Typing tool
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Typing tool
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Complete norovirus genomes
| OP205568 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5099
ORF2: 5080..6702
ORF3: 6702..7508
LOCUS OP205568 7508 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0514_R03-23 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205568
VERSION OP205568.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7508)
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JOURNAL Unpublished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 7508)
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..7508
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0514_R03-23"
/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 <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61005.1"
/translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQP
GVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVNIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEET
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRRQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGVTEAFGVPIKQIQIHKSGEFCRLRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVFEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..995
/gene="ORF1"
/product="p48"
mat_peptide 996..2093
/gene="ORF1"
/product="NTPase"
mat_peptide 2094..2624
/gene="ORF1"
/product="p22"
mat_peptide 2625..3023
/gene="ORF1"
/product="VPg"
mat_peptide 3024..3566
/gene="ORF1"
/product="Pro"
mat_peptide 3567..5096
/gene="ORF1"
/product="RdRp"
gene 5080..6702
/gene="ORF2"
CDS 5080..6702
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61006.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6702..7508
/gene="ORF3"
CDS 6702..7508
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61007.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARVTTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRDLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaagg
61 aaaaatcttc aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg
121 gggctaggcc caaacagcct gccccgagag atgaaccaca aaagccccca agaccaccaa
181 ctcccgagtt ggtcaagagg ataccccctc ctccacctaa tggcgaagaa gaagaagaac
241 cagtcattag gtatgatgtt aagagtggga tctctggcct gcccgagctc acaacagtcc
301 cccaaccggg cgtggccaac acagcattca gtgttccacc actgagcttg agagagaaca
361 gggaggccaa ggaaccgcta acaggggcaa tattagagat gtgggacgga gagatatacc
421 actatggcct gtacgtggag aaaggcttag tgttgggtgt gcacaaacca cctgcagcca
481 taagcatggc aagagtggag ctgacgccac tgtcattgta ctggcgtgtg gtgtacactc
541 cccaatacct catctcccct gaaactctca ggaggctcaa cggagaggcg ttcccttaca
601 ccgccttcga caacaactgc tatgcctttt gctgctgggt gttagacctc aatgactcat
661 ggcttagcag gaggatggtg caaagaacaa cgggcttctt cagaccttac caagagtgga
721 acagaaaacc tctgcccacc atggatgact ccaaaataaa gaaggtagca aatatattcc
781 tatgttcatt gtccacatta ttcaccagac ccataaaaga cctcatagga aaaattaaac
841 cattaaacat attgaacatc ctggcaacgt gtgactggac gtttgccgga atagtggagt
901 ctctgatatt acttgctgaa ctcttcggag ttttctggac acccccagat gtgtctgcta
961 tgatcgctcc cttactcggg gactacgagt tgcaagggcc agaagacctc gccgttgaac
1021 tcgtacctgt ggtgatggga gggattggtt tggtgttggg attcaccaaa gagaaaattg
1081 gaaaaatgtt gtcctcagca gcatcaacac tcagggcttg caaagatctt ggcgcctatg
1141 gcttagagat actcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaatg
1201 agctagccat ggtgagggcc atagaggatg ccgtactaga tcttgaggca atagaaaata
1261 accacatgac aaccctgctg aaagataaag acagcttagc aacatacatg aaaacactgg
1321 acatggagga ggagaaagcc agaaggttgt ccacaaaatc tgcatcccct gacatagttg
1381 ggacaatcaa cgccctgctg gctcgaatag cagcagccag gtcattagtc cacagggcca
