Typing tool
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Typing tool
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Complete norovirus genomes
| OP162340 | GI.6 | |
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| GI.P11 |
ORF1: 1..5355
ORF2: 5339..6961
ORF3: 6961..7590
LOCUS OP162340 7593 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GI isolate RIVM-NOV-2016-0478_R02-17 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP162340
VERSION OP162340.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7593)
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JOURNAL Unpublished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 7593)
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..7593
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0478_R02-17"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="Netherlands"
/collection_date="2016-11-28"
/note="genotype: GI.6[P11]"
gene <1..5355
/gene="ORF1"
CDS <1..5355
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUL90923.1"
/translation="SKDVVATNVASNNNANNTSATSRFLSRFKGLGGGASPPNPIKIK
STEMALGLIGKTAQEAVGASGLPPKQQRDRPPRTQEEVQYGMGWTERPVDQNVKSWEE
LDTSTKEEILDSHKEWFDAGGLGPCTMPSTCEQAKDDSPPGEQVRWSVRDGVNLGVNR
LTTVNGPEWNLCPLPPIDLRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTVGVHS
PQAAFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLRELENEPWPYAAITNNCFEFCC
QVMNLEDTWLQRRLITSGRFHHPSQSWSQQTPEFQQDSKLELVRDAILAAVNGLVSQP
FKNFLGKLKPLNVLNILSNCDWTFMGVVEMVILLLELFGVFWNPPDVSNFIASLLPDF
HLQGPEDLARDLVPVILGGIGLAIGFTRDKVTKVMKSAVDGLRAATQLGQYGLEIFSL
LKKYFFGGDQTERTLKGIETAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEEEKAR
KLSAKNADPHVISSTNALISRIAMARSALAKAQAEMTSRMRPVVIMMCGPPGIGKTKA
AEHLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNKLQAI
ADSAPLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVYCSAP
EVEQIRRVSPGDTSALKDCFKSDFSHLKMELAPQGGFDNQGNTPFGKGVMKPTTINRL
LIQAVALTMERQDEFRLQGKMYDFDDDRVSAFTTMARDNGLGILSMASLGKKLRGVTS
MDGLKNALKGYKIGACTIKWQAKVYSLESDGNSVNIREEKNVLTQQQQSVCAASIALT
RLRVARAVAYASCIQSAITSILQIAASALVVNRAVKRMFGTRTAALSLEGPPKEHKCR
VHQAKAAGKGPIGHDDMVDKYGLCETEEDEEVVHTEIPSATMEGKNKGKNKKGRGRKN
NYNAFSRRGLNDEEYEEYKKIREEKGGNYSIQEYLEDRQRYEEELAEVQAGGDGGIGE
TEMEIRHRVFYKSKSKKHHQEERRQLGLVTGSDIRKRKPIDWTPPKSAWADDEREVDY
NERINFEAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVIPTSAKEFFGEPLASIAIHR
AGEFTLFRFSKKIRPDLTGMILEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRI
QGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVYKRANDWVVCGVHAAATKSGNTV
VCAVQASEGETTLEGGDKGHYAGHEIIKHGCGPALSTKTKFWKSSPEPLPPGVYEPAY
LGGRDPRVSGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSSLEQVMDTPVP
WSYSDACQSLDKTTSSGFPHHKKKNDDWNGTAFIRELGEQAAHANNMYEQAKSMKPMY
