Typing tool
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Typing tool
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Complete norovirus genomes
| OP205547 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS OP205547 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0168_R03-02 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205547
VERSION OP205547.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7491)
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JOURNAL Unpublished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 7491)
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..7491
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0168_R03-02"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-03-09"
/note="genotype: GII.4 Sydney[P31]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60942.1"
/translation="DASVAAVANSNDDIAKSSSDGVFSNMAVTFKRALGARPKQPPLK
EIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPEEANTAF
SVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
TPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNI
LNILATCDWTFASIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQA
LKNIAIKRCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGCLKPKDD
EEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
KRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPVKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL
IKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPK
LSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIRKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRG
VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKP
TRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPF
ETMIPHSQRPIQLMSLLGEAALHGPAFYSRISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..972
/gene="ORF1"
/product="p48"
mat_peptide 973..2070
/gene="ORF1"
/product="NTPase"
mat_peptide 2071..2607
/gene="ORF1"
/product="p22"
mat_peptide 2608..3006
/gene="ORF1"
/product="VPg"
mat_peptide 3007..3549
/gene="ORF1"
/product="Pro"
mat_peptide 3550..5079
/gene="ORF1"
/product="RdRp"
gene 5063..6685
/gene="ORF2"
CDS 5063..6685
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60943.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEVPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6685..7491
/gene="ORF3"
CDS 6685..7491
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60944.1"
/translation="MAGAFFAGLASDILGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGRFSTPQPSGALPGRANLRDAVPARGPSSNSP
NSSVATSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRGLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gacgcttccg ttgccgctgt tgccaacagc aacgacgaca tcgcaaaatc ttcaagtgac
61 ggtgtgtttt ctaacatggc tgtcactttt aagcgggccc tcggggcgcg gcctaaacag
121 ccgcccctga aggagatacc acccagaccc ccgcgaccac ccacaccaga actggtcaaa
181 aagatccccc ctcccccacc caacggggag gatgaactag tggtctctta cagcgccaga
241 gatggcgttt ccggactgcc tgagctcacc actgtcaggc aaccggaaga agccaacacg
301 gcgttcagtg tccccccact caaccaaagg gagagcaggg acgctaagga gccactaact
361 ggaacaatta ttgaaatgtg ggatggagaa atctaccatt acggcctgta cgtggaacga
421 ggtcttgtac ttggtgtgca caagccaccg gcagccatca gccttgccaa ggtcgagcta
481 acaccgctct ctttgttctg gagacctgta tacacccccc agtatctcat ctccccagac
541 acccttagga gattgcacgg agagtcattc ccctacactg catttgacaa caattgctac
601 gccttttgtt gttgggtatt agacctaaac gactcatggc taagcaggag aatgattcag
661 agaacaacag gtttctttag gccgtaccag gactggaaca agaaacccct ccccactatg
721 gatgactcca aattaaagaa ggtagccaac atattcttgt gcactttgtc ttcgctattc
781 accagaccca ttaaggacat aatagggaag ttgaaacctc ttaacatcct taacattctg
841 gctacatgtg attggacttt cgcaagcata gtggaatctt taatactctt agcagaactc
901 tttggagttt tctggacacc cccagatgtg tctgcgatga tcgccccctt gctaggtgat
961 tatgaactgc aaggacctga ggaccttgca gtggaactgg tccctatagt gatggggggg
1021 ataggtttgg tgttaggatt taccaaagag aagattggaa agatgctatc atccgctgca
