3015 GD, Netherlands
COMMENT ##Assembly-Data-START##
Assembly Method :: Spades v. 3.15.4; BWA-MEM v. 0.7.17
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7547
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/NL/2020/GII.3[P21]/Rotterdam/I129S18_P19-
d1533"
/isolation_source="feaces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands: Rotterdam"
/collection_date="30-Jan-2020"
/note="genotype: GII.3[P21]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="WMX17839.1"
/translation="MKMASNDASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARP
KQPPPRDKPPKPPRPPTPELVKSIPPPPPNGEDEPTISYNVKEGVSGLPELSTVTQPE
ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYIAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVILCALASLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEKNELEMVRAIEDAVLDLEAIENNHMTTLLKDRDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREV
AKKIASTLTGDQRVGLIPRNGVDHWDSYRGERIVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIMITTNLANPAPLDYVNFEACSRRIDFLVYAESPEVEK
AKRDFPGQPDMWKDAFKPDCSHIKLTLAPQGGFDKNGNTPYGKGVMKTLTASSLVARA
SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
TELKQALKNISVKKCQLVYGGSTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLR
NARIRYYVKCVQEALYSIIQIAGAAFITTRIARRMNIQNLWSKPQVEDLEETNNVEGC
PKPKSDEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEFKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILG
PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
NGETFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDL
STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 5..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6731
/gene="ORF2"
CDS 5085..6731
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WMX17840.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAALAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLSRMYNGYAGG
FEVQVILAGNAFTAGKIIFAAIPPHFPIDNLSAAQITMCPHVIVDVRQLEPVNLPLPD
IRNSFFHYNQGSESRMRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFAFNFLVPP
TVESKTKPFSIPVLTISEMSNSRFPVPIDSLHTSPTDNIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRPASRASDQADTATPRSFNNHWHIQLDNLNGTPYDPSEDIPGP
LGTPDFRGKIFGVASQRNPDATTRAHEAKIDTASPRFTPKLGSLVISTESEDFDQNQP
TRFTPVGVGVDQEADFQQWTLPNYAGQLTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSDGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFITIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6731..7495
/gene="ORF3"
CDS 6731..7495
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WMX17841.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKHLQNA
SFNHDKEMLKAQIEATKNLQASMISIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRHWAPGATSTTSLSGGFTNQTVHRSTPNFKVNQAPKSAPSGGSSVRSNSTQITSLSS
HSSGSSRSSGSTVVSSIPSSNRTRDWVTQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgcaaaca gcaacaacga
61 caacgcaaaa tcttcaagtg acggagtact atctaatatg gccgtcactt tcaaacgagc
121 cctcggggcg cggcctaaac agccgccccc gagggacaaa ccaccaaagc ccccaagacc
181 ccccacacca gaattggtta aatcaatccc ccctccccca cccaacgggg aggacgaacc
241 aaccatttct tacaacgtaa aagagggtgt ttctggtttg cctgagctct caactgtcac
301 ccaaccagaa gagaactcta cagcatttag cgttccccct cttagtcaga gggagaacag
361 agatgcaaag gaaccattga ctggaactat tctggagatg tgggatgggg agatctacca
421 ttatggctta tatgtggaac gagggctagt gctaggtgtg cacaaaccac cagcagccat
481 cagccttgcc aaggttgagc taaccccctt gtccttgtat tggaggccag tgtacacccc
541 acagtacctc atttcccctg atactctcag aaagttgcat ggggaaacgt tcccttatat
601 agcctttgac aacaactgtt acgccttctg ctgttgggtg cttgacttga acgattcatg
661 gctgagcaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggactggaa
721 taggaagccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atgttatcct
781 ctgtgctctc gcatcattgt ttacaagacc aattaaggac attattggaa agttgaaacc
841 cctaaacatc ctcaacatcc tagccacatg tgattggact tttgcgggca tagtagaatc
901 cctgatcctc ttggctgaac tgtttggagt tttctggaca cccccagatg tgtctgcaat