TAALKDELVKPEKVYQKVKKRLLWGADLGTVIRAARAFGPFCDAIKSHTIKLPIKVGM
NSIEDGPLIYAEHSKYKYHFDADYTAWDSTQNRQIMTESFSIMCRLTASPELASVVAQ
DLLAPSEMDVGDYVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDVIQSM
SYFSFYGDDEIVSTDIEFDPAKLTQVLKEYGLKPTRPDKSEGPIIVRKSVDGLVFLRR
TISRDAAGFQGRLDRASIERQIYWTRGPNHSDPFETLVPHQQRKIQLISLLGEASLHG
EKFYRKISSKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVNDDGV
"
mat_peptide <1..1185
/gene="ORF1"
/product="p48"
mat_peptide 1186..2274
/gene="ORF1"
/product="NTPase"
mat_peptide 2275..2871
/gene="ORF1"
/product="p22"
mat_peptide 2872..3285
/gene="ORF1"
/product="VPg"
mat_peptide 3286..3828
/gene="ORF1"
/product="Pro"
mat_peptide 3829..5352
/gene="ORF1"
/product="RdRp"
gene 5339..6961
/gene="ORF2"
CDS 5339..6961
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUL90924.1"
/translation="MMMASKDAPTSPDGASGAGQLVPEANTAEQISMDPVAGASTAIA
TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLSQMYNG
WVGNMRVRILLAGNAFTAGKIIICCVPPGFDARILTIAQATLFPHLIADVRTLEPVEL
PLEDVRNVLFHNSSQPQPTMRLVAMLYTPLRTGGGSGGTDAFVVAGRVLTCPAPDFSF
LFLVPPSVEQKTRVFSVPNIPLKDLSNSRVPVPVQGMFMSPDVNQSVQFQNGRCQIDG
QLQGTTPVSLSQLCKIRGKTSSNARVLNLSEVDGTPFIPLESPAPVGFPDLGGCDWHV
NFTFQAQNQDPSQSVTFATNDASFVPYLGSISPHNGGDFHAGDIIGSLGWISAPSDNS
QLNVWTIPKYGSSLPDVTHLAPAVFPPGFGEVILYFYSTFPGSGQSSQLQVPCLLPQE
FITHFCNEQAPIAGEAALLHYVDPDTGRNLGEFKLYPDGFMTCVPNSVSSGPQTLPIN
GVFVFVSWVSRFYQLKPVGTASAARRLGLRRI"
gene 6961..7590
/gene="ORF3"
CDS 6961..7590
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUL90925.1"
/translation="MAQAVIGAIAASAAGSILGAGIQAGAEAGLQAQRYQQDLQLQQN
SFKHDKEMLGYQVQASNALLAKNLNTRYALLQAGGLSSADAARAVAGAPVTRIVDWNG
TRIAAPTSSTTTLRSGGFMAVPIPLSSKTKQPVMSGQDNPNYAASSISRTASWVQSQN
SMRSVSPFHSDALRTVWVTPPGSSSTSSVQSSFYGVFNTDRLPLFANRR"
ORIGIN
1 tcgaaagacg tcgttgcgac taatgttgca agcaataaca acgctaacaa cactagtgct
61 acatctcgat ttctgtcgag atttaagggt ttaggtggtg gcgcgagccc ccctaacccc
121 ataaagatca aaagcacaga aatggccttg ggtttgattg gcaagacagc ccaagaggca
181 gtaggtgcca gtggcctacc gcccaaacag caaagagatc ggccccccag aacccaggag
241 gaagttcagt acggcatggg gtggactgaa aggcccgtgg accagaatgt taagtcatgg
301 gaggaacttg acacctccac caaggaagaa attttggaca gccacaaaga atggttcgac
361 gccggcggtt tgggcccgtg caccatgccc tcaacttgtg aacaggctaa agatgatagc
421 ccacctggtg agcaagtcag atggtcagtg cgtgatggag tcaaccttgg agtgaaccgt
481 ctcacgacag tgaatggccc cgagtggaac ctctgccctt taccccccat tgacctaagg
541 aatatggaac cagccagtga acccaccatt ggagacatga tagagtttta tgaaggccac
601 atctaccact actccatata cattgggcaa gggaagacag ttggtgttca ttccccacag
661 gcagcattct cagtggctag agtaaccatc caacctatag ctgcttggtg gagggtttgt
721 tatatacccc agcccaaaca tagactgagt tatgaccaac ttagggaatt ggaaaatgaa
781 ccctggccat atgcagctat caccaacaat tgttttgagt tttgttgtca agtcatgaat
