Typing tool
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Typing tool
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Complete norovirus genomes
| OP205559 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS OP205559 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0444_R03-14 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205559
VERSION OP205559.1
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JOURNAL Unpublished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-2018-0444_R03-14"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-11-10"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60978.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DEPQKPPRPPTPELVKRIPPPPPNGEEEEEPAIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK
QAIRTVTIKRCRIIYGGSTYDLESDGKGKVLVEKVRNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIMQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEAPKSED
DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCVSLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDVKLDPEQLTAKLKEYGLKP
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="UUV60979.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHTTGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG
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="UUV60980.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRASLRDAVPSRGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTSRQPLFAHIRKRGESRV"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagacgaacc acaaaagccc ccaagaccac caactcccga gttggtcaag
181 aggatacccc ctcctccacc taatggcgaa gaagaagagg aaccagccat taggtatgag
241 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgtggcc
301 aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg
361 ctaacagggg caatattaga gatgtgggac ggagagatat accactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtacacaaa ccacctgcag ccataagcat ggcaagagtg
481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaacaac
601 tgctatgcct tttgctgctg ggtgttagac ctcaatgact cgtggcttag caggaggatg
661 gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgccc
721 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttattcacca gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaac
841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg 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 cactcagggc ttgcaaagat cttggtgcct atggcttgga gatactcaaa
1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg
1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg
1381 ctggctcgaa tagcagcagc caggtcatta gtccacaggg ccaaggaaga gctatctagc
1441 aggataagac cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg
1501 gccagggagg tagcaaggaa ggtagcatcc actctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg
1621 gacgactatg gcatgagtaa ccccattcac gatgctcttc gcatacaaga attggctgat
1681 acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt
1741 gaagtcataa taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt
1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag
1861 gcaaaacggg attttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt
1921 tcacacatca agctacagct tgcacctcag ggcggctttg acaagaatgg caacacccca
1981 catgggaaag gggtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggt
2041 ctactgcatg aaaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat
2101 tttgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg
2161 gtggatacca tgaaagttgg caatcaacta aaaggagtga aaaccatgga agaactcaaa
2221 caagcaatca ggactgtgac catcaagagg tgccggatca tctacggtgg ctccacttat
2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaggaa cacctctgtg
2341 cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg aatcaggtac
2401 tatgttaaat gtgtgcaaga agcagtctat tccatcatgc aaattgccgg cgctgcgttt
2461 gtcaccacgc gcattgcgcg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2521 gatcaaaatg agtcagaggc taaggaagag gcccccaagt cagaagatga cgagttcatt
2581 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc
2641 aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 aggataagag aagagagaaa tgggaaatac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa ggaagagagg
2881 gccacattag ggctggtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggga agctgtgggc cgatgacaac aggagtgttg actacaatga gaaactggac
3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3061 tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg cataacagaa
3121 gcatttggag tccccatcaa acagattcag atccacaaat caggtgaatt ttgccgattc
3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggcgcgcct
3241 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac
3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca
3541 actcttgagg gtggagatga taaaggaaca tactgtgggg cacccatttt aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3661 ccagggacat atgagcctgc ctaccttggt ggccgtgatc cgcgtgttaa gggtgggccc
3721 tccttgcagc aggtgatgag agaccagttg aagccattca ctgaacccag gggcaaacct
3781 ccaaggccaa gtgtactgga agcagccaaa caaaccatta tcaatgttct cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcactaga caaaaccacc
3901 tccagcgggc atccccatca tgtccgaaag aatgaattct ggaatggtga gaccttcact
3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg
4021 acaccagtgt atacagcagc actcaaggat gagctagtta agactgagaa aatctatgga
4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg
4141 tcatttggtg ggctcatgga cgagatgaag gcacactgcg tatcactccc agtacgagtt
4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatac
4261 cactatgatg cagactactc tcgttgggat tcaacacaac aaagggcagt 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 caccaaactg tcccctgaca ttatacaagc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgacg taaaattgga ccctgaacag
4621 ttaaccgcca agttgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgaggga
4681 cccctgatca tcagtgaaga tttgaacgga ctcacttttc tccgaaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaaactggac caaagttcaa ttttgaggca gatgtactgg
4801 actagaggac caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc
4861 atacagctta tggcactgct tggtgaagcc tctcttcacg ggccctcttt ctatagtaga
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 caatgaggtt atggctttgg agcccgttgt
5161 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5221 aaataatttt gtacaagccc ctggtgggga gtttacagtg tcccctagaa acgctccagg
5281 tgaaatatta tggagcgcgc ccctaggccc tgacctaaat ccctacctat cccatttggc
5341 cagaatgtac aatggctatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc
5401 gttcaccgcc gggaagatta tatttgcagc agttccaccg aattttccaa ctgaaggctt
5461 aagtcctagc caggtcacta tgtttcccca tataatagta gatgttaggc aattagaacc
5521 tgtgctgatt cccttacccg acgttaggaa taacttctat cattacaatc agtcaaatga
5581 ctccactatt aagttgatag caatgttgta cacaccactt agggctaata atgctggaga
5641 tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt ttgatttcat
5701 atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac
5761 tgttgaggag atgaccaatt caagattccc catccctttg gaaaagttat tcacaggccc
5821 cagcagtgcc tttgttgttc aaccacaaaa tggcaggtgc acaactgatg gcgtgctcct
5881 aggcaccacc caactttctc ctgtcaacat ctgtaccttc agaggggatg tcacccacac
5941 cacaggtagt cacaactaca caatgaattt ggcttctcaa aactggaaca actatgaccc
6001 aacagaagaa atcccagccc ctctaggaac tccagatttt gtagggaaga ttcaaggcat
6061 gctcacccaa accacaagga cagatggttc aacacgcggc cacaaagcta cagtatacac
6121 tgggagcgcc gacttcgctc caaaactggg tagagttcaa tttgcaactg acacagacca
6181 tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc aagatggtag
6241 caccacccac cgaaacgaac cccagcagtg ggtgctccca agttactcag gcagaaatac
6301 tcacaatgta catttggccc ccgctgtagc ccccaccttt ccgggtgagc aacttctctt
6361 tttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgtctgct
6421 cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat ctgatgtggc
6481 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcataa
6541 atcaggctat gttacagtag ctcacactgg ccaacatgat ttggttatcc ctcccaatgg
6601 ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 gtccttggct ctggacttgg ttctcttatc aatgctgggg ctggggccat caaccaaaaa
6781 gttgaatttg aaaataacag aaaattgcaa caagcatcct tccaatttag tagcaatttg
6841 caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga ggccaccaaa
6901 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcttagaggg tgggttctct
6961 gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt ggactggagc
7021 gggacaaggt actgggctcc agatgctagg attacaacat acaatgcagg ccacttttcc
7081 acccctcaac catcgagggc actgccagga agagctagtc tcagggatgc tgtcccttct
7141 cggggaccct ccaataaatc ttctaactct tctactgcta cctctgtgta ctcaaatcaa
7201 actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagtctcccg
7261 tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggaatttgtc acctttcatg
7321 agaggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc tagccaaggc
7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caacacgagc
7441 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta a
//