Typing tool
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Typing tool
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Complete norovirus genomes
| OP205574 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5089
ORF2: 5070..6692
ORF3: 6692..7498
LOCUS OP205574 7498 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0343_R04-05 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205574
VERSION OP205574.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7498)
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JOURNAL Unpublished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 7498)
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..7498
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0343_R04-05"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-08-30"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5089
/gene="ORF1"
CDS <1..5089
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="UUV61023.1"
/translation="SNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPA
PRDEPQKSPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVA
NTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMA
RVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWL
SRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIK
PLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDIA
VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
EEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKS
ASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVAR
KVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPL
TLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
RDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
LLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEE
LKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHA
RIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEAPKS
EDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSE
IRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFI
TSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVAT
VLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCP
YIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGA
PKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGET
FTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMI
RCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGL
KPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED
PNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..985
/gene="ORF1"
/product="p48"
mat_peptide 986..2083
/gene="ORF1"
/product="NTPase"
mat_peptide 2084..2614
/gene="ORF1"
/product="p22"
mat_peptide 2615..3013
/gene="ORF1"
/product="VPg"
mat_peptide 3014..3556
/gene="ORF1"
/product="Pro"
mat_peptide 3557..5086
/gene="ORF1"
/product="RdRp"
gene 5070..6692
/gene="ORF2"
CDS 5070..6692
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61024.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFAGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEVNQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6692..7498
/gene="ORF3"
CDS 6692..7498
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61025.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaagg aaaaatcttc
61 aggtgaaggc ttatttacaa atatgtcttc caccttaaag aaagccctcg gggctaggcc
121 caaacagcct gccccgagag acgaaccaca aaagtcccca agaccaccaa ctcccgagtt
181 ggtcaagagg ataccccctc ctccacctaa tggcgaagaa gaagaagaac cagtcattag
241 gtatgaggtt aagagtggaa tctctggcct gcccgagctc acaacagtcc cccaaccgga
301 cgtggccaac acagcattca gtgttccacc actgagcttg agagaaaaca gggaggccaa
361 ggaaccgcta acaggggcaa tattagagat gtgggacggg gagatatacc actatggcct
421 atacgtggag aaaggcttag tgttgggtgt gcacaaacca cctgcagcca taagcatggc
481 aagagtggag ctgacgccgc tgtcattgta ctggcgtgtg gtgtacactc cccaatacct
541 catctcccct gaaactctca ggaggctcaa cggagaggcg ttcccttaca ccgccttcga
601 caacaactgc tatgcctttt gctgctgggt gttagacctc aatgactcat ggcttagcag
661 gaggatggtg caaagaacaa cgggcttctt cagaccttac caagagtgga acagaaaacc
721 cctgcccacc atggatgact ccaaaataaa gaaggtagca aatatattcc tatgttcatt