841 cttgaggaca catggttgca gaggcggcta ataacatcag gtagattcca ccatccttcc
901 cagtcttggt cacaacagac ccctgaattt cagcaggaca gtaaactgga gctggttagg
961 gatgctatac tggccgcagt gaatggcctt gtctcacaac ccttcaagaa tttcttgggc
1021 aagctcaagc ctcttaatgt attaaacatc ctatctaact gtgactggac ttttatgggg
1081 gtggtagaga tggttatact acttcttgag ctctttggcg tgttctggaa cccgcccgat
1141 gtgtctaatt ttatagcatc tctcctccct gacttccacc tccagggacc agaagacctg
1201 gcccgggatt tggtgccagt cattcttggt ggcataggac tagccattgg atttaccaga
1261 gataaagtca ccaaggtcat gaagagtgct gtggatggac tccgggccgc tacacagctg
1321 gggcaatacg ggttggaaat attctcactc ctcaagaagt atttctttgg tggggatcag
1381 accgaacgaa ccctcaaagg cattgaaaca gcagtcatag acatggaggt tttgtcctcc
1441 acatcagtga cacaattggt gagagacaag caggcagcta aagcttacat gaacatcctg
1501 gataatgaag aggaaaaggc tagaaaactc tctgctaaga atgctgaccc ccatgtaata
1561 tcctcaacaa atgccctaat atcacgtata gccatggcgc gatccgcttt ggccaaggct
1621 caggctgaga tgaccagccg aatgaggcca gttgtcatca tgatgtgtgg accccctgga
1681 attggtaaaa ctaaagcagc ggagcacttg gcaaaacgcc tagctaatga gatcaggcct
1741 ggcggaaaag tgggactggt accacgtgag gctgttgacc actgggatgg ctaccatggt
1801 gaggaagtaa tgctatggga tgactatggt atgacaaaga tacaagatga ctgcaacaag
1861 ctccaggcta ttgctgactc tgccccgctc actctcaact gtgataggat tgaaaataaa
1921 gggatgcagt ttgtgtcaga tgcaatagtc atcaccacca acgctccagg gcctgcccct
1981 gtggactttg tcaaccttgg ccctgtgtgt agacgggttg acttcctggt ctactgttcc
2041 gccccagagg tagagcagat aaggagagtc agccctggag acacgtcggc acttaaagac
2101 tgcttcaagt cagatttctc ccacctgaag atggagttag ctcctcaagg ggggtttgac
2161 aaccagggga acacaccatt cggcaagggt gtcatgaaac caacaaccat caacaggctc
2221 ctcatacaag ctgtggctct caccatggag agacaggatg agttccgtct ccaagggaag
2281 atgtatgatt ttgatgatga tagggtgtca gcctttacca ccatggcacg cgataacgga
2341 ttgggcatcc tgagtatggc gagcctaggt aagaagctgc gcggtgtcac atcgatggat
2401 ggcctgaaga atgctttgaa agggtataaa attggtgcgt gcacaatcaa gtggcaggcc
2461 aaggtgtatt cactagagtc agatggcaac agtgttaaca tcagggagga gaagaatgtc
2521 ttgactcaac aacagcagtc ggtgtgcgct gcctctattg cactcacccg tctgcgggtc
2581 gcacgcgcgg tggcgtatgc gtcatgcatt caatcagcca taacctccat actacaaatt
2641 gctgcctctg ctctagtggt caacagggcc gtgaaaagaa tgtttggcac acgcactgct
2701 gctttgtctc tagagggccc ccccaaagaa cacaaatgca gagtccacca ggctaaagcc
2761 gcaggaaaag ggcccattgg ccatgatgac atggttgata aatatggcct atgcgagact
2821 gaggaggatg aagaagtagt ccacactgag ataccatctg ccaccatgga aggtaagaac
2881 aaaggaaaga acaagaaagg gcgcggccga aagaacaact acaacgcctt ttcccgtagg
2941 gggctcaatg acgaagagta cgaggagtac aagaaaatac gggaagagaa gggtggaaat
3001 tacagcattc aggagtacct agaggataga caaagatatg aagaggagct tgctgaggtt
