Typing tool
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Typing tool
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Complete norovirus genomes
| OP205550 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7459
LOCUS OP205550 7459 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0335_R03-05 nonstructural
polyprotein (ORF1) gene, partial cds; VP1 (ORF2) gene, complete
cds; and VP2 (ORF3) gene, partial cds.
ACCESSION OP205550
VERSION OP205550.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7459)
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JOURNAL Unpublished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 7459)
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..7459
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0335_R03-05"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-08-22"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60951.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DKSQKPPRPPTPELVKKIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNKITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSED
DEFIISSKDIKEEGKKGKNKTGRGRKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFT
SKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEVMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWM
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="UUV60952.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6685..>7459
/gene="ORF3"
CDS 6685..>7459
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60953.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFGNNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQSSGALPGRTNLRDAVPARGPLSKSS
NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFA"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagacaaatc acaaaagccc ccaagaccac caactcccga gttggtcaag
181 aagatacccc ctcctccacc taatggtgaa gaagaagaag aaccagtcat taggtatgag
241 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgtggcc
301 aacacagcat tcagcgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg
361 ctaacagggg caatattaga gatgtgggat ggagagatat accactacgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagta
481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct caacggagag gcattccctt acaccgcctt tgacaacaac
601 tgctatgcct tttgttgctg ggtgttagac ctcaacgact catggcttag caggaggatg
661 gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgcct
721 accatggatg actccaaaat caagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttattcacca gacccataaa agacctcata ggaaaaatca aaccattgaa catattgaat
841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgct
901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc
961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtgcc tgtggtaatg
1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca
1081 gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga gatactcaaa
1141 ttggtcatga agtggttctt cccgaagaaa gaggaggcca atgagctagc catggtgagg
1201 gccatagagg atgctgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg
1381 ttggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga gctatctagc
1441 aggatgagac cagtagttgt catgatatct ggcaaaccag gaataggaaa aactcatctg
1501 gccagggagg tggcaagaaa ggtggcatcc accctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtcga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg
1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga gttggctgat
1681 acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt
1741 gaagtcataa taattacaac aaaccttgcc aatccagccc cacttgatta tgtcaacttt
1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag
1861 gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa gtcggacttt
1921 tcacacatca agctacagct tgcaccacag ggcggctttg ataagaatgg caacacccca
1981 catgggaaag gagtgatgaa gaccctcacc accggttctc tgattgcccg tgcatcaggc
2041 ctgctgcacg agaggatgga tgaatttgag ctccaaggtc ccacaatcac caccttcaac
2101 ttcgaccgga acaaaatcac agcattcaga caattggctg cagaaaacaa gtatggattg
2161 gtggatacca tgaaagtcgg caatcaacta aaaggagtga aaaccatgga agaactcaaa
2221 caagcaatca ggaatgtgac cattaagagg tgccggatca tctacggtgg ttccacgtat
2281 gaccttgaat ctgatggcaa gggcaaagtt ctggtggaaa aggtcaagaa cacctctgtg
2341 cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg aatcaggtac
2401 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt
2461 gtcactacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2521 gatcaaaatg aatcagagac taaggaagag gcccccaagt cagaagatga cgagtttatc
2581 atatcttcta aggacatcaa ggaagaagga aagaagggca aaaacaaaac tggccgtggc
2641 aggaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 agaataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaaa gctacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgccagag aattttccgt cccaccagga aacaacgaaa ggaagagagg
2881 gccacactag ggctagtgac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggaa agctgtgggc cgatgacaac agaagtgttg actataatga gaaactggac