1081 tccactttaa gagcttgtaa agaccttggt gcatacggac tggaaatctt aaaattggtc
1141 atgaagtggt tcttcccaaa gaaagaggaa gcaaatgaac tggctatggt gagatccatc
1201 gaggatgcag tactagacct cgaggcaatt gaaaacaacc acatgaccac cctactcaaa
1261 gacaaagaca gcttggcaac ctacatgaga acccttgacc ttgaggagga gaaagccaga
1321 aaactctcaa ccaaatctgc ctcacccgat attgtgggca caatcaacgc tcttctggca
1381 agaatcgctg ctgcacgctc cctagtgcat cgggcgaaag aagaactctc cagcaggccg
1441 agacctgtcg ttgtgatgat atcgggaaga ccagggatag ggaaaactca ccttgccagg
1501 gagctggcca agaaaatcgc ggcctccctc acaggggacc agcgtgtggg tcttatccca
1561 cgcaatggtg tcgatcactg ggacgcatac aagggcgaaa gagttgtcct atgggacgac
1621 tatggaatga gcaaccccat ccatgatgcc ctcaggttgc aggaacttgc tgacacttgc
1681 cctctcacgc taaattgtga cagaattgag aacaaaggaa aagtctttga cagtgatgcc
1741 ataattatca ccaccaacct ggccaaccca gcaccactgg attatgtcaa ttttgaagca
1801 tgctcgagac gtattgactt cctcgtgtac gcagaagccc ctgaggtgga gaaggcaaag
1861 cgtgacttcc caggtcaacc tgacatgtgg aagaacgctt tcagtcctga cttctcacac
1921 ataaaactgt cactggctcc acagggtggt tttgacaaga acggcaacac tccgcatgga
1981 aaaggggtca tgaagaccct caccactggc tccctcatcg cccgagcatc agggttactc
2041 cacgagaggc tagatgaata tgaactgcaa ggcccagccc tcaccacttt caactttgac
2101 cgcaacaaga tacttgcttt tagacagctt gctgctgaaa acaagtatgg gctgatggac
2161 acaatgagag ttggaaaaca gctcaaggat gtcaagacca tgtcagacct caagcaagca
2221 ctcaagaaca tcgcgatcaa gaggtgccag atagtgtaca atggtggcac ctatacactt
2281 gaggccgatg gcaagggtag tgtgaaagtt gacaaagtgc aaagtgccac tgtgcagacc
2341 aacaatgaac tagccggcgc cctacaccac ctaaggtgcg ctagaatcag atactatgtt
2401 aagtgcgtcc aggaggcact gtattccatc atccaaatcg ctggggccgc attcgtcacc
2461 acgcgcatcg ctaagcgcat gaatatacag aatctctggt ccaagccaca ggtggaagac
2521 acagaagaaa tgaccaataa agatggttgc ctaaaaccca aagatgatga agagtttgtc
2581 gtctcatccg acgacatcaa gactgagggc aagaaaggga agaacaagtc cggccgtggc
2641 aagaagcaca cagccttttc aagcaaaggg ctcagtgatg aggagtacga tgagtacaag
2701 agaatcagag aagaaaggaa tggcaagtac tccatagagg agtaccttca ggacagagac
2761 aggtactacg aggagttggc cattgccagg gcaaccgaag aggacttctg tgaagaagaa
2821 gaggccaaaa tccggcagag gatttttaga ccaacaagga aacaacgtaa agaagagagg
2881 gcctctctcg gcttggtcac aggctctgaa atcaggaaga gaaacccaga agacttcaaa
2941 cccaagggga agctgtgggc tgatgatgac agaagtgttg actacaatga gaaactcaac
3001 tttgaggccc caccaagcat ttggtcgcgg atagtcaact tcggttcagg ctggggcttc
3061 tgggtctccc ccagtctgtt tataacatca acccatgtca taccccaagg tgcaaaagag
3121 ttcttcggag tccctgtcaa gcaaatccag gtacacaagt caggtgaatt ctgccggttg
3181 agattcccaa agccaatcag aactgacgtg acgggcatga ttctagaaga gggtgcgccc
3241 gaggggaccg tggtcacact gctcatcaag agaccaactg gagagctcat gcctctggca
3301 gccagaatgg ggacccatgc aaccatgaaa attcagggac gcacagttgg agggcaaatg
3361 ggtatgctct taacaggatc caacgccaag agtatggacc taggcacaac accaggcgac
3421 tgcggctgcc cctacatcta caagaggggg aatgactacg tggtcatagg agtccatacg
3481 gccgctgccc gtggaggaaa caccgtcata tgtgccaccc aggggagtga gggagaagcc
3541 acacttgaag gaggtgacag taaagggacg tactgtggcg caccaatctt gggcccaggg
3601 agcgctccga agctcagcac caagactaag ttttggaggt catccacaac accactccca
3661 cctggcacct acgaaccagc ctacctcggt ggcaaagacc ccagagtcaa aggcggcccc
3721 tcattgcaac aggttatgag ggaccagcta aaaccattca cagaacccag aggcaaacca
3781 ccaagaccaa atgtgttgga agctgccaag aaaaccatta tcaatgtcct tgagcaaaca
3841 attgatccac cccaaaaatg gtcatttgcg caagcttgcg catcccttga caaaaccact
3901 tccagcggcc acccgcacca catgcggaaa aacgattgtt ggaatgggga gtcctttaca
3961 ggtaaattgg ctgatcaagc ctccaaggcc aacctaatgt ttgaagaggg aaagaatatg
4021 actccagtct acacaggtgc acttaaagat gagttggtaa agaccgataa agtttatggt
4081 aagatcagga agaggcttct gtggggttca gatctggcga ccatgatacg gtgcgcccga
4141 gcttttggag gccttatgga tgaactcaag gcgcactgtg tcacacttcc tgtcagagtt
4201 ggcatgaaca tgaatgagga tggccccatc atctttgaga agcactctag atatagatat
4261 cactatgatg ctgattattc ccggtgggac tcaacacaac aaaggggtgt gctagcagca
