Typing tool
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Typing tool
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Complete norovirus genomes
| OP205564 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5086
ORF2: 5067..6689
ORF3: 6689..7495
LOCUS OP205564 7495 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0473_R03-18 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205564
VERSION OP205564.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7495)
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JOURNAL Unpublished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 7495)
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..7495
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0473_R03-18"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-11-29"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5086
/gene="ORF1"
CDS <1..5086
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="UUV60993.1"
/translation="NDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAP
RDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQPGVAN
TAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAR
VELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLS
RRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKP
LNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAV
ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKE
EANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSA
SPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARK
VASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLT
LNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKR
DFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGL
LHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEEL
KQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHAR
IRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEETPKSE
DDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRRQRKEERATLGLVTGSEI
RKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFIT
STHVIPAGVTEAFGVPIKQIQIHKSGEFCRLRFPKPIRPDVTGMILEEGAPEGTVATV
LIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPY
IYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAP
KLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
RPSVLEAAKQTIINVFEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETF
TGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIR
CARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQR
AVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLK
PTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDP
NETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..982
/gene="ORF1"
/product="p48"
mat_peptide 983..2080
/gene="ORF1"
/product="NTPase"
mat_peptide 2081..2611
/gene="ORF1"
/product="p22"
mat_peptide 2612..3010
/gene="ORF1"
/product="VPg"
mat_peptide 3011..3553
/gene="ORF1"
/product="Pro"
mat_peptide 3554..5083
/gene="ORF1"
/product="RdRp"
gene 5067..6689
/gene="ORF2"
CDS 5067..6689
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60994.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYPGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6689..7495