3001 tttgaggccc ctccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3061 tgggtatcac caagcctgtt cataacgtca actcatgtaa tccccgcagg cataacagaa
3121 gcatttggag ttcccatcaa acaaattcag atccacaaat caggcgaatt ttgccgattc
3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggagga aggtgcgcct
3241 gagggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gctagaatgg gaactcacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt taggaacaac tcctggtgac
3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgcgccacac agggaagtga gggcgaggca
3541 actcttgaag gtggagatga caaaggaaca tactgtgggg cacccattct aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3661 ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc
3721 tccttgcagc aggtgatgag agaccagttg aagccattca ctgaacccag gggcaaaccc
3781 ccaagaccga gtgtattaga agcagccaag caaaccatca tcaatgtcct cgaacaaact
3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc
3901 tccagcgggc atccctatca cgtccgaaag aatgaattct ggaatggtga gaccttcact
3961 agtaaattgg cagaccaagc gtcaaaagca aacctaatgt ttgaggaagg gaaacacatg
4021 acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa aatctatgga
4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg
4141 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtccgagtc
4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat
4261 cactacgatg cagactactc tcgttgggat tcaacgcaac agagggcagt actagcagca
4321 gccttggaag tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag
4381 gatctgctag cccccagtgt ggtagatgtg ggagacttta aaataacaat aaatgaaggg
4441 ctcccctctg gtgtgccatg tacttctcaa tggaactcca tcgcacattg gctgctaact
4501 ctatgtgcct tgtctgaggt caccaaactg tcccctgaca ttatacaggc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaactgga ccctgaacag
4621 ctaaccgcta aattaaagga gtacggcctg aaaccaaccc gcccagacaa aaccgaggga
4681 cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccggaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaaactggac caaagctcaa ttttgaggca gatgtactgg
4801 actagaggac caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc
4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaaa
4921 atcagcaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5101 gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg agcccgttgt
5161 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5221 aagtaatttt gtacaagccc ctggtggaga gtttacagtg tcccctagaa acgctccagg
5281 tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat cccacttggc
5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaatcctcg cggggaacgc
5401 gttcaccgcc gggaagatca tatttgcagc agtcccacca aattttccaa ctgaaggctt
5461 aagtcctagc caggtcacta tgttccccca tataatagta gatgttagac aattagaacc
5521 tgtgctgatt cccttacccg atgttaggaa taacttctat cattataatc aatcaaatga
5581 ctccactatt aagttgatag caatgttgta tacaccactt agggctaaca atgctgggga
5641 cgatgtcttc acagtttcgt gccgagttct cacgagacca tcccccgact ttgatttcat
5701 attcttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc cagtcttgac
5761 cgttgaggag atgaccaatt caagatttcc cattcctttg gaaaagttgt tcacaggccc
5821 cagcagtgcc tttgtcgttc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct
5881 aggcaccaca caattgtctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat
5941 cacaggtagt cacaactaca cgatgaattt ggcttctcaa aattggaaca attatgaccc
6001 aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga ttcaaggcat
6061 gctcacccaa accacaagga cagatggttc aacgcgcggc cacaaagcta cagtgtacac
6121 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacaaacca
6181 tgattttgaa gccaaccaaa atacaaagtt caccccagtc ggtgtcatcc aagatggtag
6241 caccacccac cgaaatgaac cccaacagtg ggtgctccca agttactcag gcagaaacac
6301 tcacaatgta cacctggccc ccgctgtagc tcccaccttt ccgggtgaac aacttctctt
6361 ctttagatcc accatgcccg gatgcagcgg ataccccaac atggatttgg actgtctgct
6421 cccccaggaa tgggtgcagt acttctacca ggaggcagcc ccagcacaat ctgatgtggc
6481 tttgctaaga tttgtgaatc cagacacagg tagggttttg tttgaatgca agcttcacaa
6541 atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc cccccaatgg
6601 ttactttagg tttgattcct gggtcaacca gttctacaca ctcgccccca tgggaaatgg
6661 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 gtcctcggct ctggacttgg ttcccttatc aatgctgggg ctggggccat caatcaaaaa
6781 gttgagttcg gaaacaacag aaaattgcaa caagcatcct tccaatttag cagcaatctg
6841 caacaggctt cctttcaaca tgacaaagag atgctccaag cacaaattga ggccaccaaa
6901 aagctacaac aggaaatgat gaaggttaag caggcaatgc tcctagaggg agggttctct
6961 gaaacagatg cagcccgcgg ggcaattaac gcccccatga caaaagctct agactggagc
7021 gggacaaggt actgggctcc cgatgctagg actacaacat acaatgcagg ccgcttttcc
7081 acccctcaat catcgggggc actgccagga agaactaatc ttagggatgc tgttcctgct
7141 cggggacccc tcagtaaatc ttctaactct tctactgcca cctctgtgta ctcaaatcaa
7201 actgcttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtttc gagcctcccg
7261 tcgactgcaa ggactaggag ctgggttgag gaccaaagta ggaatttgtc acctttcatg
7321 aggggggccc acaacatatc atttgtcacc ccaccatcta gtaggtcctc tagccaaggc
7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caacacgcgc
7441 aggcagcctc tcttcgctc
//