4321 gcactagaaa tcatggttaa gttctcccca gaaccacacc tggcccaggt ggttgcagaa
4381 gacctccttt cccctagcgt aatggatgta ggtgactttc aaatatcaat aagtgagggt
4441 cttccctctg gggtgccttg cacctcccag tggaattcca tcgcccactg gctcctcact
4501 ctttgtgcac tttctgaagt cacggacctg tcccctgaca tcattcaggc caactccctt
4561 ttctccttct atggtgatga tgagattgtg agcacagata taaagttgga cccagagaag
4621 ctgacagcaa aactcaagga gtacgggctg aaaccaaccc gccccgacaa aactgaagga
4681 ccccttgtta tctctgaaga tctagatggc ctaacattcc tccggagaac tgtgacccgt
4741 gacccagctg gctggtttgg aaaattggaa cagagttcaa ttcttagaca aatgtactgg
4801 actaggggtc ccaaccatga agatccattt gaaacaatga taccacactc ccaaagaccc
4861 atacaattga tgtccttgct gggcgaggct gcactccacg gcccggcatt ttatagcaga
4921 attagcaaat tagtcattgc agagttgaag gaaggtggca tggattttta cgtgcccaga
4981 caggagccaa tgttcagatg gatgagattc tcagatctga gcacgtggga gggcgatcgc
5041 aatctggctc ccagttttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5101 gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt atggctctgg agcccgttgt
5161 tggtgccgcc attgcggcac ctgtagcggg ccaacagaat gtaattgacc cctggatcag
5221 aaacaatttt gtacaagccc ctggtggaga gttcacagta tcccccagaa acgctccagg
5281 tgaaatacta tggagcgcgc ccttgggccc tgatctaaat ccctacctat cccatttggc
5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaatcctcg cggggaacgc
5401 gttcaccgct gggaaggtca tatttgcagc agtcccacca aattttccaa ctgaaggctt
5461 gagccccagc caggtcacta tgttccccca tatagtggta gatgttaggc aactagaacc
5521 tgtactgatt cccttacccg atgttaggaa taatttttac cattacaatc aatcaaatga
5581 tcccactatt aagttgatag caatgttgta tacaccactt agggctaata atgctggtga
5641 tgatgtcttc acagtttctt gccgagttct cacgagacca tcccccgact ttgatttcat
5701 atttctagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac
5761 tgttgaggaa atgaccaatt caagatttcc cattcctttg gaaaagctgt tcacgggccc
5821 cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc acgactgatg gcgtgctcct
5881 aggtaccacc caactgtccc ctgtcaacat ctgcaccttc aggggagatg tcacccacat
5941 cacaggcagt cacaactata caatgaattt ggcttctcaa aattggaata attatgaccc
6001 aacagaagaa gtcccagccc ctctagggac tccagacttt gtggggaaga ttcaaggtgt
6061 gctcacccaa accacaagga cagatggctc aacacgtggc cacaaagcca cagtgtacac
6121 tgggagcgcc gactttgccc caaaactggg tagagttcaa tttgaaactg acacaaacca
6181 tgattttgaa gctaaccaaa acacaaagtt caccccagtc ggtgttatcc aagatggtag
6241 taccacccac cggaatgaac ctcagcagtg ggtgctccca agttactcag gcaggaacac
6301 tcacaatgtg catctggctc ccgctgtagc ccccactttt ccgggtgagc aacttctctt
6361 cttcaggtcc accatgcccg gatgcagcgg gtaccccaac atggatctgg attgtctgct
6421 cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat ctgatgtggc
6481 cctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgta agctccataa
6541 atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttattc cccccaatgg
6601 ttattttaga tttgattcct gggtcaacca gttctacaca cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgcag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 atccttggct ctggacttgg ttcccttatc aatgctgggg ctggggccat caaccaaaaa
6781 gttgagtttg aaaacaacag aaaattgcaa caagcatcct tccaatttag cagcaatcta
6841 caacaggctt cctttcaaca tgacaaagag atgctccaag cacaaattga ggccaccaaa
6901 aagttacaac aggaaatgat gagagtcaag caggcaatgc tcctagaggg tgggttctct
6961 gagacggatg cggcccgtgg ggcaatcaac gcccccatga caaaagctct ggattggagc
7021 gggacaaggt actgggctcc cgatgctagg atcacaacat acaatgcagg ccgtttttcc
7081 acccctcaac catcgggagc actgccagga agagctaacc ttagggatgc tgtccctgct
7141 cggggtccct ccagtaattc tcctaactct tctgtcgcta cttctgttta ttcaaatcaa
7201 actacttcaa cgagacttgg ttctacagct ggttctggcg ccagtgtctc gagcctcccg
7261 tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggggtttgtc acctttcatg
7321 aggggggccc acaatatatc gtttgtcacc ccaccatcta gcagatcctc tagccaaggc
7381 acagtctcaa ccgtgcccaa agagattttg gactcctgga ctggcgcttt caacacgcgc
7441 aggcagccac tcttcgctca cattcgtagg cgaggggagt cacgggtgta a
//