/gene="ORF3"
CDS 6689..7495
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60995.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARVTTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRDLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 taacgacgct accgttgccg ttgcttgcaa caacaacaac gacaaggaaa aatcttcagg
61 tgaaggctta ttcacaaata tgtcttccac cttaaagaaa gccctcgggg ctaggcccaa
121 acagcctgcc ccgagagatg aaccacaaaa gcccccaaga ccaccaactc ccgagttggt
181 caagaggata ccccctcctc cacctaatgg cgaagaagaa gaagaaccag tcattaggta
241 tgatgttaag agtgggatct ctggcctgcc cgagctcaca acagtccccc aaccgggcgt
301 ggccaacaca gcattcagtg ttccaccact gagcttgaga gagaacaggg aggccaagga
361 accgctaaca ggggcaatat tagagatgtg ggacggagag atataccact atggcctgta
421 cgtggagaaa ggcttagtgt tgggtgtgca caaaccacct gcagccataa gcatggcaag
481 agtggagctg acgccactgt cattgtactg gcgtgtggtg tacactcccc aatacctcat
541 ctcccctgaa actctcagga ggctcaacgg agaggcgttc ccttacaccg ccttcgacaa
601 caactgctat gccttttgct gctgggtgtt agacctcaat gactcatggc ttagcaggag
661 gatggtgcaa agaacaacgg gcttcttcag accttaccaa gagtggaaca gaaaacccct
721 gcccaccatg gatgactcca aaataaagaa ggtagcaaat atattcctat gttcattgtc
781 cacattattc accagaccca taaaagacct cataggaaaa attaaaccat taaacatatt
841 gaacatcctg gcaacgtgtg actggacgtt tgccggaata gtggagtctc tgatattact
901 tgctgaactc ttcggagttt tctggacacc cccagatgtg tctgctatga tcgctccctt
961 actcggggac tacgagttgc aagggccaga agacctcgcc gttgaactcg tacctgtggt
1021 gatgggaggg attggtttgg tgttgggatt caccaaagag aaaattggaa aaatgttgtc
1081 ctcagcagca tcaacactca gggcttgcaa agatcttggc gcctatggct tagagatact
1141 caaattggtc atgaagtggt tcttcccaaa gaaagaggag gccaatgagc tagccatggt
1201 gagggccata gaggatgccg tactagatct tgaggcaata gaaaataacc acatgacaac
1261 cctgctgaaa gataaagaca gcttagcaac atacatgaaa acactggaca tggaggagga
1321 gaaagccaga aggttgtcca caaaatctgc atcccctgac atagttggga caatcaacgc
1381 cctgctggct cgaatagcag cagccaggtc attagtccac agggccaagg aagagctatc
1441 tagcaggata agaccagtag ttgttatgat atctggcaaa ccaggaatag gcaaaactca
1501 tctggccagg gaggtggcaa gaaaggtagc atccactctc acaggggatc aaagagtcgg
1561 actcatacca agaaacggtg tggaccattg ggatgcatac aaaggtgaga gagtcgtgct
1621 gtgggacgac tatggcatga gtaaccccat tcatgatgct cttcgcatac aagaattggc
1681 tgatacgtgt ccccttacct taaattgtga cagaattgaa aataagggaa aagtttttga
1741 cagtgaagtc ataataatta caacaaacct tgccaaccca gccccacttg attatgtcaa
1801 ctttgaggcc tgttccagga gaattgattt cctggtgtac gctgaggcac cagaagtaga
1861 aaaggcaaaa cgggattttc ctggtcagcc agatatgtgg aaggacgcct ttaagtcgga
1921 cttttcacac atcaagctac agcttgcacc tcagggtggc tttgacaaga atggcaacac
1981 cccacatggg aaaggggtga tgaagaccct cactaccggt tctctgattg cccgtgcatc
2041 aggcctactg catgagagga tggatgaatt tgaactccaa ggtcccacaa tcaccacctt
2101 caattttgac cggaacagaa tcacagcatt cagacaattg gctgcagaaa acaagtatgg
2161 attggtggat accatgaaag ttggcaacca actaaaagga gtgaaaacca tggaagagct
2221 caaacaagca atcaggaatg tgaccatcaa gaggtgccgg atcatctacg gtggctccac
2281 gtatgacctt gaatctgatg gcaagggcaa agttttggtg gaaaaggtca agaacacctc
