Typing tool
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Typing tool
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Complete norovirus genomes
| OP205572 | GII.3 | |
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| GII.P12 |
ORF1: 1..5099
ORF2: 5080..6726
ORF3: 6726..7487
LOCUS OP205572 7487 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0440_R04-03 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205572
VERSION OP205572.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7487)
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JOURNAL Unpublished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 7487)
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..7487
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0440_R04-03"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-11-03"
/note="genotype: GII.3[P12]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV61017.1"
/translation="KMASNDASAAAAANNNSDNAKSSSDGMLSSMAVTFKRALGARQK
PPPPREIPQRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVWQPDE
TNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISL
AKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSW
LCRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKV
RPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEANELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLSTK
SASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELA
RKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCP
LTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA
KRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS
GLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLLDTMRVGKQLKDVKTMS
ELKQALKNVAIKSCQIVYGGCTYRLESDGKGDVKVDRVQNATVQTNNELAGALHYLRC
ARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEEIASKDGCL
KPQDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT
GSEIRKRNPDDFKPKGKLWADDDRSVDYNERLNFEAPPSIWSRIVNFGSGWGFWVSPS
LFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGT
VVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGP
GSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPR
GRPPKPSVLEAAKKTIVNVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWN
GESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLA
TMIRCARAFGGLMEELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVKFSPEPHLAQKVAEDLLSPSVMDVGDFKISINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKE
YGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPN
HEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..989
/gene="ORF1"
/product="p48"
mat_peptide 990..2087
/gene="ORF1"
/product="NTPase"
mat_peptide 2088..2624
/gene="ORF1"
/product="p22"
mat_peptide 2625..3023
/gene="ORF1"
/product="VPg"
mat_peptide 3024..3566
/gene="ORF1"
/product="Pro"
mat_peptide 3567..5096
/gene="ORF1"
/product="RdRp"
gene 5080..6726
/gene="ORF2"
CDS 5080..6726
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61018.1"
/translation="MKMASNDATPSNDGAAGLVPEINNEAMALDPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPEFSFNFLVPP
TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTAGRFTPKLGSLEISTESGDFDQNQP
TRFTPVGIGVDHEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRVQ"
gene 6726..7487
/gene="ORF3"
CDS 6726..7487
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61019.1"
/translation="MAGAFIAGLAGDILTNTVGSLVNAGANAINQKVDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPSATSTTSMSGGFTNQAVHRTTPNFKMNQAPRSTPSSGSSRSLSTQVTSLSSH
SSGSSRSSGSTVVSSLPSSNRTRDWVNQQNFNLEPHLPGSLRTAFVTPPSSTASSSGT
VSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNI"
ORIGIN
1 tgaagatggc gtctaacgac gcttccgctg ccgctgctgc taataacaac agcgacaacg
61 caaaatcttc aagtgacgga atgctttcta gcatggctgt cacttttaaa cgagccctcg
121 gggcgcggca aaaaccgcct cccccgaggg aaataccaca gaggcctcca cggccaccca
181 ccccagaact ggtcaaaaag atccctcctc ccccacccaa tggggaggat gagctagtgg
241 tctcttatag cgccaaagat ggcgtctctg gtttgcctga acttaccact gtctggcaac
301 cggatgagac caacacggca ttcagtgttc cccctctcaa ccagagggag aacagggacg
361 ccaaggagcc gctgaccgga acaatcctgg aaatgtggga cggggagatc tatcattatg
421 gtctgtatgt ggagcgaggc cttgtacttg gtgtgcacaa accaccagct gccatcagcc
481 tcgccaaggt tgaattagca ccactctctc tgttttggag gccagtgtac acaccacagt
541 atctcatctc tccagacact cttaggagac tgcatggaga gtcgttcccc tacacagcct
601 ttgataacaa ctgctatgcc ttctgttgtt gggttctgga cctaaacgac tcgtggttgt
661 gcaggagaat gatccagaga acaactggct tcttcaggcc ttaccaagaa tggaacagga
721 aacccctccc caccatggat gactctaaat tgaagaaggt agctaacata ttcttgtgtg
781 cgctatcttc gctattcact aggcccatca aagatataat aggaaaggtg agaccgctca
841 acatccttaa catcctggcc tcatgtgatt ggacttttgc aggcatagtg gaatctttga
901 tcctcttggc agagctcttt ggagttttct ggacaccccc agatgtgtct gcgatgatcg
961 cccccttact aggtgactac gaactgcagg ggcctgagga ccttgcagtg gaactcgtac
1021 cagtagtgat gggagggatt ggtttggtgt taggattcac caaagagaag atcggaaaaa
1081 tgttgtcatc cgctgcttcc accttaagag cctgtaaaga ccttggtgca tacgggctgg
1141 aaatcctaaa attggtcatg aaatggttct tcccaaagaa agaggaagca aatgagctag
1201 ctatggtgag gtccatcgag gatgcggtgc tggacctcga agcaattgag aacaaccaca
1261 tgactgccct cctcaaagac aaagacagct tggcaaccta catgaggacc cttgacctcg
1321 aggaggagaa agccaggaag ctttcaacca agtctgcttc acctgacatc gtgggcacaa
1381 tcaacgctct tctggcgaga atcgccgctg cacgttccct ggtgcatcgg gcgaaagagg
1441 aactctccag cagaccaaga cctgttgttg ttatgatatc aggtaggcca gggataggga
1501 aaactcacct tgccagggag ctagccagga agatcgcagc ttcactcaca ggggaccagc
1561 gcgtgggtct catccctcgc aatggcgttg accactggga tgcgtacaag ggagaaagag
1621 tcgtcctgtg ggacgattat ggaatgagca atcccatcca cgacgccctc aggttacagg
1681 aacttgctga cacctgcccc cttacgctaa actgtgacag gattgagaac aaaggaaagg
1741 tctttgacag tgatgccata atcatcacca ccaatctagc caacccagca ccattggact
1801 atgtcaactt tgaagcatgc tcgaggcgca ttgacttcct cgtgtacgca gaagcccctg
1861 aggtcgagaa agcaaagcgt gatttcccag gtcaacctga catgtggaag aacgcattta
1921 gctctgactt ctcgcacata aaactggcgc tggctcccca gggtggtttc gacaagaacg
1981 gaaacacccc acacgggaaa ggcgtcatga aaaccctcac cactggttcc ctcatcgccc
2041 gagcatcagg gctactccac gagaggttgg atgaatacga gctgcagggc ccaactccca
2101 ccacctttaa ctttgaccgc aacaaggtgc ttgcgttcag acaacttgct gccgaaaaca
2161 agtacggatt gttggacaca atgagagttg gaaaacagct caaggatgtt aagaccatgt
2221 cagagctcaa acaggcactc aagaatgtcg caattaagag ttgtcagata gtgtacggtg