781 gtccacatta ttcaccagac ccataaaaga cctcatagga aaaattaagc cattaaacat
841 attgaacatc ctggcaacgt gtgactggac gtttgccgga atagtggagt ctctgatatt
901 acttgctgaa ctcttcggag ttttctggac acccccagat gtgtctgcta tgatcgctcc
961 cttactcggg gactacgagt tgcaagggcc agaagacatc gccgttgaac tcgtacctgt
1021 ggtaatggga gggattggtc tggtgttggg attcaccaaa gagaaaattg gcaaaatgtt
1081 gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg gcttagagat
1141 actcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaatg agctagccat
1201 ggtgagggcc atagaggatg ccgtactaga tcttgaggca atagaaaaca accacatgac
1261 aaccctgttg aaagacaaag acagcttagc aacgtacatg aaaacactgg acatggagga
1321 ggagaaagcc agaaggttgt ccacaaaatc tgcatcccct gacatagttg ggacaatcaa
1381 cgccctgctg gctcggatag cagcagccag gtcactagtc cacagggcca aggaagagct
1441 atctagcagg ataagaccag tagttgttat gatatctggc aaaccaggaa taggcaaaac
1501 tcatctggcc agggaggtgg caagaaaggt agcgtccact ctcacagggg atcaaagagt
1561 cggacttata ccaagaaacg gtgtggacca ttgggatgca tataaaggtg agagagtcgt
1621 gctgtgggac gactatggca tgagtaaccc cattcatgat gcccttcgca tacaagaatt
1681 ggctgatacg tgtcccctta ccttaaattg tgacagaatt gaaaataagg gaaaagtttt
1741 tgatagtgaa gtcataataa ttacaacaaa ccttgccaac ccagccccac ttgattatgt
1801 caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg caccagaagt
1861 agaaaaggca aaacgggatt ttcctggtca gccagatatg tggaaggacg ccttcaagcc
1921 ggacttttca cacatcaagc tacagcttgc acctcagggc ggctttgaca agaatggcaa
1981 caccccacat gggaaagggg tgatgaagac cctcactacc ggttctctga ttgcccgtgc
2041 atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca caatcaccac
2101 cttcaatttc gatcggaaca gaatcacagc attcagacaa ttggctgcag aaaacaagta
2161 tggattggtg gataccatga aagttggcaa tcaactaaaa ggagtgaaaa ccatggaaga
2221 actcaaacaa gcaatcagga atgtgaccat caagaggtgc cggatcatct acggtggctc
2281 cacgtatgac cttgaatctg atggcaaggg caaagtcttg gtagaaaagg tcaagaacac
2341 ctctgtacag accaacaacg agttggccgg ggccctacac catctcaaac acgcccgaat
2401 caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa ttgccggcgc
2461 tgcgtttgtc accacgcgta ttgcacgccg catgaacata caagaactct ggtcgaagcc
2521 acaattagat caaaatgaat cagaggctaa ggaagaggcc cccaagtcag aagatgacga
2581 gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa acaaaactgg
2641 ccgtggcaag aaacacactg cattctccag caagggcttg agcgatgagg agtatgacga
2701 gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggagt atcttcaaga
2761 cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagaag acttctgtga
2821 agaggaggag atcaaaatcc gtcagagaat tttccgtccc accaggaaac aaagaaagga
2881 agagagggcc acattggggc tggtaacagg ttcagaaatc agaaaaagaa accctgatga
2941 cttcaaaccc aaaggtaagc tgtgggccga tgacaacaga agtgttgact acaatgagaa
3001 actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg gttctggctg
3061 gggcttctgg gtatcaccaa gcctgttcat aacatcaact catgtaatcc ccgcaggcat
3121 aacagaagca tttggagtcc ccatcaaaca aattcagatc cacaaatcag gtgaattttg
3181 ccgattcaga ttcccaaaac caattagacc agatgtgaca ggaatgatct tggaagaagg
3241 tgcgcctgaa ggcaccgtgg caactgtgct catcaaacgc cccaccggag agctcatgcc
3301 tcttgcagcc agaatgggga cacacgcaac catgaaaatt caaggccgca tggttggcgg
3361 acagatgggt atgttgctca ctggatcaaa tgctaaagga atggatttgg gaacaactcc
3421 tggtgactgt ggctgtcctt acatctataa aaggggcaat gactatatag tcattggggt
3481 gcacactgca gcagcccgtg gtggaaacac cgtcatctgt gccacacagg gaagtgaggg
3541 tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac ccattttagg
3601 ccctgggggt gcaccaaaat tgagcaccaa aaccaagttt tggaggtcat cgaacacgcc
3661 ccttccacca gggacatatg agcctgccta cctcggtggt cgtgatccgc gcgttaaggg
3721 tgggccctcc ttgcagcagg taatgagaga ccagttgaag ccattcactg aacccagggg
3781 caaacctcca agaccaagtg tattggaagc agccaaacaa accattatca atgttctcga
3841 acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct cacttgacaa
3901 aaccacctcc agcgggcatc cccatcacgt ccgaaagaat gaattctgga atggtgagac
3961 cttcacaggt aaattggcag accaagcatc aaaagcaaac ctaatgtttg aggaagggaa
4021 acacatgaca ccagtgtata cagcagcgct caaggacgag ctagttaaga ctgagaaaat
4081 ctatggaaag atcaagaaga gactgctctg gggctctgac ttgtccacca tgatccggtg