3061 caagcaggtg gagatggagg aatcggtgaa actgaaatgg aaatccgcca cagagtgttc
3121 tacaaatcta agagcaagaa gcaccaccag gaagaacgac gccaactggg gttagtcaca
3181 ggttctgaca tccggaaaag aaaaccaatt gactggaccc cccctaagtc agcatgggca
3241 gatgatgagc gtgaagtgga ctacaatgag aggatcaact ttgaggcgcc ccccaccttg
3301 tggagccggg tcacaaagtt tggatctggg tggggcttct gggtcagtcc cacagtcttc
3361 ataaccacaa cgcacgttat accaaccagt gcaaaagagt tctttggtga accccttgcc
3421 agcatagcca tccatagagc cggagaattc accctcttca ggttctctaa gaaaatcagg
3481 cccgatctca cgggtatgat tcttgaggaa ggttgcccag agggtacggt gtgctcagta
3541 ttaataaaaa gggactccgg tgagctactt ccactggctg taagaatggg cgcaatagca
3601 tcaatgcgca tacagggtcg ccttgtccat ggccagtctg gtatgttgct cactggggcg
3661 aatgctaaag gcatggacct cggaactatt ccaggggatt gtggagctcc ctatgtctat
3721 aagagagcaa atgactgggt ggtttgtggt gtgcacgctg ctgccactaa atcaggcaac
3781 acagtagtgt gcgccgtcca ggctagtgaa ggggaaacca cacttgaggg gggtgacaaa
3841 ggtcactatg ccggacatga gataatcaag catggatgtg ggccagccct gtcaaccaaa
3901 acaaagttct ggaaatcgtc ccctgaacca ctgccccctg gagtctatga acctgcatac
3961 ctcggtggtc gggatccaag agtgagtggt ggcccctcgc tccaacaggt attacgggat
4021 cagctaaaac catttgctga gccacgtggg cgtatgccgg aaccaggtct cctggaggcc
4081 gcagttgaga ctgtgacctc atcactggag caggttatgg ataccccagt gccatggagt
4141 tacagcgatg catgtcaatc cctagataaa actactagct ctggttttcc ccatcacaag
4201 aagaagaatg atgattggaa cggcaccgcc tttattaggg agttgggaga gcaggcagcg
4261 cacgccaata atatgtacga acaagctaag agcatgaagc ccatgtacac ggcggcgctt
4321 aaggatgaat tagtgaaacc agaaaaagtg taccaaaaag tgaagaagcg cttgctttgg
4381 ggagcagatc taggaacagt gatccgggcc gcacgggcct ttggcccatt ctgtgatgcc
4441 ataaaatccc acacaattaa attacctatc aaagttggaa tgaattcaat tgaggatggg
4501 ccattaattt atgcagagca ttcaaaatat aaatatcact ttgatgcaga ctatacggct
4561 tgggactcaa cacaaaatag gcaaattatg actgaatcat tctcaatcat gtgtcggcta
4621 actgcttctc cagaattggc ctcagtggtg gcacaagatc ttcttgcacc ctcagaaatg
4681 gacgttggcg actacgtcat aagagtgaag gaaggcctcc catctggctt cccatgcaca
4741 tcacaagtca atagcataaa ccattggttg ataacattgt gcgccctctc tgaggtgact
4801 ggcctgtcac cagatgttat ccagtccatg tcatactttt ctttttatgg tgatgatgaa
4861 atagtttcca ctgacataga atttgaccca gcaaagctga cacaagtcct taaagagtat
4921 ggcctcaaac ccacccgccc tgacaagagt gaaggtccaa taattgtgag gaagagtgtg
4981 gatggcctgg tcttcttacg tcgcaccatt tcccgcgacg ccgcggggtt ccaggggcga
5041 ctggaccgtg catccattga aaggcagatc tactggacca gagggcccaa tcactcagac
5101 ccctttgaaa ccttggtgcc ccaccagcaa agaaaaatcc aactgatatc actgttaggt
5161 gaggcctcat tgcatggtga aaaattctac aggaagatct caagtaaagt catccaagag
5221 attaagacag ggggtcttga aatgtatgtg ccagggtggc aagccatgtt ccgctggatg
5281 cggtttcacg accttggcct gtggacagga gatcgcaatc tcctgcccga attcgtaaat