961 gatcgctcct ttactgggtg attatgagct gcagggaccc gaggaccttg ctgtggagct
1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
1081 caaaatgctt tcatctgctg cttcaacctt gagggcatgc aaagatctcg gtgcatatgg
1141 gttggagatc ctcaaattgg tcatgaaatg gtttttccca aagaaagaag agaaaaacga
1201 attggaaatg gtgagagcca ttgaggatgc agtgctagat cttgaggcca ttgagaacaa
1261 ccacatgaca actctactca aggatagaga cagccttgca acctacatga gaactcttga
1321 cctagaggag gagaaggcga ggaaactctc caccaagtct gcctcgccgg atattgtggg
1381 cacaataaac tccctactgg caaggattgc agctgcccgg tctttagtgc acagggctaa
1441 ggaggagctg tcaagcaggc ctcgaccggt cgttgtgatg atctcaggga gaccaggtat
1501 agggaaaacc catctagcta gagaggtggc aaagaaaatc gcctccacac tcacaggtga
1561 tcagagggtg ggtcttattc cacgcaacgg ggtcgatcac tgggattcat acagaggtga
1621 aagaatcgtt ctctgggacg actatggaat gagcaacccc atccacgacg ccctcagact
1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg
1741 caaagttttt gacagtgacg tcataatgat aaccaccaat ttggcaaacc cagcgccact
1801 ggactacgtc aactttgaag cgtgctcaag acgcatagac ttcctcgtct atgctgaatc
1861 ccctgaagtt gaaaaggcta aacgggactt cccaggccaa ccagacatgt ggaaagatgc
1921 cttcaaacct gattgctcac acataaaatt gacattggct ccacaagggg gttttgacaa
1981 aaatggcaac actccttatg gaaagggtgt catgaagacc ctcactgcca gttccctcgt
2041 tgcccgagca tcagggctcc tccatgagag gttagacgag tatgagctgc aggggccaac
2101 tcccacgaca ttcaacttcg accgcaacaa ggttctcgct tttaggcaac ttgctgctga
2161 aaacaagtac ggccttgttg acacaatgag ggtcggatcg cagctcaaga atgtcaaaac
2221 catgacagaa ctcaagcagg ctctcaagaa catctcagtc aagaaatgcc agcttgtata
2281 tggtgggagc acgtacactc ttgaatctga tggtaagggt aatgtgcatg ttgagaaggt
2341 gaacaacacc agtgtgcaaa ctaacaatga gctctccggg gctttgcacc acctcaggaa
2401 tgccagaatc aggtactatg ttaagtgtgt ccaggaagct ctctactcca tcattcaaat
2461 tgccggggct gcattcatta ccacgcgcat tgcaaggcgc atgaacatac aaaacctttg
2521 gtccaaaccg caagtagaag atttggagga gaccaacaac gtggagggtt gtccaaaacc
2581 taaaagtgat gaagaatttg tcatctcttc tgacgacatc aaagccgagg gcaagaaagg
2641 taagaacaag actggccgtg gcaagaagca cacagccttt tccagcaaag ggcttagtga
2701 tgaagagtac gatgagttca aaaggatcag ggaagagaga aatggcaaat actccataga
2761 ggaataccta caggatagag acaaatacta tgaggaggtg gccatagcta gggcaactga
2821 ggaagacttc tgtgaagaag aagaggcaaa aatccgacaa aggatattta gaccaacaag
2881 gaaacagcgc aaagaagaaa gggcctctct cggtttggtc acaggttctg agattaggaa
2941 gagaaatcca gatgatttca agcccaaagg gaaactatgg gccgatgatg acaggaatgt
3001 tgactacaat gagaaactca gtttcgaggc tccaccaagc atttggtcac gaatagtcaa
3061 ctttggctcg gggtggggtt tctgggtctc gcccagcctc ttcataacat caacccatgt
3121 catcccccaa ggcgcacagg aattctttgg ggtgtccatc aagcaaattc aaattcacaa
3181 gtcgggtgag ttttgccggc ttagattccc aaaaccaatc aggacagatg ttacaggcat
3241 gattttggag gaaggtgctc cagaaggcac cgttgccaca cttctcatca agaggccaac
3301 tggggagctc atgcccttgg cagccaggat gggcacccac gcgaccatga gaattcaggg
3361 acgcactgtt ggtggacaga tgggcatgct gctcacaggg tctaacgcta agagcatgga
3421 cttgggcaca actcccggcg attgtggttg tccctatatc tacaaaagag ggaacgacta
3481 cgttgtcatt ggggttcaca cagccgccgc tcgtggagga aacaccgtca tctgtgcaac
3541 ccaaggaagc gagggtgagg ctgtgctaga aggtggtgac aacaagggaa cttactgtgg
3601 agcaccaata ttgggacctg ggaatgcccc caaactcagc accaaaacca aattctggag
3661 gtcttccacc acccccctgc cacccggaac ctatgaacca gcttacctag gtggcaagga
3721 ccctagagtg aagggtggcc cctcactgca acaggttatg agggatcagc taaagccatt
3781 cactgaaccc agaggcaagc caccaaaacc aagtgtgcta gaagctgcta aaaagactat
3841 aatcaatgta cttgagcaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg
3901 tgcatcatta gataagacca cctccagcgg ccatcctcac cacatgcgga agaacgactg
3961 ctggaatggg gagaccttca caggaaaact ggcagaccaa gcatcaaagg ctaacctaat
4021 gtttgaggaa ggaaagaaca tgaccccagt atacacaggg gccctaaaag atgagctagt
4081 taagactgat aagatctatg ggacaatcaa gaagagactc ctgtggggtt cagacctatc
4141 aaccatgata cggtgtgcac gagccttcgg tgggttgatg gacgaactca aagcccactg