2281 gctgcaccta caggcttgag tctgatggca agggtgatgt aaaagttgac agagttcaga
2341 acgccactgt acagaccaac aatgagcttg ccggcgcact acactatctt aggtgcgcca
2401 gaatcagata ttatgtcaag tgtgttcagg aggccctgta ttccatcatc caaatcgctg
2461 gggctgcatt tgtcaccacg cgcattgtca agcgcatgaa catacaagat ctatggtcca
2521 agccacaggt ggaggacaca gaggaaatcg ctagcaagga tgggtgccta aaaccccagg
2581 atgatgaaga gtttgttgtc tcatccgatg acatcaaaac cgagggcaag aaagggaaga
2641 acaagtctgg ccgtggcaag aagcacacag cattttcaag taaaggtctc agtgatgaag
2701 agtacgatga gtacaaaaga attagagaag aaagaaatgg caaatactcc atagaggaat
2761 acctccagga cagagacagg tattatgagg aggtggccat cgccagggca accgaagagg
2821 acttctgtga agaagaagag gccaagatcc gacagaggat cttcaggcca acaaggaaac
2881 aacgcaaaga ggagagagcc tctctcggtt tggtcacagg ttctgaaatc aggaagagga
2941 acccagacga cttcaagcct aaaggaaagc tgtgggctga tgatgacagg agtgttgact
3001 acaatgagag actcaatttt gaagccccac caagcatctg gtcgaggata gtcaactttg
3061 gctcaggttg gggcttttgg gtttccccca gcctgttcat aacatcaact catgtcatac
3121 cccagggcgc acaggagttc tttggtgtac ccatcaaaca aatccagata cacaaatcag
3181 gtgaattctg ccgcttgagg tttccaaagc cgatcagaac tgacgtgaca ggcatgatct
3241 tagaagaagg tgcacccgaa gggaccgtgg tcacattact catcaaaaga ccaactggag
3301 agctcatgcc cctggcagcc agaatgggaa cccacgcaac catgaagata caagggcgca
3361 ctgttggagg ccaaatgggc atgctcctaa ctggatccaa cgccaagagt atggacctgg
3421 gcaccacacc aggtgactgt ggctgcccct acatttacaa gagggggaat gactacgtgg
3481 tcattggggt ccatacagct gccgcccgtg gaggaaacac tgtcatttgt gccacccagg
3541 ggagcgaggg agaagccaca cttgaaggcg gtgatagcaa ggggacctac tgcggtgcac
3601 caatcttagg tccaggaagt gccccaaaac tcagcaccaa gaccaaattc tggaggtcat
3661 ccacggcacc actcccacct ggtacctatg aaccagctta cctcggtggc aaggacccca
3721 gagttaaggg tggcccttca ctgcaacaag ttatgaggga tcaactgaaa ccattcactg
3781 agcctagggg taggccacca aaaccaagtg tgctagaagc tgccaagaaa accatcgtca
3841 atgtcctaga acagacaatt gacccacctc aaaaatggtc gtttgcgcag gcatgcgcat
3901 ccctagacaa gaccacttct agcggtcatc cgcaccacat gcggaagaat gactgctgga
3961 acggggagtc cttcacagga aaattggcag atcaggcttc caaggccaac ctgatgtttg
4021 aggaggggaa gaacatgacc ccagtttaca cgggtgcgct taaggacgag ctggtcaaga
4081 ctgacaagat ttatggtaag atcaaaaaga ggcttctctg gggttcggac ctggcgacca
4141 tgattcggtg cgctcgagca ttcgggggtc tgatggagga actcaaagca cattgtgtca
4201 cactacctgt tagggtgggt atgaatatga atgaggatgg ccctatcatc tttgagagac
4261 actccagata taaatatcat tatgatgctg actactcccg gtgggattca acacaacaaa
4321 gagctgtgtt ggcagcagcc ttagaaatca tggtcaagtt ttccccagag ccacacctgg
4381 cccaaaaggt tgcagaagac cttctttctc ccagcgtgat ggacgtgggt gatttcaaaa
4441 tatcaatcaa tgagggtctc ccctccggag tgccctgcac ctcccaatgg aattccatcg
4501 cccactggct cctcactctc tgtgcactct ccgaggttac aaacctgtcc cctgacatta
4561 ttcaggctaa ctctctcttt tctttctacg gtgatgatga aattgtgagt acagacataa
4621 aattggaccc ggaaaaactg acagcaaaac tcaaggaata cgggttgaaa ccgacccgcc
4681 ctgacaaaac tgaagggcct cttgtcattt ccgaagacct gaatggccta accttcctgc
4741 ggaggaccgt gactcgcgac ccagcaggct ggtttggaaa gttggaacag agctcaatac
4801 tcagacaaat gtactggact agaggcccca accatgaaga tccatctgaa acaatgatac
