Typing tool
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Typing tool
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Complete norovirus genomes
| OP205573 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5069
ORF2: 5050..6672
ORF3: 6672..7478
LOCUS OP205573 7478 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2019-0027_R04-04 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205573
VERSION OP205573.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7478)
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JOURNAL Unpublished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 7478)
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..7478
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2019-0027_R04-04"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2019-01-03"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5069
/gene="ORF1"
CDS <1..5069
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61020.1"
/translation="VASNGNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDEPQK
PPRPPTPELVKRIPPPPPNGEEEEEPIIRYEVKSGISGLPELTTVPQPDVANTAFSVP
PLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTPL
SLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQR
TTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNI
LATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVV
MGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELA
MVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVG
TINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLT
GDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRI
ENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQP
DMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMD
EFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRN
VTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVK
CVQEAIYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDPNESEAKEEAPKSEDDEFII
SSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR
DRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPD
DFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIP
AGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPT
GELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGN
DYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKT
KFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLE
AAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLAD
QASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFG
GLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAA
LEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLL
TLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDK
TEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIP
HSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDL
STWEGDRNLAPNFVNEDGVE"
mat_peptide <1..965
/gene="ORF1"
/product="p48"
mat_peptide 966..2063
/gene="ORF1"
/product="NTPase"
mat_peptide 2064..2594
/gene="ORF1"
/product="p22"
mat_peptide 2595..2993
/gene="ORF1"
/product="VPg"
mat_peptide 2994..3536
/gene="ORF1"
/product="Pro"
mat_peptide 3537..5066
/gene="ORF1"
/product="RdRp"
gene 5050..6672
/gene="ORF2"
CDS 5050..6672
