Typing tool
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Typing tool
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Complete norovirus genomes
| OP205560 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS OP205560 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0445_R03-15 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205560
VERSION OP205560.1
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JOURNAL Unpublished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-2018-0445_R03-15"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-11-13"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60981.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DESQKPLRPPTPELVKRIPPPPPNGEEEEGPAIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENKEAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVNTMKVGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEAPKSED
DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..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="UUV60982.1"
/translation="MKMASSDANPSDGSAANLVPEVNSEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6685..7491
/gene="ORF3"
CDS 6685..7491
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60983.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSIPQPSRALPGRANPSDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRGLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagacgaatc acaaaagccc ctaagaccac caactcccga gttggtcaag
181 aggatacccc ctcctccacc taatggcgaa gaagaggaag gaccagccat taggtatgag
241 gtcaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggatgtggcc
301 aacacggcat tcagtgttcc accactgagc ttgagagaaa acaaggaggc caaggaaccg
361 ctaacagggg caatactaga gatgtgggac ggagagatat accactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg
481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtata ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaataac
601 tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg
661 gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgccc
721 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttattcacca gacccataaa ggacctcata ggaaaaatta aaccattaaa catattgaac
841 atcctggcaa cgtgtgactg gacgtttgcc gggatagtgg agtctctgat attacttgct
901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc
961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg
1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca
1081 gcagcatcaa cacttagggc ttgcaaagat cttggtgcct atggcttaga gatactcaaa
1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg
1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacagccctg
1261 ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg
1381 ctggctcgaa tagcagcagc caggtcatta gtccacaggg ccaaggaaga gctatctagc
1441 aggataagac cagtggttgt tatgatatct ggtaaaccag gaataggtaa aactcatctg
1501 gccagggagg tggcaagaaa ggtggcatct actctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg
1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat
1681 acgtgtcccc tcaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt
1741 gaagtcataa taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaatttt
1801 gaggcctgtt cccggagaat tgatttcctg gtgtacgctg aggcaccaga agtggaaaag
1861 gcaaaacggg attttcctgg ccagccagat atgtggaagg acgccttcaa gccggacttt
1921 tcacacatca agctacagct tgcacctcaa ggcggctttg acaagaatgg taacacccca
1981 catgggaaag gggtaatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc
2041 ctactacatg agaggatgga tgaattcgaa ctccaaggtc ccacaatcac caccttcaat
2101 ttcgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatgggtta
2161 gtgaatacca tgaaggttgg caatcaacta aaaggagtga aaaccatgga agaactcaaa
2221 caagcaatca ggaatgtgac catcaagagg tgccggatca tctatggtgg ctccacgtat
2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta
2341 cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg aatcaggtac
2401 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt
2461 gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2521 gatcaaaatg aatcagaagc taaggaagag gcccccaagt cagaagatga cgagttcatc
2581 atatcttcta aggacatcaa agaggaagga aagaagggca aaaacaaaac tggccgtggc
2641 aagaaacaca ctgcgttctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgccagag aattttccgc cccaccagga aacaaagaaa ggaagagagg
2881 gccacattag ggctggtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggga agctatgggc cgatgacaac agaagtgttg actacaatga gaaactggac
3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg atggggcttc
3061 tgggtgtcac caagcctgtt cataacatca actcatgtaa tccccgcagg cataacagaa
3121 gcatttggcg tccccatcaa acaaattcag atccacaaat caggtgaatt ttgccgattc
3181 agattcccaa aaccaattag gccagatgtg acaggaatga tcttggaaga aggtgcgcct
