Typing tool
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Typing tool
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Complete norovirus genomes
| OP205571 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5072
ORF2: 5053..6675
ORF3: 6675..7481
LOCUS OP205571 7481 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0495_R04-02 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205571
VERSION OP205571.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7481)
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JOURNAL Unpublished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 7481)
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..7481
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0495_R04-02"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-12-07"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5072
/gene="ORF1"
CDS <1..5072
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61014.1"
/translation="AVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDEPQ
KPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQPGVANTAFSV
PPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTP
LSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQ
RTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILN
ILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPV
VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANEL
AMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIV
GTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTL
TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDR
IENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQ
PDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERM
DEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIR
NVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYV
KCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEETPKSEDDEFI
ISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQD
RDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRRQRKEERATLGLVTGSEIRKRNP
DDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVI
PAGVTEAFGVPIKQIQIHKSGEFCRLRFPKPIRPDVTGMILEEGAPEGTVATVLIKRP
TGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRG
NDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTK
TKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVL
EAAKQTIINVFEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLA
DQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSF
GGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAA
ALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWL
LTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPD
KTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMI
PHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSD
LSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..968
/gene="ORF1"
/product="p48"
mat_peptide 969..2066
/gene="ORF1"
/product="NTPase"
mat_peptide 2067..2597
/gene="ORF1"
/product="p22"
mat_peptide 2598..2996
/gene="ORF1"
/product="VPg"
mat_peptide 2997..3539
/gene="ORF1"
/product="Pro"
mat_peptide 3540..5069
/gene="ORF1"
/product="RdRp"
gene 5053..6675
/gene="ORF2"
CDS 5053..6675
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61015.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6675..7481
/gene="ORF3"
CDS 6675..7481
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61016.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARVTTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRDLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa ggcttattca
61 caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag cctgccccga
121 gagatgaacc acaaaagccc ccaagaccac caactcccga gttggtcaag aggatacccc
181 ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgat gttaagagtg
241 ggatctctgg cctgcccgag ctcacaacag tcccccaacc gggcgtggcc aacacagcat
301 tcagtgttcc accactgagc ttgagagaga acagggaggc caaggaaccg ctaacagggg
361 caatattaga gatgtgggac ggagagatat accactatgg cctgtacgtg gagaaaggct
421 tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg gagctgacgc
481 cactgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc cctgaaactc
541 tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaacaac tgctatgcct
601 tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg gtgcaaagaa
661 caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgccc accatggatg
721 actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca ttattcacca
781 gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaac atcctggcaa
841 cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgct gaactcttcg
901 gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc ggggactacg
961 agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtgatg ggagggattg
1021 gtttggtgtt gggattcacc aaagagaaaa ttggaaaaat gttgtcctca gcagcatcaa
1081 cactcagggc ttgcaaagat cttggcgcct atggcttaga gatactcaaa ttggtcatga
1141 agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg gccatagagg
1201 atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg ctgaaagata
1261 aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa gccagaaggt
1321 tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg ctggctcgaa
1381 tagcagcagc caggtcatta gtccacaggg ccaaggaaga gctatctagc aggataagac
1441 cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg gccagggagg
1501 tggcaagaaa ggtagcatcc actctcacag gggatcaaag agtcggactc ataccaagaa
1561 acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg gacgactatg
1621 gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat acgtgtcccc
1681 ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt gaagtcataa
1741 taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt gaggcctgtt
1801 ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag gcaaaacggg
1861 attttcctgg tcagccagat atgtggaagg acgcctttaa gtcggacttt tcacacatca
1921 agctacagct tgcacctcag ggtggctttg acaagaatgg caacacccca catgggaaag
1981 gggtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc ctactgcatg
2041 agaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat tttgaccgga
2101 acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg gtggatacca
2161 tgaaagttgg caaccaacta aaaggagtga aaaccatgga agagctcaaa caagcaatca
2221 ggaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtat gaccttgaat
2281 ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta cagaccaaca