1441 aggaagagct atctagcagg ataagaccag tagttgttat gatatctggc aaaccaggaa
1501 taggcaaaac tcatctggcc agggaggtgg caagaaaggt agcatccact ctcacagggg
1561 atcaaagagt cggactcata ccaagaaacg gtgtggacca ttgggatgca tacaaaggtg
1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc cattcatgat gctcttcgca
1681 tacaagaatt ggctgatacg tgtcccctta ccttaaattg tgacagaatt gaaaataagg
1741 gaaaagtttt tgacagtgaa gtcataataa ttacaacaaa ccttgccaac ccagccccac
1801 ttgattatgt caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg
1861 caccagaagt agaaaaggca aaacgggatt ttcctggtca gccagatatg tggaaggacg
1921 cctttaagcc ggacttttca cacatcaagc tacagcttgc acctcagggt ggctttgaca
1981 agaatggcaa caccccacat gggaaagggg tgatgaagac cctcactacc ggttctctga
2041 ttgcccgtgc atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca
2101 caatcaccac cttcaatttt gaccggaaca gaatcacagc attcagacaa ttggctgcag
2161 aaaacaagta tggattggtg gataccatga aagttggcaa ccaactaaaa ggagtgaaaa
2221 ccatggaaga gctcaaacaa gcaatcagga atgtgaacat caagaggtgc cggatcatct
2281 acggtggctc cacgtatgac cttgaatctg atggcaaggg caaagttttg gtggaaaagg
2341 tcaagaacac ctctgtacag accaacaacg aattggccgg ggccctgcac catctcaaac
2401 acgcccgaat caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa
2461 ttgccggcgc tgcgtttgtc accacgcgca ttgcacgccg catgaacata caagaactct
2521 ggtcgaagcc acaattagat caaaatgaat cagaggctaa ggaagagacc cccaagtcag
2581 aagatgacga gttcatcata tcttccaagg acatcaagga ggagggaaag aagggcaaaa
2641 acaaaactgg ccgtggcaag aaacacactg cattctctag caagggcttg agcgatgagg
2701 agtatgacga gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggagt
2761 atcttcaaga cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagaag
2821 acttctgtga agaggaggag atcaaaatcc gtcagagaat tttccgtccc accaggagac
2881 aaagaaagga agagagggcc acattagggc tggtaacagg ttcagaaatc agaaaaagaa
2941 accccgatga cttcaaaccc aaagggaagc tgtgggccga tgacaacaga agtgttgact
3001 acaatgagaa actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg
3061 gttctggctg gggcttctgg gtatcaccaa gcctgttcat aacatcaact catgtaatcc
3121 ccgcaggcgt aacagaagca tttggagtcc ccatcaaaca aattcagatc cacaaatcag
3181 gtgaattttg ccgactcaga ttcccaaaac caattagacc agatgtgaca ggaatgatct
3241 tggaagaagg tgcgcctgaa ggcaccgtgg caactgtgct catcaaacgc cccaccggag
3301 agctcatgcc tcttgcagcc agaatgggaa cacacgcaac catgaaaatt caaggccgca
3361 tggttggcgg acagatgggt atgttgctca ctggatcaaa tgctaaaggt atggatttgg
3421 gaacaactcc tggtgactgt ggctgtcctt acatctataa aaggggcaat gactatatag
3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac cgtcatctgt gccacgcagg
3541 gaagtgaggg cgaggcgact cttgagggtg gagatgacaa aggaacatac tgtggggcac
3601 ccattttagg ccctgggggt gcaccaaaat tgagcaccaa aaccaaattc tggaggtcat
3661 cgaacacgcc ccttccacca gggacatatg agcctgccta cctcggtggc cgtgatccgc
3721 gtgttaaggg tgggccctct ttgcagcagg tgatgagaga ccagttgaag ccattcactg
3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accattatca
3841 atgttttcga acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct
3901 cacttgacaa aaccacctcc agcggacatc ctcaccacgt ccgaaagaat gaattctgga
3961 atggtgagac cttcactggt aaattggcag accaagcgtc aaaagcaaac ctaatgtttg
4021 aggaagggaa acacatgaca ccagtgtata cagcagcact caaggacgag ctagttaaga
4081 ctgagaaaat ctatggaaaa atcaagaaga gactgctctg gggctctgac ttgtccacca
4141 tgatccggtg cgctaggtca tttggtgggc tcatggacga gatgaaggca cactgcatat
4201 cactcccagt acgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac
4261 attccagata caaatatcac tatgatgcag actactctcg ttgggattca acacaacaaa
4321 gggcagtact agcagcagcc ttggaaatca tggtcagatt ctctgcagaa ccacaattgg
4381 cacaaatagt cgctgaggat ctactggccc ctagtgtagt agatgtagga gactttaaaa