5341 gatgatggcg tctaaggacg ccccaacatc ccctgatggc gccagtggcg ccggccagct
5401 ggtaccggag gctaatacag ctgagcaaat ttcaatggac cctgttgcgg gtgcttcaac
5461 agcaatcgcg acagctgggc aagttaacat gattgaccca tggattttca ataactttgt
5521 ccaggcacct caaggagaat tcactatttc ccctaataat acccccggtg atattttgtt
5581 tgatttacaa ctaggacccc accttaaccc atttctagcc catctctcac agatgtacaa
5641 tggttgggtc ggcaatatgc gtgtgcgcat actgttggcc gggaatgcct tcacagctgg
5701 aaagataatc atttgctgtg tcccccctgg ttttgatgcc agaatactca caatagctca
5761 agcaactctc ttcccacact taattgctga tgtaaggacc cttgagcctg tggagcttcc
5821 tttggaggat gtgcgcaatg ttctcttcca caacagtagc caaccgcagc caacaatgcg
5881 gttggttgct atgttgtaca ctcccctccg cactggtggt ggttccggag gcactgatgc
5941 ctttgtggtc gcgggtaggg tgcttacgtg ccccgccccc gactttagtt ttctgtttct
6001 agtcccccct tccgttgaac aaaagactag agttttcagt gtccccaata tacccctgaa
6061 ggatctctca aattcccgtg tccctgtgcc agtgcagggc atgtttatgt ccccagatgt
6121 taatcaatca gtccagtttc agaatggacg ctgccaaatt gatggccaac tccaaggcac
6181 cactccagtc tcgctcagcc aactctgcaa gattaggggt aaaacttcta gcaatgctag
6241 ggtgcttaac ttaagtgagg tagatggcac acccttcatc ccacttgaat caccagcgcc
6301 agttggtttt cccgacttgg gaggttgtga ttggcatgta aatttcactt tccaggctca
6361 aaatcaggac ccatctcaaa gtgtaacctt tgcaactaat gatgctagct ttgtccccta
6421 tctaggtagt atctctcctc acaatggggg agattttcat gcaggtgaca tcataggtag
6481 ccttggttgg atttcagccc cgtctgataa ttcacaactt aatgtttgga caataccaaa
6541 gtatggatct agtctcccag atgtcactca tcttgcccct gctgtgttcc ccccaggctt
6601 tggggaggtg atcttgtact tctattccac cttcccaggt tctggacaat ccagccaact
6661 tcaagtccca tgcttgttgc ctcaggagtt tatcacccac ttctgtaacg aacaggctcc
6721 catcgctggg gaggctgccc tcctccacta cgtggaccct gatacggggc gaaacttggg
6781 agaatttaaa ctttaccctg atgggtttat gacctgtgtc cccaatagtg ttagtagtgg
6841 ccctcaaacc ctccctatca atggagtctt tgtctttgtt tcatgggtat ctagattcta
6901 tcaactcaag cctgtgggaa cggcctcagc ggctagaagg cttggattgc ggcgcatata
6961 atggcccaag ctgtcatcgg tgccatagcc gcatctgccg ctggtagcat actaggggca
7021 ggcatacagg ctggtgctga ggctggtctc caggctcaac ggtatcagca ggatctgcag
7081 ttgcaacaaa attctttcaa gcatgataag gaaatgttag gttaccaagt tcaggctagt
7141 aatgctcttt tagctaagaa tcttaacact agatatgctc ttctgcaggc agggggccta
7201 tctagcgctg atgctgctcg ggcagtggct ggtgctcctg tcacccgtat agtggactgg
7261 aatggcacgc gcattgcagc gcccacttca agcaccacta cactcagatc tggtggtttt
7321 atggctgtcc ctataccatt gtcttcaaag accaagcaac cagtgatgtc tgggcaggat
7381 aatccaaatt atgctgcttc ttctatctct agaactgctt catgggtgca atctcaaaat
7441 tctatgaggt ctgtttctcc ttttcacagt gatgctttga gaaccgtttg ggttacacca
7501 cccggttcat catcaacttc atctgtgcaa tctagtttct atggtgtttt taatacagat
7561 agattgcctc tgttcgcaaa cagaaggtaa taa
//