Typing tool
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Typing tool
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Complete norovirus genomes
| OP205555 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS OP205555 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0382_R03-10 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205555
VERSION OP205555.1
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JOURNAL Unpublished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-2018-0382_R03-10"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-10-05"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60966.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DEPQKPPRPSTPELVKRVPPPPPNGEEEEEPVIRYEVKGGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLMDTMKVGNQLKGVKTMEELK
QAIKNVTIKRCRIIYGGSTYDLESDGRGKVLVEKVKNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSED
GEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
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="UUV60967.1"
/translation="MKMASSDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRSTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
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="UUV60968.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPPGALSGRANLRDAVPARGPSIKSS
NSSAATSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTHRQPLFAHIRKRGESRV"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagacgaacc acaaaaaccc ccgagaccat caacccccga gttggtcaag
181 agggtacccc ctcccccacc taatggtgaa gaggaagaag aaccagtcat taggtatgag
241 gttaagggtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgtggcc
301 aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg
361 ctaacagggg caatattgga gatgtgggat ggagagatat accactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg
481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt tgacaacaac
601 tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg
661 gtgcagagaa caacgggctt ctttagacct taccaagagt ggaacagaaa acccctgccc
721 accatggatg actccaaaat taagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttattcacca gacctataaa agacctcata ggaaaaatta aaccattaaa catattgaac
841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat actacttgct
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 atggcttaga gatactcaaa
1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgaga
1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ttgaaagaca aagacagctt agcaacatat atgaaaacac tggacatgga ggaggagaaa
1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat taacgccctg
1381 ctggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga gctatctagc
1441 aggataagac cagtagttgt tatgatatct ggcaaaccag ggataggcaa aacccatctg
1501 gccagggagg tggcaagaaa ggtggcatcc actctcacag gggatcaaag agttggactc
1561 ataccaagaa acggtgtgga ccactgggat gcatacaaag gtgagagagt cgtgctgtgg
1621 gacgactacg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgac
1681 acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgatagt
1741 gaagtcataa taattacaac aaaccttgcc aatccagccc cacttgatta tgtcaacttt
1801 gaggcctgtt ccaggagaat tgatttcctg gtgtatgctg aggcaccaga agtggaaaag
1861 gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt
1921 tcacacatca agttacagct tgcacctcag ggcggctttg acaagaatgg caacacccca
1981 catgggaaag gagtgatgaa gaccctcact accggttcac tgattgcccg tgcatcaggc
2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat
2101 ttcgaccgga acagaatcac agcattcagg caattggctg cagaaaacaa gtatggattg
2161 atggacacca tgaaagttgg caatcaacta aaaggagtga aaaccatgga agaactcaaa
2221 caagcaatca agaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtac
2281 gaccttgaat ctgatggcag gggcaaagtt ttagtggaaa aggtcaagaa tacctctgta
2341 cagaccaaca acgagttggc cggggccctg caccacctca aacacgcccg aatcaggtat
2401 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt
2461 gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaacta
2521 gatcaaaatg aatcagagac taaggaagag gcccccaagt cagaagatgg cgagttcatc
2581 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc
2641 aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 aggataaggg aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa ggaagagagg
2881 gccacattag ggctagtgac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggga agctgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac
3001 tttgaggccc ctccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3061 tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg cataacagaa
3121 gcatttggag tccccatcaa acaagttcag atccacaaat caggtgaatt ttgccgattc
3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct
3241 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg gaacacacgc aaccatgaaa atccaaggcc gcatggttgg cggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac
3421 tgtggctgcc cttacatcta taaaaggggc aatgactaca tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgtgctacac agggaagtga gggtgaggca
3541 actcttgagg gtggagatga taaaggaaca tactgtgggg cacccattct aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3661 ccagggacat atgagcctgc ctacctcggt ggtcgtgatc cgcgtgttaa gggtgggccc
3721 tccttgcagc aggtaatgag agaccaattg aagccattca ctgaacccag gggcaagcct
3781 ccaagaccaa gtgtattgga ggcagccaaa caaaccatta tcaatgtcct cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatacgcg caggcgtgtg cctcacttga caaaaccacc
3901 tccagcgggc atccccatca cgtccgaaag aatgaattct ggaatggtga gaccttcact
3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt tcgaggaagg gaaacacatg
4021 acgccagtgt atacagcagc actcaaggac gagctagtca agactgagaa aatctatgga
4081 aagatcaaga agagactgct ttggggctct 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 gatctgctgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg
4441 ctcccatctg gtgtgccatg cacttctcaa tggaattcca tcgcacactg gctgctaact
4501 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc aaattccatg
4561 ttctcatttt atggtgatga tgagattgtc agcaccgaca taaaattgga ccctgaacag
4621 ttaaccgcta aattgaagga gtatggcctg aaaccaactc gcccagacaa gaccgaagga
4681 cccctgatca tcagtgaaga tttgaatggg ctcactttcc tccgaaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaagctggac caaagctcaa ttttgaggca gatgtactgg
4801 actagaggac caaatcatga agaccccaat gagacaatga taccccactc tcaaagaccc
4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccatcttt ctacagtaaa
4921 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgagattt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5101 gtccgcagcc aacctcgtac cagaggtcag caatgaggtt atggctttgg agcccgttgt
5161 tggtgccgcc attgcggcac ctgtggcggg tcaacaaaat gtaattgacc cctggattag
5221 aaataatttt gtacaagccc ctggtgggga gtttacagta tcccctagaa acgctccagg
5281 tgaaatacta tggagcgcgc ccctaggccc tgatctaaat ccctacctat cccatttggc
5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc
5401 gttcaccgcc gggaaggtca tatttgcagc agtcccacca aattttccaa ctgaaggatt
5461 aagtcccagc caggtcacta tgttccccca tatagtagta gatgttaggc aattagaacc
5521 tgtgctgatt cccttacccg atgttaggaa taatttctat cattacaatc agtcaaatga
5581 ccccactatt aagttgatag caatgttgta tacaccactt agggctaata atgctgggga
5641 tgatgttttc acagtttcgt gcagagttct cacgaggcca tcccccgatt ttgatttcat
5701 atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac
5761 tgttgaggag atgaccaatt caaggttccc catccctttg gaaaagttgt tcacgggccc
5821 cagcagtgcc tttgttgttc aaccacaaaa cggcagatgt acaactgatg gcgtgctcct
5881 aggcaccacc caactgtctc ctgtcaacat ctgcactttc agaggggatg tcacccacat
5941 cacaggtagt cgcaactaca caatgaattt ggcttctcaa aattggaaca actatgaccc
6001 aacagaagaa attccagccc ctctaggaac tccagatttt gtggggaaga ttcaaggcat
6061 gctcacccaa accacaagaa cagatggttc aacacgcggc cacaaagcca cagtgtacac
6121 tgggagcgcc gactttgctc caaaactggg tagagtccaa tttgaaactg acacagacca
6181 tgatttcgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc aagatggcag
6241 caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaagtac
6301 ccacaatgta catctggccc ccgctgtagc ccccaccttc ccgggtgagc aacttctctt
6361 cttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgtctgct
6421 cccccaggaa tgggtgcaat acttctacca agaggcagcc ccagcgcaat ctgatgtggc
6481 tctgttaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcacaa
6541 atcaggctac gttacagtgg ctcacactgg ccaacatgat ttggttatcc cccccaatgg
6601 ttactttagg tttgactcct gggtcaacca gttctacacg cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 gtccttggct ctgggcttgg ttcccttatc aatgctgggg ctggggccat caaccaaaaa
6781 gtagagtttg aaaataacag aaaattacaa caggcatcct tccaatttag cagcaatctg
6841 caacaagcat cctttcaaca tgacaaagag atgctccaag cacaaattga ggccaccaaa
6901 aagttacaac aggaaatgat gagagttaaa caggcaatgc tcctagaggg tgggttctct
6961 gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagtttt ggactggagc
7021 gggacgaggt actgggctcc cgatgctagg actacaacat acaatgcagg ccgcttttcc
7081 acccctcaac caccgggtgc actgtcagga agagctaatc ttagggatgc tgtccctgct
7141 cggggaccct ccattaaatc ttctaactct tctgctgcca cctctgtata ctcaaatcaa
7201 actgtttcaa cgagacttgg ttctacagct ggttctggga ccagtgtctc gagcctcccg
7261 tcaactgcga ggactaggag ctgggttgag gatcaaagta ggaatttgtc acctttcatg
7321 aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc cagccaaggc
7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caatacgcac
7441 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta a
//