2341 acgaattggc cggggccctg caccatctca aacacgcccg aatcaggtac tatgtcaaat
2401 gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt gtcaccacgc
2461 gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta gatcaaaatg
2521 aatcagaggc taaggaagag acccccaagt cagaagatga cgagttcatc atatcttcca
2581 aggacatcaa ggaggaggga aagaagggca aaaacaaaac tggccgtggc aagaaacaca
2641 ctgcattctc tagcaagggc ttgagcgatg aggagtatga cgagtacaag aggataagag
2701 aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac aggtactatg
2761 aggagctcgc catcgccaag gccacggaag aagacttctg tgaagaggag gagatcaaaa
2821 tccgtcagag aattttccgt cccaccagga gacaaagaaa ggaagagagg gccacattag
2881 ggctggtaac aggttcagaa atcagaaaaa gaaaccccga tgacttcaaa cccaaaggga
2941 agctgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac tttgaggccc
3001 ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc tgggtatcac
3061 caagcctgtt cataacatca actcatgtaa tccccgcagg cgtaacagaa gcatttggag
3121 tccccatcaa acaaattcag atccacaaat caggtgaatt ttgccgactc agattcccaa
3181 aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct gaaggcaccg
3241 tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca gccagaatgg
3301 gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg ggtatgttgc
3361 tcactggatc aaatgctaaa ggtatggatt tgggaacaac tcctggtgac tgtggctgtc
3421 cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact gcagcagccc
3481 gtggtggaaa caccgtcatc tgtgccacgc agggaagtga gggcgaggcg actcttgagg
3541 gtggagatga caaaggaaca tactgtgggg cacccatttt aggccctggg ggtgcaccaa
3601 aattgagcac caaaaccaaa ttctggaggt catcgaacac gccccttcca ccagggacat
3661 atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc tctttgcagc
3721 aggtgatgag agaccagttg aagccattca ctgaacccag gggcaaacct ccaagaccaa
3781 gtgtattgga agcagccaaa caaaccatta tcaatgtttt cgaacaaacc ctggaccctc
3841 cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc tccagcggac
3901 atcctcacca cgtccgaaag aatgaattct ggaatggtga gaccttcact ggtaaattgg
3961 cagaccaagc gtcaaaagca aacctaatgt ttgaggaagg gaaacacatg acaccagtgt
4021 atacagcagc actcaaggac gagctagtta agactgagaa aatctatgga aaaatcaaga
4081 agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg tcatttggtg
4141 ggctcatgga cgagatgaag gcacactgca tatcactccc agtacgagtt ggcatgaata
4201 tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat cactatgatg
4261 cagactactc tcgttgggat tcaacacaac aaagggcagt actagcagca gccttggaaa
4321 tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag gatctactgg
4381 cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg ctcccatctg
4441 gtgtgccatg cacttcccaa tggaactcca tcgcacactg gctgctaact ctctgtgcct
4501 tgtctgaagt caccaaactg tcccctgaca ttatacaagc aaattccatg ttctcatttt
4561 acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag ttgaccgcca
4621 agttgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgaggga cccctgatca
4681 tcagtgaaga tctgaacgga ctcactttcc tccgaaggac ggtgactcgt gacccagctg
4741 gctggtttgg aaaactggac cagagttcaa ttttgaggca gatgtactgg actagaggac
4801 caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc atacagctca
4861 tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaga atcagtaaat
4921 tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg caggaaccca
4981 tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc aatctggctc
5041 ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg gtccgcagcc
5101 aacctcgtac cagaggtcaa caatgaggtt atggctttgg agcccgttgt tggtgccgct
5161 attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag aaataatttt
5221 gtacaagccc ctggtgggga gttcacagtg tcccctagaa acgctccagg tgaaatacta
5281 tggagcgcgc ccctaggccc tgatctaaat ccctacctat cccatttggc cagaatgtac
5341 aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc gttcaccgcc
5401 gggaagatta tatttgcagc agtcccacca aattttccaa ctgaaggctt aagtcccagc
5461 caggtcacta tgttccccca tataatagta gatgttagac aattagaacc tgtgctgatt
5521 cccttacccg atgttaggaa taatttctat cattacaatc agtcaaatga ttccactatt
5581 aagttgatag caatgttgta cacaccactt agggctaata atgctggaga tgatgttttc
5641 acagtttcgt gccgagttct cacgaggcca tcccccgatt ttgatttcat atttttagtg
5701 ccccccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac tgttgaggag
5761 atgaccaatt caaggttccc catccctttg gaaaagttgt tcacaggccc cagtagtgcc
5821 tttgttgttc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct aggcaccacc
5881 caactttctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat cacaggtagt
5941 cgcaactaca cgatgaattt ggcttcccaa aattggaaca actatgaccc gacagaagaa
6001 atcccagccc ctctagggac tccagatttt gtagggaaga ttcaaggcat gctcacccaa
6061 accacaagga cagacggttc aacacgcggc cacaaagcaa cagtgtacac tgggagcgcc
6121 gactttgctc caaaactggg tagagttcaa tttgaaactg acacagacca tgattttgaa
6181 gctaatcaaa acacaaaatt taccccagtc ggtgtcatcc aagatggtag caccacccac
6241 cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaatac tcacaatgta
6301 catctggccc ctgctgtagc ccccaccttt ccgggtgagc aacttctctt tttcagatcc
6361 accatgcccg gatgcagcgg gtaccccaac atggatttgg actgcctgct cccccaggaa
6421 tgggtgcagt acttctacca agaggcagcc ccagcacaat ccgatgtggc tctgctaaga
6481 tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcataa atcaggctat
6541 gttacagtgg ctcacactgg ccaacatgat ttggttatcc cccccaatgg ttactttagg
6601 tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg aacggggcgt
6661 agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat gtccttggct
6721 ctggacttgg ttcccttatc aatgctgggg ctggggccat caaccaaaaa gttgaatttg
6781 aaaataacag aaaattgcaa caagcatcct tccaatttag cagcaatctg caacaggctt
6841 cctttcaaca tgataaagag atgctccaag cacaaattga ggccactaaa aagctacaac
6901 aggaaatgat gaaagttaag caggcaatgc tcttagaggg tgggttctct gagacagatg
6961 cagcccgcgg ggcaatcaat gcccccatga caaaagtttt ggattggagc gggacaaggt
7021 actgggctcc agatgctagg gttacaacat acaatgcagg ccacttttcc acccctcaac
7081 catcgagggc actgccagga agagctaatc ttagggatgc tgtccctgct cggggaccct
7141 ccaacaaatc ttctaactct tctactgcta cctctgtgta ctcaaatcaa actatttcaa
7201 cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagtctcccg tcaactgcaa
7261 ggactaggag ctgggttgag gatcaaaata gggatttgtc tcctttcatg aggggggccc
7321 acaacatatc atttgtcacc ccaccatcta gcagatcctc tagccaaggc acagtctcaa
7381 ccgtgcctaa agagattttg gactcctgga ctggcgcttt taacacgcgc aggcagcctc
7441 tcttcgctca cattcgtaag cgaggggagt cacgggtgta a
//