Typing tool
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Typing tool
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Complete norovirus genomes
| OP205584 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5099
ORF2: 5080..6702
ORF3: 6702..7505
LOCUS OP205584 7505 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0479_R04-18 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205584
VERSION OP205584.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7505)
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JOURNAL Unpublished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 7505)
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..7505
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0479_R04-18"
/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..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61053.1"
/translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKGGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKIGNQLKGVKT
MEELKQAIRNVTIRRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSSS
LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVAGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGRIKKRLLWGSDLS
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="UUV61054.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPTPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6702..7505
/gene="ORF3"
CDS 6702..7505
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61055.1"
/translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAAPARGPSNKSS
NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
FVTPPSSRSSSQGTVSTVPREILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaagg
61 aaaaatcttc aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg
121 gggctaggcc caaacagcct gccccgagag acgaaccaca aaaaccccca agaccaccaa
181 ctcccgagtt ggtcaagagg ataccccctc ctccacctaa tggcgaagga gaagaagagc
241 cagtcattag gtatgaggtt aagggtggga tctctggtct gcccgagctc acaacagtcc
301 cccaaccgga cgtggccaac acagcattca gtgttccacc actgagcttg agagaaaaca
361 gggaggccaa ggaaccgtta acaggggcga tattagagat gtgggatgga gagatatacc
421 actatggcct gtacgtggag aaaggtttag tgttgggtgt gcacaaacca cctgcagcca
481 taagcatggc aagagtggag ctgacgccgc tgtcattgta ctggcgtgtg gtgtacactc
541 cccagtacct catctcccct gaaactctca ggaggctcaa cggagaggcg ttcccttaca
601 ccgccttcga caacaactgc tatgcctttt gctgctgggt gttagacctc aatgactcat
661 ggcttagcag gaggatggtg caaagaacaa cgggcttctt cagaccttac caagagtgga
721 acagaaagcc cctgcctacc atggatgact ccaaaattaa gaaggtagca aatatattcc
781 tatgttcatt gtccacgttg ttcaccagac ccataaaaga cctcatagga aaaattaaac
841 cattaaacat attaaacatc ctggcaacgt gtgactggac gtttgccgga atagtggagt
901 ctctgatatt acttgctgaa ctcttcggag ttttctggac gcccccagat gtgtctgcta
961 tgatcgctcc cttactcggg gactacgagt tgcaagggcc agaagacctc gccgttgaac
1021 tcgtacctgt ggtaatggga gggattggtt tggtgttggg attcaccaaa gagaaaattg
1081 gcaaaatgtt gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg
1141 gcttagagat actcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaatg
1201 agctagccat ggtgagggcc atagaggatg ccgtactaga tcttgaggca atagaaaata
1261 accacatgac aaccctgttg aaagacaaag acagcttagc aacatacatg aaaacactgg
1321 acatggagga ggagaaagcc agaaggttgt ccacaaagtc tgcatcccct gacatagttg
1381 ggacaatcaa cgccctgctg gctcgaatag cagcggccag gtcattagtt cacagggcca
1441 aggaagagtt atctagcagg ataagaccag tagttgttat gatatctggt aaaccaggaa
1501 taggcaaaac tcatctggcc agggaggtgg caagaaaggt ggcatccacc ctcacagggg
