Typing tool
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Typing tool
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Complete norovirus genomes
| OP162337 | GI.3 | |
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| GI.P3 |
ORF1: 1..5396
ORF2: 5380..7017
ORF3: 7017..7664
LOCUS OP162337 7664 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GI isolate RIVM-NOV-2016-0143_R01-20 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP162337
VERSION OP162337.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7664)
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JOURNAL Unpublished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 7664)
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..7664
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0143_R01-20"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="Netherlands"
/collection_date="2016-01-13"
/note="genotype: GI.3[P3]"
gene <1..5396
/gene="ORF1"
CDS <1..5396
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUL90914.1"
/translation="MASNDAIAVADVSNNNANTNNDNIGSRLMARIRGRMGPQRGETT
KKITDANMALNLLRRSQTPSPSRQESPPKSQRDRPPRTASEVKKVLGWDVEPEHQEST
AKAWCDLTQEEKEEIMRNNEKLFDAGGITPSTLPSTFERADPVDSPTEQQPVTWSASG
GVDIGVNDLTTVSGPFWNMCPLPPLDARNNGPAKEPLIGDMIEFYEGHIFHYAIYIGQ
GKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYDQLKELENEPWPYASIT
NNCYEFCCRVMALDDTWLERRLVSTGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVLSA
INGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGVVELIVLLAELFDVFWTPPDISSF
IASLLPEFHLQGPEDLARDLVPLILGGIGLAIGFTRDKVTKVMKSAVDGLRSATQLGQ
YGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLARTYMNVL
DNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIMMCGP
PGIGKTKAAEHLAGRLANEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKITE
DCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFINLGPVCRRVD
FLVYCSAPEIEQMRRTHPGDANAIKDLYKRDYSHLKMELAPQGGFDSQGNTPFGKGIM
KPTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVSAFTSLARANGLGLLSMATLG
KRLRSVKSMEGLRNALVGYKIGECDIIWNTRVYSIKSDGSTVTIKEKQTPTSPQYQAI
STATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPMLEG
KHKEHNCRVHRAEAAGHGPIGHDGVIERYGLCESEQEEEGEQTVELPTANKEGKNKGK
TKKGRGRKSNFNAFSRRGLSDEEYEEYKKIREEKSGNYSIQEYLEDRQRYEEELAEVQ
AGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGSEIRKRKPIDWTPPKN
DWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKEVF
GEDLSNVAIHRVGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCTIMIKRDSGELLPLA
VRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVCGV
HAAATKSGNTVVCAIQGGDGEATLEGGGQNKGHYAGHPILRYGNGPSLSTKTKFWKST
PQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVETV
TNAIEQVMDTPVAWSYSDACMSLDKTTSSGHPHHKKKNDDWNGNSFVRELGDQAAHAN
SMYELGKSMKPVYTAALKDELVKPDKVYTKIKKRLLWGADLGTVIRAARAFGPFCEAI
