Typing tool
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Typing tool
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Complete norovirus genomes
| OP205580 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS OP205580 7513 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0511_R04-12 nonstructural
polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP205580
VERSION OP205580.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7513)
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JOURNAL Unpublished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 7513)
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..7513
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0511_R04-12"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-12-10"
/note="genotype: GII.4 Sydney[P16]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV61041.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRGEPQKPPRPPTPELVKRIPPPPPNGGEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLNRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILFAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVERVKNTSVQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
TPKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQRWSYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 5..1000
/gene="ORF1"
/product="p48"
mat_peptide 1001..2098
/gene="ORF1"
/product="NTPase"
mat_peptide 2099..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..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61042.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61043.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNTGRFSTPQPSRALPGRDNLRDAVPARGSSNKSS
NSSAATSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
121 cctcggggca aggcccaaac agcctgcccc gagaggcgaa ccacaaaagc ccccaagacc
181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg gagaagaaga
241 agaaccagtc atcaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
301 agtccctcaa ccagacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga
361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg atggagagat
421 ataccactac ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
481 agccataagt atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta
541 cactccccaa tacctcatct cccctgagac tctcaggagg ctcaacggag aggcattccc
601 ttacaccgcc ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga
661 ctcatggctt aacaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga
721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa attaagaagg tagcaaatat
781 attcctatgt tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat
841 taaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ctggaatagt
901 ggagtctctg atattgtttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagagg acctcgccgt
1021 tgaactcgta cctgtggtaa tgggagggat tggcctggtg ttgggattca ccaaagagaa
1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc
1201 caatgagcta gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga
1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat
1381 agttgggaca atcaacgctc tgctggctcg aatagcagcg gccaggtcat tagtccacag
1441 ggccaaggaa gagttatcta gcaggataag accagtagtt gttatgatat ctggcaaacc
1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac
1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa
1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct
1681 tcgcatacaa gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa
1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc
1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
1861 tgaggcacca gaagtggaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacctc agggcggttt
1981 tgataagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc
2041 tctgattgcc cgtgcatcag gcctattgca tgagaggatg gatgaatttg aactccaagg
2101 ccccacaatc accaccttca atttcgaccg gaacagaatc acagcattca gacaattggc
2161 tgcagaaaac aagtatggat tggtggacac catgaaagtt ggcaatcaac taaaaggagt
2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgtcggat
2281 catttacggt ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga
2341 aagggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccatct
2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
2461 acaaattgcc ggcgctgcgt ttgtcaccac ccgcattgca cgccgcatga acatacaaga
2521 actctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggagg agacccccaa
2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
2701 cgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga
2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
2881 gaaacaaagg aaggaagaaa gggccacatt agggttagtg acaggttcag aaatcagaaa
2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt
3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag
3061 ctttggttct ggctggggct tctgggtatc accaagtctg ttcataacat caactcatgt
3121 aatccccgcg ggcataacag aagcatttgg agtccccatc aaacagattc agatccacaa
3181 atcaggtgaa ttttgccgat ttagattccc aaaaccaatt aggccagacg tgacaggaat
3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac
3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
3361 ccgcatggtt ggcggacaga tgggcatgtt gctcactgga tcaaatgcta aaggaatgga
3421 tttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
3481 tatagccatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac
3541 acaaggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg
3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc accaaaacta aattttggag
3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcttaccttg gtggtcgtga
3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtaatg agagaccagt tgaagccatt
3781 cactgaaccc aggggtaaac ctccaagacc aagtgtactg gaagcagcca aacaaaccat
3841 tatcaatgtc ctcgaacaaa ccctggatcc tccacaaaga tggtcatacg cacaggcgtg
3901 tgcctcactt gacaaaacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt
3961 ctggaatggt gagaccttca ctggcaaatt ggcagaccaa gcatcaaaag caaacctaat
4021 gtttgaggaa gggaaacata tgacaccagt gtatacagca gcactcaagg acgagttagt
4081 caagactgag aaaatctatg gaaagatcaa gaagagattg ctctggggct ctgacttgtc
4141 caccatgatc cggtgcgcta ggtcatttgg tgggctcatg gatgagatga aggcacactg
4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
4261 gaaacactcc agatacaaat atcactatga tgcagactac tctcgttggg attcaacaca
4321 acagagggca gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca
4381 attggcacaa atagtcgctg aggatctgct ggcccctagt gtagtagatg taggagactt
4441 taaaatcaca ataaatgaag ggctcccatc tggtgtacca tgcacttccc aatggaactc
4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
4561 cattatacaa gcaaactcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
4621 cataaaactg gaccctgaac agttaaccgc caagctgaag gagtacggcc tgaaaccaac
4681 ccgaccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacttt
4741 cctccgaagg acggtgactc gcgacccagc tggctggttt gggaaactgg accaaagctc
4801 aattttgagg cagatgtact ggactagagg gccaaaccat gaagacccca atgagacaat
4861 gataccccat tctcaaagac ccatacagct catggcactg cttggtgaag cctctctcca
4921 cggaccctct ttctacagta aaatcagtaa attggtcata actgaactca aagaaggtgg
4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg
5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag
5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagtccta gccaggtcac tatgttcccc catataatag
5521 tagatgttag acaattagaa cctgtgctga ttcccttacc cgatgtcagg aataatttct
5581 atcattataa tcaatcaaat gactccacta ttaagttgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggg gatgatgttt tcacagtctc gtgccgagtt ctcacgagac
5701 catcccccga ttttgatttt atatttttag tgccacccac agttgaatca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggc cccagcagtg cctttgttgt tcaaccgcaa aatggcagat
5881 gcacaactga tggcgtgctc ctaggcacta cccaactgtc tcctgtcaac atctgcacct
5941 tcagagggga tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc
6001 aaaactggaa taactatgac ccaacagaag aaatcccagc ccctctagga actccagatt
6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg
6121 gtcacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacagac catgactttg aagccaacca aaacacaaag ttcaccccag
6241 tcggtgtcat tcaagatggt agcaccaccc accgaaatga accccaacag tgggtgcttc
6301 caagttactc aggcagaaat actcacaatg tacatctggc ccctgctgta gcccccacct
6361 tcccgggtga acaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgcctg ctcccccagg aatgggtgca gtacttctat caagaggcag
6481 ccccagcaca atctgatgtg gctctgttaa gatttgtgaa cccagataca ggtagggttt
6541 tgtttgagtg caagcttcac aaatcaggct atgtcacagt ggctcacact ggccaacatg
6601 atttggttat cccccccaat ggttacttta gatttgattc atgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt ggtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtcctcgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaact tgcaacaggc ttcctttcaa catgataaag agatgcttca
6901 agcacaaatt gaggccacca aaagactaca acaggaaatg atgaaagtta agcaggcagt
6961 gctcttagag ggtggattct ctgagacaga tgcagcccgc ggggcaatta acgctcccat
7021 gacaaaagct ttggattgga gcgggacaag gtactgggct cccgatgcta ggactacaac
7081 atacaataca ggccgcttct ccacccctca accatcgagg gcactgccag gaagagataa
7141 cctcagggat gctgtccctg ctcggggatc ctccaacaaa tcttctaact cttctgctgc
7201 cacctctgtg tactcaaatc aaactgtctc aacgagactt ggttctacag ctggttctgg
7261 aaccagtgtc tcaagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
7321 taggaatttg tcacccttca tgaggggggc tcacaacata tcatttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
7501 gtcacgggtg taa
//