3241 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3361 ggcatgttgc tcactgggtc gaatgctaag ggaatggatt tgggaacaac tcctggtgac
3421 tgtggttgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcggccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca
3541 actcttgagg gtggagatga taaaggaaca tactgtgggg cacccatttt aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3661 ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc
3721 tccttgcagc aggtaatgag agaccagttg aagccattca ctgaacccag gggcaaacct
3781 ccaagaccaa gtgtattgga agcagccaaa cagaccatta tcaatgttct cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatatgca caggcgtgtg cctcacttga caaaaccacc
3901 tccagcgggc atccccatca cgtccgaaag aatgaattct ggaatggtga gaccttcact
3961 ggcaaattgg cagaccaagc atcaaaagca aacctaatgt tcgaggaagg gaaacatatg
4021 acaccagtgt acacagcagc actcaaggat gagctagtta agactgagaa aatctatgga
4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg
4141 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtacgagtt
4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatac
4261 cactatgatg cagactactc tcgttgggat tcaacacaac agagggcagt actagcagca
4321 gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag
4381 gatctactgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg
4441 ctcccatctg gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact
4501 ctctgtgcct tgtctgaagt cactaaactg tcccctgaca ttatacaagc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag
4621 ttaaccgcca agttgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgaggga
4681 cccctgatca tcagtgagga tttgaacggg ctcactttcc tccgaaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaaactggac caaagttcaa ttttgaggca gatgtactgg
4801 actagaggac caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc
4861 atacagctca tggcactgct tggtgaagcc tctcttcatg gaccctcttt ctacagtaga
4921 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5101 gtccgcagcc aacctcgtac cagaggtcaa cagtgaggtt atggctttgg agcccgttgt
5161 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5221 aaataatttt gtacaagccc ctggtgggga gtttacagtg tcccctagaa acgctccagg
5281 tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat cccatttggc
5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc
5401 gttcaccgcc gggaagatta tatttgcagc tgtcccacca aattttccaa ctgaaggctt
5461 aagtcctagc caggtcacta tgttccccca tataatagta gatgttagac aactagaacc
5521 tgtgctgatt cccttacccg atgttaggaa caatttctac cattacaatc agtcaaatga
5581 ctccactatt aagttgatag caatgttgta cacaccactt agggctaata atgctggaga
5641 tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt ttgatttcat
5701 atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc caattttaac
5761 tgttgaggag atgaccaatt caagattccc catccctttg gaaaagttgt tcacaggccc
5821 cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct
5881 aggcaccacc caactctctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat
5941 cacaggtagt cgcaactaca caatgaattt ggcctctcag aattggaaca actatgaccc
6001 aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga ttcaaggcat
6061 gctcacacaa accacaaggg cagatggttc aacacgcggc cacaaagcca cagtgtacac
6121 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacagacca
6181 tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc aagatggtag
6241 cactacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaacac
6301 tcacaatgta catttggccc ccgctgtagc ccccaccttt ccgggtgagc aacttctctt
6361 cttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgtctgct
6421 cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat ctgatgtggc
6481 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcataa
6541 atcaggctat gttacagtgg ctcacactgg ccaacatgat ctggttatcc cccccaacgg
6601 ttactttagg tttgattcct gggtcaacca gttctacaca cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 gtccttggct ctggacttgg ttccctcatc aatgctgggg ctggggccat caaccaaaaa
6781 gttgaatttg aaaataacag aaaattgcaa caagcatcct tccaatttag cagcaatctg
6841 caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga ggccaccaaa
6901 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcctagaggg tgggttctct
6961 gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt ggactggagc
7021 gggacaaggt actgggctcc agatgctagg attacaacat acaatgcagg tcacttttcc
7081 atccctcaac catcgagggc actgccagga agagctaatc ctagtgatgc tgtccctgct
7141 cggggaccct ccaacaaatc ctctaactct tctactgcca cctctgtgta ctcaaatcaa
7201 actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagcctcccg
7261 tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggggcttgtc acctttcatg
7321 agaggggccc ataacatatc atttgtcacc ccaccatcta gcagatcctc tagtcaaggc
7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caacacgcgc
7441 aggcagcctc tcttcgcaca cattcgtaag cgaggggagt cacgggtgta a
//