Typing tool
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Typing tool
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Complete norovirus genomes
| OP205566 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS OP205566 7509 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0506_R03-21 nonstructural
polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP205566
VERSION OP205566.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7509)
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JOURNAL Unpublished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 7509)
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..7509
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0506_R03-21"
/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..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60999.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPAIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEI
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRTVTIKRCRIIYGGSTYDLESDGKGKVLVEKVRNTSVQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIMQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEE
APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERSG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRKRNPDDFKPKGKLWADDNRSVDYNERLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCVSLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 1..996
/gene="ORF1"
/product="p48"
mat_peptide 997..2094
/gene="ORF1"
/product="NTPase"
mat_peptide 2095..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6703
/gene="ORF2"
CDS 5081..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61000.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6703..7509
/gene="ORF3"
CDS 6703..7509
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61001.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRASLGDAVPSRGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgctaccgtt gccgttgctt gcaacaacaa caacgacaag
61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
121 ggggctaggc ccaaacagcc tgccccgaga gacgaaccac aaaagccccc aagaccacca
181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagaggaa
241 ccagccatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc
301 ccccaaccgg acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac
361 agggaggcca aggaaccgct aacaggggca atattagaga tgtgggacgg agagatatac
421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tacacaaacc acctgcagcc
481 ataagcatgg caagagtgga gctgacgccg ctgtcattgt actggcgtgt ggtgtacact
541 ccccaatacc tcatctcccc tgaaactctc aggaggctca acggagaggc gttcccttac
601 accgccttcg acaacaactg ctatgccttt tgctgctggg tgttagacct caatgactcg
661 tggcttagca ggaggatggt gcaaagaaca acgggcttct tcagacctta ccaagagtgg
721 aacagaaaac ccctgcccac catggatgac tccaaaataa agaaggtagc aaatatattc
781 ctatgttcat tgtccacatt attcaccaga cccataaaag acctcatagg aaaaattaaa
841 ccattaaaca tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag
901 tctctgatat tacttgctga actcttcgga gttttctgga cacccccaga tgtgtctgct
961 atgatcgccc ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa
1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat
1141 ggcttggaga tactcaaatt ggtcatgaag tggttcttcc caaagaaaga ggaggccaat
1201 gagctagcca tggtgagggc catagaggat gccgtactag atcttgaggc aatagaaaat
1261 aaccacatga caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg
1321 gacatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt
1381 gggacaatca acgccctgct ggctcgaata gcagcagcca ggtcattagt ccacagggcc
1441 aaggaagagc tatctagcag gataagacca gtagttgtta tgatatctgg caaaccagga
1501 ataggcaaaa ctcatctggc cagggaggta gcaaggaagg tagcatccac tctcacaggg
1561 gatcaaagag tcggactcat accaagaaac ggtgtggacc attgggatgc atacaaaggt
1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcacga tgctcttcgc
1681 atacaagaat tggctgatac gtgtcccctt accttaaatt gtgacagaat tgaaaataag
1741 ggaaaagttt ttgacagtga agtcataata attacaacaa accttgccaa cccagccccg
1801 cttgattatg tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag
1861 gcaccagaaa tagaaaaggc aaaacgggat tttcctggtc agccagatat gtggaaggac
1921 gccttcaagc cggacttttc acacatcaag ctacagcttg cacctcaggg tggctttgac
1981 aagaatggca acaccccaca tgggaaaggg gtgatgaaga ccctcactac cggttctctg
2041 attgcccgtg catcaggcct actgcatgaa aggatggatg aatttgaact ccaaggtccc
2101 acaatcacca ccttcaattt cgaccggaac agaatcacag cattcagaca attggctgca
2161 gaaaacaagt atggattggt ggataccatg aaagttggca atcaactaaa aggagtgaaa
2221 accatggaag aactcaaaca agcaatcagg actgtgacca tcaagaggtg ccggatcatc
2281 tacggtggct ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag
2341 gtcaggaaca cctctgtgca gaccaacaac gagttggccg gggccctgca ccatctcaaa
2401 cacgcccgaa tcaggtacta tgttaaatgt gtgcaagaag cagtctattc catcatgcaa
2461 attgccggcg ctgcgtttgt caccacgcgc attgcgcgcc gcatgaacat acaagaactc
2521 tggtcgaagc cacaattaga tcaaaatgag tcagaggcta aggaagaggc ccccaagtca
2581 gaagatgacg agttcattat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa
2641 aacaaaactg gccgtggcaa gaaacacact gcattctcca gcaagggctt gagcgatgag