4141 cgctaggtca tttggtgggc tcatggacga gatgaaggca cactgcatat cactcccagt
4201 acgagttggc atgaacatga atgaagatgg cccaataata tttgagaaac attccagata
4261 caaataccac tatgatgcag actactctcg ttgggattca acacaacaga gggcagtact
4321 agcagcagcc ttggaaatca tggtcagatt ctctgcagaa ccacaattgg cacaaatagt
4381 cgctgaagat ctactggccc ctagtgtagt agatgtagga gactttaaaa tcacaataaa
4441 tgaagggctc ccatctggtg tgccatgcac ttctcaatgg aactccatcg cacactggct
4501 gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta tacaagcaaa
4561 ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa aattggaccc
4621 tgaacagcta accgccaagt tgaaggagta cggcctgaaa ccaacccgcc cagacaagac
4681 cgaggggccc ctgatcatca gtgaagattt gaacggactc actttcctcc gaaggacggt
4741 gactcgtgac ccagctggct ggtttggaaa gctggaccaa agttcaattt tgaggcagat
4801 gtactggact agaggaccaa accatgaaga ccccaatgag acaatgatac cccattctca
4861 aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac cctctttcta
4921 cagtagaatt agtaaattgg tcataactga actcaaagaa ggtgggatgg acttttacgt
4981 gccaaggcag gaacccatgt tcaggtggat gagattttct gacttgagca cgtgggaggg
5041 cgatcgcaat ctggctccca attttgtgaa tgaagatggc gtcgagtgac gccaacccat
5101 ctgatgggtc cgcagccaac ctcgtaccag aggtcaacaa tgaggttatg gctttggagc
5161 ccgttgttgg tgccgctatt gcggcacctg tagcgggcca acaaaatgta attgacccct
5221 ggattagaaa taattttgta caagcccctg gtggggagtt tacagtgtcc cctagaaacg
5281 ctccaggtga aatactatgg agcgcgcccc taggccctga cctaaatccc tacctatccc
5341 atttggccag aatgtacaat ggttatgcag gtggttttga agtgcaggta attctcgcgg
5401 ggaacgcgtt caccgccggg aagattatat ttgcagcagt cccaccaaat tttccaactg
5461 aaggcttaag tcctagccag gtcactatgt tcccccatat aatagtagat gttagacaat
5521 tagaacctgt gctgattccc ttacccgatg ttaggaataa tttctatcat tacaatcagt
5581 caaatgattc cactattaag ttgatagcaa tgttgtacac accacttagg gctaataatg
5641 ctggagatga tgttttcaca gtttcgtgcc gagttctcac gagaccatcc cccgattttg
5701 atttcatatt tttagtgcca cccacagttg agtcaagaac taaaccattc tctgtcccag
5761 ttttaactgt tgaggagatg accaattcaa gattccccat ccctttggaa aagttgttca
5821 caggccccag cagtgccttt gttgttcaac cacaaaacgg caggtgcaca actgatggcg
5881 tgctcctagg caccacccaa ctttctcctg tcaacatctg caccttcaga ggggatgtca
5941 cccacatcac aggtagtcgc aactacacaa tgaatttggc ttctcaaaat tggaacaact
6001 atgacccaac agaagaaatc ccagcccctc taggaactcc agatttcgca gggaagattc
6061 aaggcatgct cacccaaacc acaaggacag acggttcaac acgcggccac aaagctacag
6121 tgtacactgg gagcgccgac tttgctccaa aactgggtag agttcaattt gaaactgaca
6181 cagaccatga ttttgaagtt aatcaaaaca caaagttcac cccagtcggt gtcatccaag
6241 atggtagcac cacccaccga aacgaacccc aacagtgggt gctcccaagt tactcgggca
6301 gaaatactca caatgtacat ttggcccccg ctgtagcccc cacctttccg ggtgagcaac
6361 ttctcttttt cagatccacc atgcccggat gcagcgggta ccccaacatg gatttggact
6421 gtctgctccc ccaggaatgg gtgcagtact tctaccaaga ggcagcccca gcacaatctg
6481 atgtggctct gctaagattt gtgaacccag acacaggtag ggttttgttt gagtgcaagc
6541 ttcacaaatc aggctatgtt acagtggctc acactggcca acatgacttg gttatccccc
6601 ccaatggtta ctttaggttt gattcctggg tcaaccagtt ctacacgctt gcccccatgg
6661 gaaatggaac ggggcgtaga cgtgcagtat aatggctgga gctttctttg ctggattggc
6721 atctgatgtc cttggctctg gacttggttc ccttatcaat gctggggctg gggccatcaa
6781 ccaaaaagtt gaatttgaaa ataacagaaa attgcaacaa gcatccttcc aatttagcag
6841 caatctgcaa caggcttcct ttcaacatga taaagagatg ctccaagcac aaattgaggc
6901 caccaaaaag ctacaacagg aaatgatgaa agttaagcag gcaatgctcc tagagggtgg
6961 gttctctgag acagatgcag cccgcggggc aattaacgcc cccatgacaa aagctttgga
7021 ctggagcggg acaaggtact gggctccaga tgctaggatt acaacataca atgcaggcca
7081 cttttccacc cctcaaccat cgagggcact gccaggaaga gctaatctta gggatgctgt
7141 ccctgctcgg ggaccctcca ataaatcttc taactcttct actgccacct ctgtgtattc
7201 aaatcaaact atttcaacga gacttggttc tacagctggt tctggaacca gtgtctcgag
7261 cctcccgtca actgcaagga ctaggagttg ggttgaggat caaaatagga atttgtcacc
7321 tttcatgagg ggggcccaca acatatcatt tgttacccca ccatctagca gatcctctag
7381 ccaaggcaca gtctcaaccg tgcctaaaga gattttggac tcctggactg gcgctttcaa
7441 cacgcgcagg cagcctctct tcgctcacat tcgtaggcga ggggagtcac gggtgtaa
//