4201 tgtcacacta ccagtcagag ttggcatgaa catgaatgag gatggaccca taatatttga
4261 gaaacattcc agatataaat atcattatga tgcagattac tcccgctggg actcaacaca
4321 acaaagagca gtactggctg cagccctgga aataatggtc aaattctcac cagaacccca
4381 tctggctcaa gtggttgcag aggacctctt gtcccccagt gtgatggatg tgggtgattt
4441 caagatatca atcaacgagg gattaccctc tggtgttccc tgcacctcac aatggaactc
4501 cattgcccac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
4621 cattaaattg gatccagaga aattaacaac aaaattgaag gaatacggac tgaaaccaac
4681 ccgtcctgac aaaacagaag gacccttgat tatctctgaa gatttgaatg gcctaacatt
4741 cttgcggaga acggtaaccc gtgatccggc cgggtggttt ggcaaactgg accaaagctc
4801 aatactcagg cagatgtact ggaccagggg accaaaccat gaggatccct ttgaaacaat
4861 gataccacac tcccaaagac ccatacaact gatgtcatta ttgggtgaag ctgcgttgca
4921 tggcccgtca ttttacagta aaatcagcaa attggtcatc tcagaattga aagagggtgg
4981 aatggatttt tacgtgccca ggcaagaacc aatgttcaga tggatgagat tttcagactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
5101 atgacgccgc tccatctaac gatggtgccg ccggcctcgt cccagagatc aacaatgagg
5161 caatggcgct agaaccagtg gcgggtgcag cgttagcagc accccttact ggtcagcaaa
5221 atataattga tccctggatt atgaataatt ttgtacaagc acctggtggt gagttcacag
5281 tgtcccctag aaattcccct ggtgaagttc ttctcaattt ggaattaggt ccagaaataa
5341 atccctattt ggcccatctt tctagaatgt ataatggtta tgcaggtgga tttgaagtgc
5401 aggtgatcct agctggaaat gcgtttacag caggaaagat aatctttgca gctatccccc
5461 cccattttcc aattgacaac ctaagtgcag cacagatcac aatgtgtcca catgtgatcg
5521 tggatgtcag acagctggaa ccagtcaacc tcccgttgcc tgacattcgc aacagtttct
5581 ttcattataa tcaagggtct gaatcaagaa tgcgcttaat tgcaatgtta tatacacctc
5641 ttagggcaaa taattctggg gatgatgttt ttactgtgtc ttgtagagtg ttaactagac
5701 ctagtcctga ctttgcattt aatttccttg tgccacctac tgtggagtca aagacaaaac
5761 ccttttccat ccctgttctg actatctctg aaatgtccaa ttcgaggttc ccagtaccaa
5821 ttgattccct gcacaccagc cctactgata atattgttgt ccagtgtcag aatgggcgcg
5881 tcacccttga cggtgagttg atgggcacta cccagctcct acctagtcaa atctgtgctt
5941 tcaggggcgt gctcaccaga ccagcaagca gggccagtga ccaggccgat acagcaaccc
6001 ccagatcgtt caataatcat tggcacatac aattggataa tctaaatgga actccttatg
6061 atccttcaga agatatacca ggccccttgg gaacaccaga ttttcggggc aaaatctttg
6121 gcgtggccag ccagagaaat cctgatgcta caactagggc acatgaagca aagatagata
6181 cagcatctcc ccgtttcacc ccgaaattag gttcattagt aatttccact gaatctgaag
6241 actttgacca aaatcaacca acaagattca ccccagttgg cgttggggtc gaccaggagg
6301 cagactttca acaatggact cttcccaact atgctggcca gctcacccac aacatgaact
6361 tagccccagc tgttgctccc aacttccctg gtgaacaact ccttttcttc cgctcacagt
6421 taccatcttc tggtgggcga tccgatggaa ttctggactg cctggtcccc caagaatggg
6481 tacagcactt ctaccaagaa tcagccccct cccaatctca ggtagccctg gttaggtatg
6541 tcaatcctga cactggtaga gtgttatttg aggccaaact gcacaaattg ggtttcataa
6601 ctatagccaa aaatggtgac tctccaataa cagtccctcc caatggatac ttcagatttg
6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aacagggaat gggcgtagaa
6721 ggattcaata atggctgggg cttttatagc aggattggct ggtgacatgc tcacaaatac
6781 tgtgggatct ttagttaatg caggggctaa tgccattaat caaacaattg attttgaaaa
6841 caataaacat ttgcaaaatg cttcttttaa tcatgataag gaaatgttga aagcacaaat
6901 tgaggcaaca aagaatttac aggccagcat gatttctatc aaacaagggg ttttgaccgc
6961 tggcggcttt tcccctactg atgcggcccg cggggcaatc aacgccccca tgacaaaagt
7021 cctagattgg aatggcacga gacactgggc accaggtgcc acctccacaa cctcgttgtc
7081 gggtggcttt acaaatcaaa ctgtgcacag atctacacca aattttaaag tgaaccaggc
7141 ccccaaatcc gcacccagtg gtgggtcttc agtaaggtca aattcaaccc aaatcactag
7201 cttgagctca cactcgtccg ggtcgtctcg gtccagcggg tctacagttg tcagctcaat
7261 accatcctct aacaggacta gggattgggt cacccaacaa aactttaatt tggaaccaca
7321 catgcctggg tctcttagaa cagcttttgt cactccacca tctagtacag cctctagctc
7381 aggcacagtc tcaactgtac ctaaaaatgt tttggactcc tggacatctg cgtttaacac
7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
7501 agattattat aaatttgatt taaattagat ttaatttgga atctttt
//