2341 tgtacagacc aacaacgaat tggccggggc cctgcaccat ctcaaacacg cccgaatcag
2401 gtactatgtc aaatgtgtgc aagaagcagt ctattccatc atacaaattg ccggcgctgc
2461 gtttgtcacc acgcgcattg cacgccgcat gaacatacaa gaactctggt cgaagccaca
2521 attagatcaa aatgaatcag aggctaagga agagaccccc aagtcagaag atgacgagtt
2581 catcatatct tccaaggaca tcaaggagga gggaaagaag ggcaaaaaca aaactggccg
2641 tggcaagaaa cacactgcat tctctagcaa gggcttgagc gatgaggagt atgacgagta
2701 caagaggata agagaagaga ggaatgggaa gtactctata gaggagtatc ttcaagacag
2761 agacaggtac tatgaggagc tcgccattgc caaggccacg gaagaagact tctgtgaaga
2821 ggaggagatc aaaatccgtc agagaatttt ccgtcccacc aggagacaaa gaaaggaaga
2881 gagggccaca ttagggctgg taacaggttc agaaatcaga aaaagaaacc ccgatgactt
2941 caaacccaaa gggaagctgt gggccgatga caacagaagt gttgactaca atgagaaact
3001 ggactttgag gcccccccaa gcatatggtc taggattgtg agctttggtt ctggctgggg
3061 cttctgggta tcaccaagcc tgttcataac atcaactcat gtaatccccg caggcgtaac
3121 agaagcattt ggagtcccca tcaaacaaat tcagatccac aaatcaggtg aattttgccg
3181 actcagattc ccaaaaccaa ttagaccaga tgtgacagga atgatcttgg aagaaggtgc
3241 gcctgaaggc accgtggcaa ctgtgctcat caaacgcccc accggagagc tcatgcctct
3301 tgcagccaga atgggaacac acgcaaccat gaaaattcaa ggccgcatgg ttggcggaca
3361 gatgggtatg ttgctcactg gatcaaatgc taaaggtatg gatttgggaa caactcctgg
3421 tgactgtggc tgtccttaca tctataaaag gggcaatgac tatatagtca ttggggtgca
3481 cactgcagca gcccgtggtg gaaacaccgt catctgtgcc acgcagggaa gtgagggcga
3541 ggcgactctt gagggtggag atgacaaagg aacatactgt ggggcaccca ttttaggccc
3601 tgggggtgca ccaaaattga gcaccaaaac caaattctgg aggtcatcga acacgcccct
3661 tccaccaggg acatatgagc ctgcctacct cggtggccgt gatccgcgtg ttaagggtgg
3721 gccctctttg cagcaggtga tgagagacca gttgaagcca ttcactgaac ccaggggcaa
3781 acctccaaga ccaagtgtat tggaagcagc caaacaaacc attatcaatg ttttcgaaca
3841 aaccctggac cctccacaaa aatggacata cgcacaggcg tgtgcctcac ttgacaaaac
3901 cacctccagc ggacatcctc accacgtccg aaagaatgaa ttctggaatg gtgagacctt
3961 cactggtaaa ttggcagacc aagcgtcaaa agcaaaccta atgtttgagg aagggaaaca
4021 catgacacca gtgtatacag cagcactcaa ggacgagcta gttaagactg agaaaatcta
4081 tggaaaaatc aagaagagac tgctctgggg ctctgacttg tccaccatga tccggtgcgc
4141 taggtcattt ggtgggctca tggacgagat gaaggcacac tgcatatcac tcccagtacg
4201 agttggcatg aatatgaatg aagatggccc aataatattt gagaaacatt ccagatacaa
4261 atatcactat gatgcagact actctcgttg ggattcaaca caacaaaggg cagtactagc
4321 agcagccttg gaaatcatgg tcagattctc tgcagaacca caattggcac aaatagtcgc
4381 tgaggatcta ctggccccta gtgtagtaga tgtaggagac tttaaaatca caataaatga
4441 agggctccca tctggtgtgc catgcacttc ccaatggaac tccatcgcac actggctgct
4501 aactctctgt gccttgtctg aagtcaccaa actgtcccct gacattatac aagcaaattc
4561 catgttctca ttttacggtg atgacgagat tgtcagcacc gacataaaat tggaccctga
4621 acagttgacc gccaagttga aggagtacgg cctgaaacca acccgcccag acaagaccga
4681 gggacccctg atcatcagtg aagatttgaa cggactcact ttcctccgaa ggacggtgac
4741 tcgtgaccca gctggctggt ttggaaaact ggaccagagt tcaattttga ggcagatgta
4801 ctggactaga ggaccaaatc atgaagaccc caatgagaca atgatacccc attctcaaag
4861 acccatacag ctcatggcac tgcttggtga agcctctctt cacggaccct ctttctacag