1561 accaaagagt cggactcata ccaagaaacg gtgtggacca ttgggatgca tacaaaggtg
1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc cattcacgat gctcttcgca
1681 tacaagaatt ggctgatacg tgtcccctta ccttaaattg tgacagaatc gaaaacaagg
1741 gaaaagtttt tgacagtgaa gtcataataa ttacaacaaa ccttgccaac ccagccccac
1801 ttgattatgt caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg
1861 caccagaagt agaaaaggca aaacgggatt ttcctggtca gccagatatg tggaaggacg
1921 ccttcaagcc ggacttttca cacatcaagc tacagcttgc acctcagggc ggctttgaca
1981 agaatggcaa caccccacat gggaaaggag tgatgaagac cctcactacc ggttctctga
2041 ttgcccgtgc atcaggcctc ctgcatgaga ggatggatga gtttgagctc cagggcccca
2101 caatcaccac cttcaatttc gaccggaaca gaatcacagc attcagacaa ctggctgcag
2161 aaaacaagta tggattggtg gatactatga aaattggcaa tcaactaaaa ggagtgaaaa
2221 ccatggaaga actcaaacaa gcaatcagaa atgtgaccat caggaggtgc cggatcatct
2281 acggcggctc cacgtatgac cttgaatctg atggcaaggg caaagttttg gtggaaaagg
2341 tcaagaacac ctctgtacag accaacaacg agttggccgg ggccctgcac catcttaaac
2401 acgcccgaat caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa
2461 ttgccggcgc tgcgtttgtc accacgcgca ttgcacgccg catgaacata caagaactct
2521 ggtcgaagcc acaattagat caaaatgaat cagagactaa ggaggaggcc cccaaatcag
2581 aagatgacga gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa
2641 acaagactgg ccgtggcaag aaacacactg cattttccag caagggcttg agcgatgagg
2701 agtatgacga gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggaat
2761 accttcaaga cagagacagg tactatgagg agcttgccat tgccaaggcc acggaagaag
2821 acttctgtga agaggaggag atcaaaatcc gtcagagaat tttccgtccc accaggaaac
2881 aaaggaagga agagagggcc acattaggac tggtgacagg ttcagaaatc agaaaaagaa
2941 accctgatga cttcaaaccc aaagggaagc tgtgggctga tgacaacaga agtgttgact
3001 ataatgagaa actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg
3061 gttctggctg gggcttctgg gtatcatcaa gcctgttcat aacatcaact catgtaatcc
3121 ccgcaggcat aacagaagca tttggagtcc ccatcaaaca aattcagatc cacaaatcag
3181 gtgaattttg ccgattcaga ttcccaaaac caattagacc agacgtggca gggatgatct
3241 tggaagaagg tgcgcctgaa ggcaccgtgg caactgtgct catcaaacgc cccaccggag
3301 agctcatgcc tcttgcagcc agaatgggaa cacacgcaac catgaaaatt caaggtcgca
3361 tggttggcgg acagatgggt atgttgctca ctggatcaaa tgctaaagga atggatttgg
3421 ggacaacccc tggtgactgt ggctgtccct acatctacaa aaggggcaat gactatatag
3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac cgtcatctgt gccacacagg
3541 gaagtgaggg tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac
3601 ccattctagg ccctgggggt gcaccaaagt tgagcaccaa aaccaaattt tggaggtcat
3661 cgaacacgcc ccttccacca gggacatatg agcctgccta cctcggtggc cgtgatccgc
3721 gtgttaaggg tgggccttcc ttgcagcagg taatgagaga ccagttgaag ccattcactg
3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accattatca
3841 atgtcctcga acaaaccctg gatcctccac aaaaatggac atacgcacag gcgtgtgcct
3901 cacttgacaa aaccacttcc agcgggcatc cccatcatgt ccgaaagaat gaattctgga
3961 atggtgagac cttcactggc aaattggcag accaagcatc aaaagcaaac ctaatgtttg
4021 aggaagggaa gcacatgaca ccagtgtata cagcagcact caaggacgag ctagtcaaga
4081 ctgagaaaat ctatggaagg atcaagaaga gactgctctg gggctctgac ttgtccacca
4141 tgatccggtg cgctaggtca tttggtggac tcatggacga gatgaaggca cactgcatat
4201 cactcccagt acgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac
4261 attccagata caaataccac tatgatgcag actactctcg ttgggactca acacaacaga
4321 gggcagtact agcagcagcc ttggaaatca tggtcagatt ctctgcagaa ccacaactgg
4381 cacaaatagt cgctgaggat ctgctggccc ctagcgtagt ggatgtggga gactttaaaa