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61021.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFAGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEVNQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6672..7478
/gene="ORF3"
CDS 6672..7478
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61022.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSP
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 ccgttgcaag caacggcaac aacgacaagg aaaaatcttc aggtgaaggc ttatttacaa
61 atatgtcttc caccttaaag aaagccctcg gggctaggcc caaacagcct gccccgagag
121 acgaaccaca aaagccccca agaccaccaa ctcccgagtt ggtcaagagg ataccccctc
181 ctccacctaa tggcgaagaa gaagaagaac caatcattag gtatgaggtt aagagtggaa
241 tctctggcct gcccgagctc acaacagtcc cccaaccgga cgtggctaac acagcattca
301 gtgttccacc actgagcttg agagaaaaca gggaggccaa ggaaccgcta acaggggcaa
361 tattagagat gtgggacggg gagatatacc actatggcct gtacgtggag aaaggcttag
421 tgttgggtgt gcacaaacca cctgcagcca taagcatggc aagagtggag ctgacgccgc
481 tgtcattgta ctggcgtgtg gtgtacactc cccaatacct catctcccct gaaactctca
541 ggaggctcaa cggagaggcg ttcccttaca ccgccttcga caacaactgc tatgcctttt
601 gctgctgggt gttagacctc aatgactcat ggcttagcag gaggatggtg cagagaacaa
661 cgggcttctt cagaccttac caagagtgga acagaaaacc cctgcccacc atggatgact
721 ccaaaataaa gaaggtagct aatatattcc tgtgttcatt gtccacatta ttcaccagac
781 ccataaaaga cctcatagga aaaattaagc cattaaacat attgaacatc ctggcaacgt
841 gtgactggac gtttgccgga atagtggagt ctctgatatt acttgctgaa ctcttcggag
901 ttttctggac acccccagat gtgtctgcta tgatcgctcc cttactcggg gactacgagt
961 tgcaagggcc agaagacctc gccgttgaac tcgtacctgt ggtaatggga gggattggtc
1021 tggtgttggg attcaccaaa gagaaaattg gcaaaatgtt gtcctcagca gcatcaacac
1081 tcagggcttg caaagatctt ggtgcctatg gcttagagat acttaaattg gtcatgaagt
1141 ggttcttccc aaagaaagag gaggccaatg agctagccat ggtgagggct atagaggatg
1201 ccgtactaga tcttgaggca atagaaaaca accacatgac aaccctgttg aaagacaaag
1261 acagcttagc aacgtacatg aaaacactgg acatggagga ggagaaagcc agaaggttgt
1321 ccacaaaatc tgcatcccct gacatagttg ggacaatcaa cgccctgctg gctcggatag
1381 cagcagccag gtcactagtc cacagggcca aggaagagct atctagcagg ataagaccag
1441 tagttgttat gatatctggc aaaccaggaa taggcaagac tcatctggcc agggaggtgg
1501 cgagaaaggt agcgtccact ctcacagggg atcaaagagt cggacttata ccaagaaacg
1561 gtgtggacca ttgggatgca tataaaggtg agagagtcgt gctgtgggac gactatggca
1621 tgagtaaccc catccatgat gcccttcgca tacaagaatt ggctgatacg tgtcccctta
1681 ccttaaattg tgacagaatt gaaaataagg gaaaagtttt tgatagtgaa gtcataataa
1741 ttacaacaaa ccttgccaac ccggccccac ttgattatgt caactttgag gcctgttcta
1801 ggagaattga tttcctggtg tacgctgagg caccagaagt agaaaaggca aaacgggatt
1861 ttcctggtca gccagatatg tggaaggacg ccttcaagcc ggacttttca cacatcaagc
1921 tacagcttgc acctcagggc ggctttgaca agaatggcaa caccccacat gggaaagggg
1981 tgatgaagac cctcactacc ggttctctga ttgcccgtgc atcaggccta ctgcatgaga
2041 ggatggatga atttgaactc caaggtccca caatcaccac cttcaatttc gaccggaaca
2101 gaatcacagc attcagacaa ttggctgcag aaaacaagta tggattggtg gataccatga
2161 aagttggcaa tcaactaaaa ggagtgaaaa ccatggaaga actcaaacaa gcaatcagga
2221 atgtgaccat caagaggtgc cggatcatct acggtggctc cacgtatgac cttgaatctg