KPHVIKLPIKVGMNAIEDGPLIYAEHSKYKFHYDADYTAWDSTQNREIMMESFNIMCK
LTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWILTLCALS
EVTGLSPDVIQSQSYFSFYGDDEIVSTDIEFDPIRLTQILKEYGLKPTRPDKTDGPII
IRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHEDPFETLVPHSQRKV
QLISLLGEAALHGEKFYRKIAGRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSLWTGD
RDLLPDYVNDDGV"
mat_peptide <1..1211
/gene="ORF1"
/product="p48"
mat_peptide 1212..2300
/gene="ORF1"
/product="NTPase"
mat_peptide 2301..2900
/gene="ORF1"
/product="p22"
mat_peptide 2901..3320
/gene="ORF1"
/product="VPg"
mat_peptide 3321..3863
/gene="ORF1"
/product="Pro"
mat_peptide 3864..5393
/gene="ORF1"
/product="RdRp"
gene 5380..7017
/gene="ORF2"
CDS 5380..7017
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUL90915.1"
/translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMEPVAGAATAAA
TAGQVNMIDPWIMNNYVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLAQMYNG
WVGNMKVKVLLAGNAFTAGKIIISCIPPGFAAQNISIAQATMFPHVIADVRVLEPIEV
PLEDVRNVLFHNNDNTPTMRLVCMLYTPLRASGSSSGTDPFVIAGRVLTCPSSDFSFL
FLVPPNVEQKTKPFSVPNLPLNTLSNSRVPSLIKSMMVSRDHGQMVQFQNGRVTLDGQ
LQGTTPTSASQLCKIRGSVFHANGGNGYNLTELDGSPYHAFESPAPIGFPDLGECDWH
MEASPTTQFNTGDVIKQINVKQESAFAPHLGTVQVDGLSDVSVNTNMIAKLGWVSPVS
DGHKGDVDPWVIPRYGSTLTEAAQLAPPIYPPGFGEAIVFFMSDFPIAHGTNGLSVPC
TIPQEFVTHFVNEQAPTRGEAALLHYLDPDTNRNLGEFKLYPDGFMTCVPNSSGTGPQ
TLPINGVFVFVSWVSRFYQLKPVGTAGPARRLGIRRS"
gene 7017..7664
/gene="ORF3"
CDS 7017..7664
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUL90916.1"
/translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQKN
SFIHDKEMMGLQVEASTALLQNSLGTRYNMLTKAGMTSADAARMVVGAPATRVVDWNG
TRIAAPMSTATTLRSGGFMTVPTVYRGSKNKQSIGGGFSNVNYDPPVSSSRTSQWVSS
QNSMRSTLEPFHPGALRTTWVTPPGSTSTSTISTVSTVPKFFNTERLPLFANRGK"
ORIGIN
1 tgatggcgtc taacgacgct attgccgttg ctgatgtcag caataacaat gctaacacca
61 acaatgataa cattggatcc cgcctcatgg cgaggatccg tgggcgcatg ggcccacaac
121 gtggtgaaac aaccaaaaaa ataacagacg ccaatatggc gcttaatctg ttacgccggt
181 cacaaacacc ctccccatcc cggcaagaga gccctcctaa gagccagaga gaccgccccc
241 ctcgtactgc ttctgaggtg aagaaagtgt tggggtggga tgttgaacca gaacaccagg
301 aaagcacggc caaggcatgg tgcgacctca cgcaagaaga gaaggaggag ataatgcgca
361 ataatgaaaa gcttttcgat gctgggggaa tcaccccatc aactttgcct agcacgtttg
421 aaagggccga cccagttgat agccccactg aacagcaacc tgtgacatgg tctgctagtg
481 gtggggtcga tattggtgtc aatgatttga ccaccgtcag tggcccattt tggaatatgt
541 gccccctccc gccactggat gctcggaata atggccccgc caaggaaccc ctcataggag
601 atatgataga gttctatgag ggtcatatat tccattatgc catctatatt ggacaaggta
661 agaccattgg ggtccactca ccgcaagcag ctttctccat accaaggata accatccatc
721 ctctggtagc ctggtggcgc gtgtgctacg ttccaactaa ccagcagcgc ctcacttatg
781 accagctcaa agagttggag aatgagccat ggccctacgc ttccattaca aataactgct