4921 tagaatcagt aaattggtca taactgaact caaagaaggt gggatggact tttacgtgcc
4981 aaggcaggaa cccatgttca ggtggatgag gttttctgac ttgagcacgt gggagggcga
5041 tcgcaatctg gctcccaatt ttgtgaatga agatggcgtc gagtgacgcc aacccatctg
5101 atgggtccgc agccaacctc gtaccagagg tcaacaatga ggttatggct ttggagcccg
5161 ttgttggtgc cgctattgcg gcacctgtag cgggccaaca aaatgtaatt gacccctgga
5221 ttagaaataa ttttgtacaa gcccctggtg gggagttcac agtgtcccct agaaacgctc
5281 caggtgaaat actatggagc gcgcccctag gccctgatct aaatccctac ctatcccatt
5341 tggccagaat gtataatggt tatgcaggtg gttttgaagt gcaggtaatt ctcgcgggga
5401 acgcgttcac cgccgggaag attatatttg cagcagtccc accaaatttt ccaactgaag
5461 gcttaagtcc cagccaggtc actatgttcc cccatataat agtagatgtt agacaattag
5521 aacctgtgct gattccctta cccgatgtta ggaataattt ctatcattac aatcagtcaa
5581 atgattccac tattaagttg atagcaatgt tgtacacacc acttagggct aataatgctg
5641 gagatgatgt tttcacagtt tcgtgccgag ttctcacgag gccatccccc gattttgatt
5701 tcatattttt agtgcccccc acagttgagt caagaactaa accattctct gtcccagttt
5761 taactgttga ggagatgacc aattcaaggt tccccatccc tttggaaaag ttgttcacag
5821 gccccagtag tgcctttgtt gttcaaccac aaaacggcag gtgcacaact gatggcgtgc
5881 tcctaggcac cacccaactt tctcctgtca acatctgcac cttcagaggg gatgtcaccc
5941 acatcacagg tagtcgcaac tacacgatga atttggcttc ccaaaattgg aacaactatg
6001 acccaacaga agaaatccca gcccctctag ggactccaga ttttgtaggg aagattcaag
6061 gcatgctcac ccaaaccaca aggacagacg gttcaacacg cggccacaaa gcaacagtgt
6121 acactgggag cgccgacttt gctccaaaac tgggtagagt tcaatttgaa actgacacag
6181 accatgattt tgaagctaat caaaacacaa aatttacccc agtcggtgtc atccaagatg
6241 gtagcaccac ccaccgaaat gaaccccaac agtgggtgct cccaagttac ccaggcagaa
6301 atactcacaa tgtacatctg gcccctgctg tagcccccac ctttccgggt gagcaacttc
6361 tctttttcag atccaccatg cccggatgca gcgggtaccc caacatggat ttggactgcc
6421 tgctccccca ggaatgggtg cagtacttct accaagaggc agccccagca caatccgatg
6481 tggctctgct aagatttgtg aatccagaca caggtagggt tttgtttgag tgcaagcttc
6541 ataaatcagg ctatgttaca gtggctcaca ctggccaaca tgatttggtt atccccccca
6601 atggttactt taggtttgat tcctgggtca accagttcta cacgcttgcc cccatgggaa
6661 atggaacggg gcgtagacgt gtagtataat ggctggagct ttctttgctg gattggcatc
6721 tgatgtcctt ggctctggac ttggttccct tatcaatgct ggggctgggg ccatcaacca
6781 aaaagttgaa tttgaaaata acagaaaatt gcaacaagca tccttccaat ttagcagcaa
6841 tctgcaacag gcttcctttc aacatgataa agagatgctc caagcacaaa ttgaggccac
6901 taaaaagcta caacaggaaa tgatgaaagt taagcaggca atgctcttag agggtgggtt
6961 ctctgagaca gatgcagccc gcggggcaat caatgccccc atgacaaaag ttttggattg
7021 gagcgggaca aggtactggg ctccagatgc tagggttaca acatacaatg caggccactt
7081 ttccacccct caaccatcga gggcactgcc aggaagagct aatcttaggg atgctgtccc
7141 tgctcgggga ccctccaaca aatcttctaa ctcttctact gctacctctg tgtactcaaa
7201 tcaaactatt tcaacgagac ttggttctac agctggttct ggaaccagtg tctcgagtct
7261 cccgtcaact gcaaggacta ggagctgggt tgaggatcaa aatagggatt tgtctccttt
7321 catgaggggg gcccacaaca tatcatttgt caccccacca tctagcagat cctctagcca
7381 aggcacagtc tcaaccgtgc ctaaagagat tttggactcc tggactggcg cttttaacac
7441 gcgcaggcag cctctcttcg ctcacattcg taagcgaggg gagtcacggg tgtaa
//