2281 atggtaaggg caaagtcttg gtagaaaagg tcaagaatac ctctgtacag accaacaacg
2341 agttggccgg ggccctacac catctcaaac acgcccgaat caggtactat gtcaaatgcg
2401 tgcaagaagc aatctattcc atcatacaaa ttgccggcgc tgcgtttgtc accacgcgta
2461 ttgcacgccg catgaacata caagaactct ggtcgaagcc acaattagat ccaaatgaat
2521 cagaggctaa ggaagaggcc cccaaatcag aagatgacga gttcatcata tcttctaagg
2581 acatcaagga ggaaggaaag aagggcaaaa acaaaactgg ccgtggcaag aaacacactg
2641 cattctccag caagggcttg agcgatgagg agtacgacga gtacaagagg ataagagaag
2701 agagaaatgg gaagtactct atagaggagt atcttcaaga cagagacagg tactatgagg
2761 agctcgccat tgccaaggcc acggaagaag acttctgtga agaggaggag atcaaaatcc
2821 gtcagagaat tttccgtccc accaggaaac aaagaaagga agagagggcc acattggggc
2881 tggtaacagg ttcagaaatc agaaaaagaa accctgatga cttcaaaccc aaaggtaagc
2941 tgtgggccga tgacaacaga agtgttgact acaatgagaa actggacttt gaggcccccc
3001 caagcatatg gtctaggatt gtgagctttg gttctggctg gggcttctgg gtatcaccaa
3061 gcctgttcat aacgtcaact catgtaatcc ccgcaggcat aacagaagca tttggagtcc
3121 ccatcaaaca aattcagatc cacaaatcag gtgaattttg ccgattcaga tttccaaaac
3181 caattagacc agatgtgaca ggaatgatct tggaagaagg tgcgcctgaa ggcaccgtgg
3241 caactgtgct catcaaacgc cccaccggag agctcatgcc tcttgcagcc agaatgggga
3301 cacacgcaac catgaaaatt caaggccgca tggttggcgg acagatgggt atgttgctca
3361 ctggatcaaa tgctaaagga atggatttgg gaacaactcc tggtgactgt ggctgtcctt
3421 acatctataa aaggggcaat gactatatag tcattggggt gcacactgca gcagcccgtg
3481 gtggaaacac cgtcatttgt gccacacagg gaagtgaggg tgaggcaact cttgagggtg
3541 gagatgacaa aggaacatac tgtggggcac ccattttagg ccctgggggt gcaccaaaat
3601 tgagcaccaa aaccaagttt tggaggtcat cgaacacgcc ccttccacca gggacatatg
3661 agcctgccta cctcggtggc cgtgatccgc gcgttaaggg tgggccctcc ctgcagcagg
3721 taatgagaga ccagttgaag ccattcactg aacccagggg caaacctcca agaccaagtg
3781 tattagaagc agccaaacaa accattatca atgttctcga acaaaccctg gaccctccac
3841 aaaaatggac atacgcacag gcgtgtgcct cacttgacaa aaccacctcc agcgggcacc
3901 cccatcacgt ccgaaagaat gaattctgga atggtgagac cttcacaggt aaattggcag
3961 accaagcatc aaaagcaaac ctaatgtttg aggaagggaa acacatgaca ccagtgtata
4021 cagcagcact caaggacgag ctagttaaga ctgagaaaat ctatggaaag atcaagaaga
4081 gactgctctg gggctctgac ttgtccacca tgatccggtg cgctaggtca tttggtgggc
4141 tcatggacga gatgaaggca cactgcatat cactcccagt acgagttggc atgaacatga
4201 atgaagatgg cccaataata tttgagaaac attccagata caaataccac tatgatgcag
4261 actactctcg ttgggattca acacaacaga gggcagtact agcagcagcc ttggaaatca
4321 tggtcagatt ctctgcagaa ccacaattgg cacaaatagt cgctgaggat ctactggccc
4381 ctagtgtagt agatgtagga gactttaaaa tcacaataaa tgaagggctc ccatctggtg
4441 tgccatgcac ttctcaatgg aactccatcg cacactggct gctaactctc tgtgccttgt
4501 ctgaagtcac caaactgtcc cctgacatta tacaagcaaa ttccatgttc tcattttacg
4561 gtgatgacga gattgtcagc accgacataa aattggaccc tgaacagcta accgccaagt
4621 tgaaggagta cggcctgaaa ccaacccgcc cagacaagac cgaggggccc ctgatcatca
4681 gtgaagattt gaacggactc actttcctcc gaaggacggt gactcgtgac ccagctggct
4741 ggtttggaaa gctggaccaa agttcaattt tgaggcagat gtactggact agaggaccaa
4801 accatgaaga ccccaatgag acaatgatac cccattctca aagacccata cagctcatgg