841 atgagttttg ctgcagagtg atggcacttg atgatacatg gcttgagagg aggttagtca
901 gcactggaaa attcaatcac cccacacaag attggtcaca ggataccccg gattttcacc
961 aggactcgaa acttgagatg gtaagagatg ccgtgctatc agctattaat ggccttgtgt
1021 cacagccttt taaaaacatt ttgtcaaaga tcaaaccatt aaatgttctc aatctcttgt
1081 caaattgcga ttggactttc atgggggttg tggaactgat tgtgctccta gcggagttgt
1141 ttgatgtgtt ctggacccca ccagacatct caagtttcat tgcctcacta ttacctgaat
1201 ttcacctgca gggcccagaa gacctagcta gggacttggt ccctctcatc ctaggtggca
1261 taggcctggc tattggcttt acaagagaca aagtgacgaa agtgatgaag agtgccgtcg
1321 atgggttgag atcggcgaca caactcgggc agtacgggct ggaaatattc tcaatcatca
1381 agaaatattt ctttggtggg gaccaaacgg aaaagaccct gcggggtatt gaggatgcag
1441 tgatagacat ggaggtgtta tctagcacca acgtgacaca attggttaaa gacaagaaat
1501 tggccagaac ctacatgaat gtgctagaca atgaagagga aaaagcaagg aaactctcag
1561 tccgtagtgc tgatccgcac atagtgacct cagtcaacaa tctgatatca cgaatatcta
1621 tggcaagatc agccttggcc aaagcccagg ctgagatgac atctcgccca cgccctgtgg
1681 tcataatgat gtgtggcccc cccggcatcg gaaaaaccaa ggccgccgaa cacctggctg
1741 gccgattggc aaacgagatt agaccaggag gtaaggttgg acttgtgccc cgggaatcca
1801 tagatcactg ggacggatac catggcgagg atgtcctact atgggatgac tatggcatgt
1861 caaagataac agaggactgt aataagctac aagccatagc tgacactgca cccctgtcac
1921 ttaattgtga caggatagag aacaaaggca tgcaattctc ctcagatgca ataatcataa
1981 ccaccaatgc ccctggcccg gcccctgtgg actttatcaa cctaggccct gtgtgcaggc
2041 gagtggactt tttagtttac tgttctgccc ctgaaattga gcaaatgaga aggacccatc
2101 ctggtgatgc caatgccatc aaagacctat acaaaaggga ctactcgcac ttaaaaatgg
2161 aattggcccc acaaggtggt tttgatagtc agggtaacac accatttggg aagggcatta
2221 tgaaacccac gaccctcaat aggctactca tccaggcaac agcattagct atggagcggc
2281 aagacgagtt ccagctccaa ggggctgtct acaactttga tgaagacagg gtgtccgctt
2341 tcacaagcct ggcccgagct aacggcttgg ggcttttaag catggcaaca ttgggtaaaa
2401 ggctcagaag tgtcaaatct atggagggcc tgcgtaacgc attggtgggc tacaaaatag
2461 gagagtgtga tataatctgg aacactagag tgtattcaat taaaagtgat ggtagtactg
2521 tcacaatcaa ggaaaaacaa accccaactt caccccaata ccaagccatt agcacagcca
2581 ctcttgcact ctctaggttg cgggccgcta gagctcttgc gtacgcctcc tgcctacaga
2641 gtgcagtgct gtcaatactt caagtggctg gctctgccct ggtggtgagc agagccgtta
2701 agcgcatgtt tggcacgcgc actgaacaac ctatgttgga aggcaagcac aaagaacaca
2761 actgtagagt gcaccgcgca gaggcagctg gccatggtcc cattgggcac gatggagtca
2821 tcgaacgcta tggcctctgt gagagtgagc aagaagaaga aggcgagcaa acagttgagc
2881 tacccactgc caataaagaa ggcaaaaaca agggcaagac caaaaagggc cgtggacgaa
2941 aatccaattt taatgctttc tcaagacgag gcctcagtga tgaagagtat gaagaataca
3001 agaagatcag agaagaaaag agtggcaatt acagcatcca ggagtacctc gaggaccgcc
3061 aacgatatga ggaagaactt gctgaagtgc aggctggtgg ggatggtgga attggtgaaa