4441 tcacaataaa tgaggggctc ccatctggtg tgccatgcac ttctcaatgg aattccatcg
4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta
4561 tacaagcaaa ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa
4621 aattggaccc tgaacagtta accgctaagt tgaaggagta cggcctgaaa ccaacccgcc
4681 cagacaagac cgagggaccc ctgatcatca gtgaagattt gaacggactc actttcctcc
4741 gaaggacggt gactcgtgac ccagctggct ggtttggaaa actggaccaa agttcaattt
4801 tgaggcagat gtactggact agaggaccaa atcatgaaga tcccaatgag acaatgatac
4861 cccattctca aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac
4921 cctctttcta cagtagaatc agtaaattgg tcataactga actcaaagaa ggcgggatgg
4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttctct 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 tacagtatcc
5281 cctagaaacg ctccaggtga aatactatgg agcgcgcccc taggccctga cctaaatccc
5341 tacttatccc atttggccag aatgtacaat ggctatgcag gtggttttga agtgcaggta
5401 attctcgcgg ggaacgcgtt caccgccggg aagatcatat ttgcagcagt tccaccaaat
5461 tttccaactg aaggcttaag tcctagccag gtcactatgt tcccccatat aatagtagat
5521 gttagacaat tagaacctgt gctgattccc ttacccgatg ttaggaataa tttctatcat
5581 tacaatcagt caaatgattc cactattaag ttgatagcaa tgttgtacac accacttagg
5641 gctaataatg ctggggatga tgttttcaca gtttcgtgcc gagttctcac gagaccatcc
5701 cccgattttg atttcatatt tttagtgcca cccacagttg agtcaagaac aaaaccattt
5761 tctgtcccag ttttaactgt tgaggagatg accaattcaa gattccccac ccctttggaa
5821 aagttgttca caggccccag tagtgccttt gttgttcaac cacaaaacgg caggtgcaca
5881 actgatggcg tgcttctagg caccacccaa ctttctcctg tcaacatctg caccttcaga
5941 ggggatgtca cccacatcac aggtagtcac aactacacaa tgaatttggc ttctcaaaat
6001 tggaacaact atgacccaac agaagaaatc ccagcccctc taggaactcc agattttgta
6061 gggaagattc aaggcatgct cacccaaacc acaaggacag atggttcaac acgcggccac
6121 aaagctacag tgtacactgg gagcgccgac tttgctccaa aactgggtag agttcaattt
6181 gaaactgaca caaaccatga ctttgaagct aaccagaaca caaagttcac cccagtcggt
6241 gtcattcaag atggtggcac cacccaccga aacgaacccc aacagtgggt gctcccaagt
6301 tactcaggca gaaatactca caatgtacat ctggcccccg ctgtagcccc cacctttccg
6361 ggtgagcagc ttctcttctt cagatccacc atacccggat gcagcgggta ccccaacatg
6421 gatttggact gtctgctccc ccaggaatgg gtgcagtact tctaccaaga ggcagcccca
6481 gcacaatctg atgtggctct gttaagattt gtgaatccag acacaggtag agttttgttt
6541 gagtgcaagc ttcacaaatc aggttatgtt acagtggctc acactggcca acatgatttg
6601 gttatccccc ccaatggtta ctttaggttt gattcctggg tcaatcagtt ctatacgctt
6661 gcccccatgg gaaatggaac ggggcgtaga cgtgtagtat aatggctgga gctttctttg
6721 ctggattggc atctgatgtc cttggctctg gacttggttc ccttatcagt gctggtgctg
6781 gggccatcaa ccaaaaagtt gagtttgaaa ataatagaaa attgcaacaa gcatccttcc
6841 aatttagcag caatctgcag caggcttcct tccaacatga taaagagatg ctccaagcac
6901 aaattgaagc caccaaaaag ctacagcagg aaatgatgaa agttaagcag gcaatgctcc
6961 tagagggtgg gttctctgag acagatgcag cccgcggggc aattaacgcc cccatgacaa
7021 aagctttgga ctggagcggg acaaggtact gggctcccga tgctaggact acaacataca
7081 atgcaggccg cttttccacc cctcaaccat cgggggcact gccaggaaga gctaatctta
7141 gggatgctgc ccctgctcgg ggaccctcca acaaatcttc taattcttct attgccacct
7201 ctgtgtattc aaaccaaact atttcaacga gacttggttc tacagctggt tctggaacca
7261 gtgtctcgag cctcccgtca actgcaagga ctaggagctg ggttgaggat caaaatagga
7321 atttgtcacc tttcatgagg ggggcccaca acatatttgt caccccacca tctagtagat
7381 cctctagcca aggcacagtc tcaaccgtgc ctagagagat tttggactcc tggactggcg
7441 ctttcaacac gcgcaggcag cctctcttcg ctcacattcg taagcgaggg gagtcacggg
7501 tgtaa
//