4441 tcacaataaa tgaagggctc ccatctggtg tgccatgcac ttcccaatgg aactccatcg
4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta
4561 tacaagcaaa ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa
4621 aattggaccc tgaacagttg accgccaagt tgaaggagta cggcctgaaa ccaacccgcc
4681 cagacaagac cgagggaccc ctgatcatca gtgaagattt gaacggactc actttcctcc
4741 gaaggacggt gactcgtgac ccagctggct ggtttggaaa actggaccag agttcaattt
4801 tgaggcagat gtactggact agaggaccaa atcatgagga ccccaatgag acaatgatac
4861 cccattctca aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac
4921 cctctttcta cagtagaatc agtaaattgg tcataactga actcaaagaa ggtgggatgg
4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca
5041 cgtgggaggg cgatcgcaat ctggctccca attttgtgaa tgaagatggc gtcgagtgac
5101 gccaacccat ctgatgggtc cgcagccaac ctcgtaccag aggtcaacaa tgaggttatg
5161 gctttggagc ccgttgttgg tgccgctatt gcggcacctg tagcgggcca acaaaatgta
5221 attgacccct ggattagaaa taattttgta caagcccctg gtggggagtt cacagtgtcc
5281 cctagaaacg ctccaggtga aatactatgg agcgcgcccc taggccctga tctaaatccc
5341 tacctatccc atttggccag aatgtataat ggttatgcag gtggttttga agtgcaggta
5401 attctcgcgg ggaacgcgtt caccgccggg aagattatat ttgcagcagt cccaccaaat
5461 tttccaactg aaggcttaag tcccagccag gtcactatgt tcccccatat aatagtagat
5521 gttagacaat tagaacctgt gctgattccc ttacccgatg ttaggaataa tttctatcat
5581 tataatcagt caaatgattc cactattaag ttgatagcaa tgttgtacac accacttagg
5641 gctaataatg ctggagatga tgttttcaca gtttcgtgcc gagttctcac gaggccatcc
5701 cccgattttg atttcatatt tttagtgccc cccacagttg agtcaagaac taaaccattc
5761 tctgtcccag ttttaactgt tgaggagatg accaattcaa ggttccccat ccctttggaa
5821 aagttgttca caggccccag tagtgccttt gttgttcaac cacaaaacgg caggtgcaca
5881 actgatggcg tgctcctagg caccacccaa ctttctcctg tcaacatctg caccttcaga
5941 ggggatgtca cccacatcac aggtagtcgc aactacacga tgaatttggc ttcccaaaat
6001 tggaacaact atgacccgac agaagaaatc ccagcccctc tagggactcc agattttgta
6061 gggaagattc aaggcatgct cacccaaacc acaaggacag acggttcaac acgcggccac
6121 aaagcaacag tgtacactgg gagcgccgac tttgctccaa aactgggtag agttcaattt
6181 gaaactgaca cagaccatga ttttgaagct aatcaaaaca caaaatttac cccagtcggt
6241 gtcatccaag atggtagcac cacccaccga aacgaacccc aacagtgggt gctcccaagt
6301 tactcaggca gaaatactca caatgtacat ctggcccctg ctgtagcccc cacctttccg
6361 ggtgagcaac ttctcttttt cagatccacc atgcccggat gcagcgggta ccccaacatg
6421 gatttggact gcctgctccc ccaggaatgg gtgcagtact tctaccaaga ggcagcccca
6481 gcacaatccg atgtggctct gctaagattt gtgaatccag acacaggtag ggttttgttt
6541 gagtgcaagc ttcataaatc aggctatgtt acagtggctc acactggcca acatgatttg
6601 gttatccccc ccaatggtta ctttaggttt gattcctggg tcaaccagtt ctacacgctt
6661 gcccccatgg gaaatggaac ggggcgtaga cgtgtagtat aatggctgga gctttctttg
6721 ctggattggc atctgatgtc cttggctctg gacttggttc ccttatcaat gctggggctg
6781 gggccatcaa ccaaaaagtt gaatttgaaa ataacagaaa attgcaacaa gcatccttcc
6841 aatttagcag caatctgcaa caggcttcct ttcaacatga taaagagatg ctccaagcac
6901 aaattgaggc cactaaaaag ctacaacagg aaatgatgaa agttaagcag gcaatgctct
6961 tagagggtgg gttctctgag acagatgcag cccgcggggc aatcaatgcc cccatgacaa
7021 aagttttgga ttggagcggg acaaggtact gggctccaga tgctagggtt acaacataca
7081 atgcaggcca tttttccacc cctcaaccat cgagggcact gccaggaaga gctaatctta
7141 gggatgctgt ccctgctcgg ggaccctcca acaaatcttc taactcttct actgctacct
7201 ctgtgtactc aaatcaaact atttcaacga gacttggttc tacagctggt tctggaacca
7261 gtgtctcgag tctcccgtca actgcaagga ctaggagctg ggttgaggat caaaataggg
7321 atttgtctcc tttcatgagg ggggcccaca acatatcatt tgtcacccca ccatctagca
7381 gatcctctag ccaaggcaca gtctcaaccg tgcctaaaga gattttggac tcctggactg
7441 gcgcttttaa cacgcgcagg cagcctctct tcgctcacat tcgtaagcga ggggagtcac
7501 gggtgtaa
//