3121 ctgaagcaga gattcgccat cgggttttct ataaatcaaa atccggcatg agaaagcaac
3181 gccaagaaga acggcgtcag ttgggtctcg ttagcggttc tgagatccgc aaacgcaagc
3241 ccatagactg gaccccccct aagaatgatt ggtcagaaga caccaggact gtcaactatg
3301 atgaacacat tagctttgaa gcccctccct caatttggag tagggtggtg aagtttggca
3361 gtggttgggg tttttgggtg agttcaacag tgttcataac cacaacccat gtcataccac
3421 ctggggccaa agaagtcttt ggtgaagacc tcagtaatgt ggccatccat agagttggtg
3481 aattcaccca gttccgtttc tccaaaaaga tgagacctga cctcaccggt atggttttag
3541 aagaaggttg cccagaggga acagtgtgca ccataatgat caagagagat tctggtgagt
3601 tgctgccgct cgccgttcgg atgggggcag tggcatcaat gaagatccaa ggcaaactta
3661 tgcatgggca atcaggaatg ttactcaccg gtgctaacgc caaaggcatg gaccttggga
3721 ctatacccgg tgattgtggg gcaccctatg tccacaagag gggaaatgac tgggtggtct
3781 gtggggtaca tgcagccgcc acaaaatcag gcaacactgt ggtgtgcgct atacaaggtg
3841 gcgatggtga agccactcta gaaggcggcg gtcaaaacaa gggccactat gcagggcatc
3901 cgatactaag gtatgggaat ggcccttcac tatcaaccaa aacaaaattt tggaaatcaa
3961 ccccccagcc tttgcctcct ggtacatatg agccagctta ccttggaggc agagacccca
4021 gagttgaggg gggcccatcc ttacaacagg tgttaaggga ccagttaaaa ccatttgccg
4081 agccccgtgg cagattaccc gaagcgggct tgttggaagc tgcagttgaa acggtcacca
4141 atgctattga acaggtcatg gacacaccgg tggcatggag ctatagtgat gcttgcatgt
4201 cactagataa gacaaccagt tccggccacc cccatcacaa gaagaaaaat gatgattgga
4261 atgggaattc atttgtgaga gaattgggtg accaggcggc acacgctaac agcatgtatg
4321 agcttggtaa gtccatgaaa cctgtgtata cagcagccct aaaggatgag ctagtcaaac
4381 cagataaggt gtacacaaaa atcaaaaaga gactgctttg gggcgcggac ctcggtaccg
4441 tcattcgcgc tgccagagca tttggaccat tttgtgaggc cataaaaccc catgtaatta
4501 agttgcctat taaggtgggt atgaatgcca tagaggatgg ccccttgatt tatgctgagc
4561 actccaagta taaattccat tatgatgctg actatacagc ttgggactca acacaaaaca
4621 gagaaatcat gatggaatct ttcaacatta tgtgcaaact tacagccaat ccctccttgg
4681 ccgcagtggt ggcacaggat ctactctccc catctgaaat ggatgttggt gactatgtga
4741 tcagtgtcaa agatggttta ccatctggct ttccatgcac ttcacaggtg aacagcatca
4801 accactggat actgaccctg tgtgcactgt cagaagtcac tggcttgtcc ccagatgtga
4861 tacagtcaca atcctacttc tcattttatg gtgatgatga aatagtctca acagatatag
4921 aatttgaccc aattagattg acacaaatat tgaaggaata tggtttgaag cctacaagac
4981 ctgacaaaac tgatggccca attattatta gacaacaggt tgatggcctg gtcttcctcc
5041 ggcgcaccat ttctaaggat gccattggat accagggacg actcgaccgt aactctattg
5101 aaaggcagct ttggtggact cgtggaccaa accatgagga cccatttgag acactggtcc
5161 cacattcaca gagaaaggtc caattaatat ccttgttagg tgaagcagca ctccacggtg
5221 aaaagttcta caggaagata gctggtaggg tcattcaaga agtcaaagag ggagggcttg
5281 aaatctacat ccctggttgg caggccatgt tccgctggat gcgattccat gatctaagct
5341 tgtggacagg agaccgcgat ctcctgcccg attatgtaaa tgatgatggc gtctaaggac