4861 cactgcttgg tgaagcctct cttcacggac cctctttcta cagtagaatt agtaaattgg
4921 tcataactga actcaaagaa ggtgggatgg acttttacgt gccaaggcag gaacccatgt
4981 tcaggtggat gagattttct gacttgagca cgtgggaggg cgatcgcaat ctggctccca
5041 atttcgtgaa tgaagatggc gtcgagtgac gccaacccat ctgatgggtc cgcagccaac
5101 ctcgtaccag aggtcaacaa tgaggttatg gctttggagc ccgttgttgg tgccgctatt
5161 gcggcacctg tagcgggcca acaaaatgta attgacccct ggattagaaa taattttgta
5221 caagcccctg gtggggagtt tacagtgtcc cctagaaacg ctccaggtga aatactatgg
5281 agcgcgcccc taggccctga cctaaatccc tacctatccc atttggccag aatgtacaat
5341 ggttatgcag gtggttttga agtgcaggta attctcgcgg ggaacgcgtt caccgccggg
5401 aagattatat ttgcagcagt cccaccaaat tttccaactg aaggcttaag tcctagccag
5461 gtcactatgt tcccccatat aatagtagat gttagacaac tagaacctgt gctgattccc
5521 ttacctgatg ttaggaataa tttctatcat tacaatcagt caaatgatcc cactattaag
5581 ttgatagcaa tgttgtacac accacttagg gctaataatg ctggagatga tgttttcaca
5641 gtttcgtgcc gagttctcac gagaccatcc cccgattttg atttcatatt tttagtgcca
5701 cccacagttg agtcaagaac taaaccattc tctgtcccag ttttaactgt tgaggagatg
5761 accaattcaa gattccccat ccctttggaa aagttgttca caggccccag cagtgccttt
5821 gttgttcaac cacaaaacgg caggtgcaca actgatggcg tgctcctagg caccacccaa
5881 ctttctcctg tcaacatctg caccttcaga ggggatgtca cccacatcac aggtagtcgc
5941 aactacacaa tgaatttggc ttctcaaaat tggaacaact atgacccaac agaagaaatc
6001 ccagcccctc taggaactcc agattttgca gggaagattc aaggcatgct cacccaaacc
6061 acaaggacag acggttcaac acgcggccac aaagctacag tgtacactgg gagcgccgac
6121 tttgctccaa aactgggtag agttcaattt gaaactgaca cagaccatga ttttgaagtt
6181 aatcaaaaca caaagttcac cccagtcggt gtcatccaag atggtagcac cacccaccga
6241 aacgaacccc aacagtgggt gctcccaagt tactcaggca gaaatactca caatgtacat
6301 ttggcccccg ctgtagcccc cacctttccg ggtgagcaac ttctcttttt cagatccacc
6361 atgcccggat gcagcgggta ccccaacatg gatttggact gtctgctccc ccaggaatgg
6421 gtgcagtact tctaccaaga ggcagcccca gcacaatctg atgtggctct gctaagattt
6481 gtgaacccag acacaggtag ggttttgttt gagtgcaagc ttcacaaatc aggctatgtt
6541 acagtggctc acactggcca acatgacttg gttatccccc ccaatggtta ctttaggttt
6601 gattcctggg tcaaccagtt ctacacgctt gcccccatgg gaaatggaac ggggcgtaga
6661 cgtgcagtat aatggctgga gctttctttg ctggattggc atctgatgtc cttggttctg
6721 gacttggttc ccttatcaat gctggggctg gggccatcaa tcaaaaagtt gaatttgaaa
6781 ataacagaaa attgcaacaa gcatccttcc aatttagcag caatctgcaa caggcttcct
6841 ttcaacatga taaagagatg ctccaagcac aaattgaggc caccaaaaag ctacaacagg
6901 aaatgatgaa agttaagcag gcaatgctcc tagagggtgg gttctctgag acagatgcag
6961 cccgcggggc aattaacgcc cccatgacaa aagctttgga ttggagcggg acaaggtact
7021 gggctccaga tgctaggatt acaacataca atgcaggcca cttttccacc cctcaaccat
7081 cgagggcact gccaggaaga gctaatctta gggatgctgt ccctgctcgg ggaccctcca
7141 ataaatctcc taactcttct actgccacct ctgtgtattc aaatcaaact atttcaacga
7201 gacttggttc tacagctggt tctggaacca gtgtctcgag cctcccgtca actgcaagga
7261 ctaggagttg ggttgaggat caaaatagga atttgtcacc tttcatgagg ggggcccaca
7321 acatatcatt tgtcacccca ccatctagca gatcctctag ccaaggcaca gtctcaaccg
7381 tgcctaaaga ggttttggac tcctggactg gcgctttcaa cacgcgcagg cagcctctct
7441 tcgctcacat tcgtaggcga ggggagtcac gggtgtaa
//