4861 cacactccca gaggcccata caactgatgt ctttgctggg tgaggcagca ctccacggcc
4921 cagcattcta cagcaaaatc agtaaactgg tcattgcaga attgaaggag ggtggcatgg
4981 atttttacgt gccaagacaa gaaccaatgt tcagatggat gagattctcg gatctgagca
5041 cgtgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgaatgac
5101 gccaccccat ctaatgatgg tgccgccggc ctcgtcccag agatcaacaa tgaggcaatg
5161 gcgctagatc cagtggcggg tgcagcgata gcagcacccc tcaccggcca gcaaaatata
5221 attgatccct ggattatgaa taattttgtg caagcacctg gtggtgagtt cacagtgtct
5281 cctaggaatt cccctggtga agtgctcctc aatttggaat tgggcccaga gataaacccc
5341 tatctggccc atcttgctag aatgtataat ggttatgcag gtgggtttga agtgcaggta
5401 gtcctggctg gaaatgcgtt tacagcagga aagataatct ttgcagctat accccctaac
5461 ttcccaattg acaatctaag tgcagcacag atcacaatgt gcccacatgt gattgtggat
5521 gtcaggcagc tggaaccggt caacctcccg atgcctgacg ttcgcaataa cttcttccac
5581 tacaaccaag ggtctgattc gagattgcgc ttggttgcaa tgctgtacac acctcttagg
5641 gcaaataact ctggggatga tgttttcact gtgtcttgta gagtgctgac tagacctagt
5701 cctgaatttt catttaactt ccttgtgcca cccactgtgg agtcaaagac aaaacctttt
5761 accctcccaa ttctgactat ctctgaaatg tctaattcta ggtttccagt gccgattgat
5821 tctctgcaca ccagcccaac tgagaatatt gttgtccagt gtcaaaatgg acgcgtcact
5881 cttgatggcg agttgatggg caccactcag ctcttaccta gtcaaatctg tgctttcagg
5941 ggcgtgctca ctagatcaac aagcagggct agcgaccagg ccgacacagc aacccctaga
6001 ttgtttaatt attattggca catacaattg gataatctaa atgggactcc ttatgatcct
6061 gcagaagaca taccaggccc cctagggaca ccagatttcc ggggcaaagt ctttggcgtg
6121 gccagccaaa gaaaccccga cagtacaact agagcacatg aagcaaaggt ggacacaaca
6181 gctggtcgct tcaccccaaa actaggctca ttagagatat ccactgaatc tggtgacttt
6241 gaccaaaacc aaccaacaag attcacccca gttggcattg gggttgacca cgaggcagac
6301 ttccaacaat ggtccttacc cgattactct ggccagttca ctcacaacat gaacttagcc
6361 ccagctgttg ctcccaactt ccctggtgag cagctccttt tcttccgctc acagttacca
6421 tcttctggtg ggcgatccaa tgggattcta gattgcctgg tcccccaaga atgggtccag
6481 cacttctacc aagaatcagc ccccgcccaa acccaggtgg ctctggttag atatgtcaac
6541 cctgacactg gtagagtgtt gtttgaggcc aagctgcaca aattaggttt catgactata
6601 gctaagaatg gtgactctcc aataactgtc cccccaaatg gatactttag gtttgaatct
6661 tgggtgaacc cattttatac acttgccccc atgggaactg ggaatgggcg tagaagagtt
6721 caataatggc tggtgctttt atagcaggat tagctggtga tatactcaca aatactgtag
6781 ggtctctggt taatgcaggg gctaatgcta ttaatcaaaa agttgatttt gaaaataata
6841 aatatttgca aaatgcttct ttcaatcatg ataaggaaat gttaaatgca cagattgagg
6901 caacaaagag attacaggct gacatgattg ctatcaaaca gggggttttg accgctggcg
6961 gcttttcccc cactgatgca gctcgcgggg caattaacgc ccccatgaca aaagtcctag
7021 attggaatgg aacaaggtac tgggcaccaa gtgccacctc tacaacctcg atgtcgggtg
7081 gcttcacaaa ccaggctgtg cacagaacca cgccaaattt taaaatgaac caggccccca
7141 gatccacacc cagcagtggg tcttcaaggt cactctcaac ccaagtcact agtctgagct
7201 cacactcgtc cgggtcgtct cgatccagcg ggtctacagt tgttagctcg ttaccatcct
7261 ccaacaggac tagggactgg gtcaatcagc aaaatttcaa tttggaacca cacttgcctg
7321 ggtcacttag gacggctttt gtcactccac catctagtac agcctctagt tcaggcactg
7381 tctcaaccgt gcccaaaaat gttttggact cctggacatc tgcgtttaac acgcgcagac
7441 agccgctatt cgcacacctt cgtagaaggg gggagtcaaa tatttag
//