2701 gagtatgacg agtacaagag gataagagaa gagagaagtg ggaaatactc tatagaggag
2761 tatcttcaag acagagacag gtactatgag gagctcgcca ttgccaaggc cacggaagaa
2821 gacttctgtg aagaggagga gatcaaaatc cgtcagagaa ttttccgtcc caccaggaaa
2881 caaagaaagg aagagagggc cacattaggg ctggtaacag gttcagaaat cagaaaaaga
2941 aaccctgatg acttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac
3001 tacaatgaga gactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt
3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtaatc
3121 cccgcaggca taacagaagc atttggagtc cccatcaaac agattcagat ccacaaatca
3181 ggtgaatttt gtcgattcag attcccaaaa ccaattagac cagatgtgac aggaatgatc
3241 ttggaagaag gcgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc
3361 atggttggcg gacagatggg tatgttgctc actggatcaa atgctaaagg aatggatttg
3421 ggaacaactc ctggtgactg tggctgtcct tacatctata aaaggggcaa tgactatata
3481 gtcattgggg tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
3541 ggaagtgagg gtgaggcaac tcttgagggc ggagatgata aaggaacata ctgtggggca
3601 cccattttag gccctggggg tgcaccaaaa ttgagcacca aaaccaaatt ttggaggtca
3661 tcgaacacgc cccttccacc agggacatat gagcctgcct accttggtgg ccgtgatccg
3721 cgtgttaagg gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcact
3781 gaacccaggg gcaaacctcc aagaccaagt gtactggaag cagccaaaca aaccattatc
3841 aatgttctcg aacaaaccct ggaccctcca caaaaatgga catacgcaca ggcgtgtgcc
3901 tcactagaca aaaccacctc cagcgggcat ccccatcatg tccgaaagaa tgaattctgg
3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa cctaatgttt
4021 gaggaaggga aacacatgac accagtgtat acagcagcac tcaaggatga gctagttaag
4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgcgta
4201 tcactcccag tacgagttgg catgaatatg aatgaagatg gcccaataat atttgagaaa
4261 cattccagat acaaatacca ctatgatgca gactactctc gttgggattc aacacaacaa
4321 agggcagtac tagcagcagc cttggaaatc atggtcagat tctctgcaga accacaattg
4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtagg agactttaaa
4441 atcacaataa atgaagggct cccatctggt gtgccatgca cttctcaatg gaactccatc
4501 gcacactggc tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt
4561 atacaagcaa attccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata
4621 aaattggacc ctgaacagtt aaccgccaag ttgaaggagt acggcctgaa accaacccgc
4681 ccagacaaga ccgagggacc cctgatcatc agtgaagatt tgaatggact cactttcctc
4741 cgaaggacgg tgactcgtga cccagctggc tggtttggaa aactagacca aagttcaatt
4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata
4861 ccccattctc aaagacccat acagcttatg gcactgcttg gtgaagcctc tcttcacgga
4921 ccctcttttt atagtagaat cagtaaattg gtcataactg aactcaaaga aggtgggatg
4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtgtc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ctaggccctg acctaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggctatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaagattata tttgcagcag ttccaccaaa
5461 ttttccaact gaaggcttaa gtcctagcca ggtcactatg tttccccata taatagtaga
5521 tgttaggcaa ttagaacctg tgttgattcc cttacccgat gttaggaata acttctatca
5581 ttacaatcag tcaaatgact ccactattaa gctgatagca atgttgtaca caccacttag
5641 ggctaataat gctggagatg atgttttcac agtttcgtgc cgagttctca cgagaccatc
5701 ccccgatttt gatttcatat ttttagtgcc acccacagtt gagtcaagaa ctaaaccatt
5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca tccctttgga
5821 aaagttattc acaggcccca gcagtgcctt tgttgttcaa ccacaaaatg gcaggtgcac
5881 aactgatggc gtgctcctag gcaccaccca actttctcct gtcaacatct gtaccttcag
5941 aggggatgtc acccacatca caggtagtcg caactacaca atgaatttgg cttctcaaaa
6001 ctggaacaac tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt
6061 ggggaagatt caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca
6121 caaagctaca gtatacactg ggagcgccga cttcgctcca aaactgggta gagttcaatt
6181 tgaaactgac acagaccatg attttgaagc taatcaaaac acaaagttca ccccagtcgg
6241 tgtcatccaa gatggtagca ccacccaccg aaacgaaccc cagcagtggg tgctcccaag
6301 ttactcaggc agaaatactc acaatgtaca tttggccccc gctgtagccc ccacctttcc
6361 gggtgagcaa cttctctttt tcagatccac catgcccgga tgcagcgggt accccaacat
6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
6541 tgagtgcaag cttcataaat caggctatgt tacagtagct cacactggcc aacatgattt
6601 ggttatccct cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgtagta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggcc
6781 ggggccatca accaaaaagt tgaatttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagta gcaatttgca acaggcttcc tttcaacatg ataaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc
6961 ttagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca
7021 aaaactttgg actggagcgg gacaaggtac tgggctccag atgctaggat tacaacatac
7081 aatgcaggcc acttttccac ccctcaacca tcgagggcac tgccaggaag agctagtctt
7141 ggggatgctg tcccttctcg gggaccctcc aataaatctt ctaactcttc tactgctacc
7201 tctgtgtact caaatcaaac tatttcaacg aggcttggtt ctacagctgg ttctgggacc
7261 agtgtctcga gtctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg
7321 aatttgtcac ctttcatgag aggggcccac aacatatcat ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
7501 cgggtgtaa
//