5401 gccccaacaa acatggatgg caccagtggt gccggccagc tggtaccaga ggcaaacaca
5461 gctgagccta tatcaatgga gcccgtggct ggggcagcaa cagctgccgc aactgctggc
5521 caagttaata tgattgaccc ctggataatg aacaattatg tacaagcccc ccaaggtgaa
5581 tttaccatat cgcctaataa cacaccaggt gatattttgt ttgatttaca attaggcccc
5641 caccttaacc ctttcttatc tcatttggcc caaatgtata atggctgggt tggcaatatg
5701 aaagtgaagg ttctattggc tggtaatgct ttcacggctg gtaaaataat cattagttgc
5761 ataccccctg gctttgccgc acaaaatatt tctattgccc aggccaccat gttcccccat
5821 gtcatagctg atgttagggt tttggaacct attgaggtgc cattggaaga tgtgaggaat
5881 gtgctcttcc acaacaatga caacacgcca actatgcggt tggtgtgcat gttatacacc
5941 cccttgcggg ccagtggtag ctcgtcagga actgacccct ttgtgattgc tgggcgtgtt
6001 ttgacatgcc caagttctga ttttagcttt ttgtttttag tcccccccaa tgtagagcaa
6061 aagactaaac ctttcagtgt cccaaacctt ccattgaaca ccctctcaaa ttcgagagtc
6121 ccctctctaa tcaaatcaat gatggtgtcc agggaccatg ggcagatggt tcagtttcaa
6181 aatggtaggg tcaccctaga tgggcagctg caaggcacca cacccacatc agctagtcag
6241 ctgtgcaaaa tcaggggcag tgtcttccat gccaatggtg ggaatgggta caacttaaca
6301 gaactggatg ggagcccata ccacgcattt gagagccccg caccaatagg gtttccagat
6361 ctaggtgaat gtgattggca catggaggct tctcctacca cccaatttaa tactggagat
6421 gtcataaaac aaattaatgt taaacaagag tcagcatttg ccccccacct tggcaccgtg
6481 caggtagacg gcctgagtga tgtgagtgtc aacaccaaca tgatagctaa attaggatgg
6541 gtgtctcccg tcagtgatgg acacaaaggg gatgtcgacc cgtgggtcat tccacgctat
6601 ggttcaacct tgactgaggc cgcccaatta gcccccccaa tatatccccc aggctttggt
6661 gaggccattg tgtttttcat gtcagatttt cccattgccc atggcaccaa tggcttgagt
6721 gtgccctgca ctatacccca agaatttgtc acccattttg tcaatgaaca ggcccctact
6781 agaggggaag cagccttgct acactatctg gaccctgata ctaatagaaa tcttggtgag
6841 tttaaattat atcctgatgg cttcatgaca tgtgtgccta attccagtgg cactggtcca
6901 caaactcttc caatcaatgg tgtttttgtt tttgtgtcct gggtttctag attttatcaa
6961 ttaaagcctg tgggaacagc cggcccggct cgtaggcttg ggattaggag atcataatgg
7021 ctcaagccat acttggagcc atagcagcaa cagcagccgg tagtgctgtt ggtgctggta
7081 tacaagctgg aaccgaagct gccctacagc atcaaagatt tcagcaagat ttgaccttac
7141 aaaagaattc cttcattcat gataaagaga tgatgggcct acaggtagag gcttcaaccg
7201 cactcctcca aaacagcttg ggtacgaggt acaatatgtt gaccaaagca gggatgacat
7261 ccgcagacgc ggcacgtatg gtagtggggg cacccgcgac tcgtgtcgtt gactggaacg
7321 ggactaggat cgccgcaccc atgtcaactg cgacgacact taggtctggt ggtttcatga
7381 ccgtaccaac tgtttatagg ggtagtaaaa ataaacaatc aattggtggt ggtttttcta
7441 atgtaaatta tgatccccca gtctcctctt cccgcacttc tcaatgggtc tcttctcaaa
7501 attcaatgcg ttccactctg gaaccatttc atccaggtgc tctgagaacc acatgggtta
7561 ccccacctgg gtcaacttct acttctacaa tttctacagt ttccactgta ccaaaattct
7621 tcaatacaga aaggttaccc ttattcgcaa ataggggtaa gtga
//