Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP162335 | GI.5 | |
|
|---|---|---|---|
| GI.P5 |
ORF1: 1..5364
ORF2: 5348..6979
ORF3: 6979..7605
LOCUS OP162335 7605 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GI isolate RIVM-NOV-2016-0166_R01-05 nonstructural
polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP162335
VERSION OP162335.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7605)
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JOURNAL Unpublished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 7605)
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..7605
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0166_R01-05"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="Netherlands"
/collection_date="2016-02-16"
/note="genotype: GI.5[P5]"
gene <1..5364
/gene="ORF1"
CDS 1..5364
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUL90908.1"
/translation="MMMASKDVVAATAASKNCASDNSNTIKNRLLAKLKNIGNNNQPI
KIENTHMALGLIGRGPSPTPPIEPPKQQRDRAPRSAAETQQAMGWVEQPLDQNLPTWE
ELSEAEKRDIMARNENWFDAGGLAPASIPSTHERAHNDEPPGHQIRWSANAGVDLGVG
DLTSVSGPAWNMCPMPPMDQRNAGPAKEPLIGDMLEFYEGRIYHYAIYIGQGKSIGVH
SPQAAFSIARITIHPIAAWWRVCYVPSTEQRLNYDQLKELENEPWPYAAVTNNCYEFC
CRVMGVQDTWLERRLINSGRFNHPTQDWSKDTPDFQQDSKLEIVRDAVLAAINGLVSK
PFKDLLGKLKPLNVLNLLSNCDWTFMGVVETVILLMELFGIFWNPPDVSSFIASLLPD
MHLQGPEDLAKDLIPLILGGIGLAIGFTKDKVTKVMKSAVEGLRAATQLGQYGLEIFA
VLKKYFFGGDQTEKTLKDIEAAVIDMEVISTTAITQLVRDKQSARTYMAILDAEEEKA
RKLSVKHADPHVVSTTNALIARISLARSALAKAQAEMTNRVKPVVIMMCGPPGIGKTK
AAEYLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMSKIADDCNKLQA
IADTAPLTLNCDRIEKKGLQFVSDAIIITTNAPGPAPVDFVNLGPVCRRVDFLVYCSA
PDVEQTRRTNPGDTGALKDCFKSDFSHLKMELAPQGGFDNQGNTPFGKGVMRPTTLNR
LLIQAVALTMERQDEFQMQGPTYDFDADRIAAFTSLARANGLGLIDMAKLGKKLRGVD
SIHGLKNALNGYTITPCSIKWQARIYNIESDGTTVKIKEDTAAQTQRQHTIDTAVLAL
TRLRAARAAAYASCLQSAITTILQMAGSALVINRAVKRMFGTHTNTISLEGPPKEHRC
RVHVAKANGGGPIGHDDVIERFGLCETEEDDDSQELKVSLPTATHEGKNKGKTKKGRG
RRANYNAFSRRGLNDEEYEEYKKIREEKNGNYSIQEYLEDRQRYEEEMAEVQAGGDGG
IGETEMEIRHRVFYKSKTRKNRQEERHQLGLVTGSDIRKRKPIDWTPPKNEWADDNRE
VDYNEKISFEAPPTLWSRVVKFGSGWGFWVSPTVFITTTHVIPTSVREFFGEPLDTIA
IHRAGEFTQLRFSRKIRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIAS
MKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSG
NTVVCAVQAGEGETTLEGGDKGHYAGHEIIKHSKGPALSSKTKFWRSTTEPLPPGVYE
PAYLGGRDPRVKGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSVLEQVMDT
PVPWTYADACQSLDKTTSSGHPYHKRKNDDWNGTAFIGELGEQAAHANNMYEQGKPMK
PLYTAALKDELVKPEKVYQKIKKRLLWGADLSTVIRAARAFGPFCDAIKPHVIKLPIK
VGMNSIEDGPMIYAEHARFKNHFDADYSAWDSTQNRQIMTESFSIMCRLTATPELASV
VAKDLLAPSEMDVGDYIIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDVI
QSQSYFSFYGDDEIVSTDIDFDPARLTQVLKEYGLRPTRPDKSEGPIVLRRQIDGLVF
LRRTISKDAAGFQGRLDRGSIERQLWWTRGPNHDDPNETLIPHPQRKVQLISLLGEAS
LHGEKFYRKIAAKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVND
DGV"
mat_peptide 1..1188
/gene="ORF1"
/product="p48"
mat_peptide 1189..2277
/gene="ORF1"
/product="NTPase"
mat_peptide 2278..2880
/gene="ORF1"
/product="p22"
mat_peptide 2881..3294
/gene="ORF1"
/product="VPg"
mat_peptide 3295..3837
/gene="ORF1"
/product="Pro"
mat_peptide 3838..5361
/gene="ORF1"
/product="RdRp"
gene 5348..6979
/gene="ORF2"
CDS 5348..6979
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUL90909.1"
/translation="MMMASKDASPSADGANGAGQLVPEVNNAEPLPLDPVAGASTALA
TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLSQMYNG
WVGNMRVRVILAGNAFTAGKVIICCVPPGFQSRTLSIAQATLFPHVIADVRTLEPIEI
PLEDVRNTLYHTNDNQPTMRLLCMLYTPLRTGGGSGGTDAFVVAGRVLTCPSSDFNFL
FLVPPTVEQKTRPFSVPNIPLQLLSNSRVPNLIQSMVLSPDQAQNVQFQNGRCTTDGQ
LLGTTPVSVSQILKFRGKVSAGSKVINLTELDGSPFLAFEAPAPTGFPDLGTSDWHVE
MSLNSNSQSSGNPILLRDIQPNSSDFVPHLGSVSVTAAIEVAGDYTGTIQWTSQPSNV
TPVPDVNFWTIPHYGSNLAEASQLAPVVYPPGFGEAIVYFMSPIPGPNTAHKPNLVPC
LLPQEFVTHFVSEQAPSMGEAALVHYVDPDTNRNLGEFKLYPEGFITCVPNGTGPQQL
PLNGVFVFASWVSRFYQLKPVGTASSARGRLGVRR"
gene 6979..7605
/gene="ORF3"
CDS 6979..7605
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUL90910.1"
/translation="MAQAIIGAIAASAAGSALGAGIQAGAEAALQSQRFQQDLTLQQN
SFKHDKEMMSYQVEMSNVLLAKNLNTRYALLQSGGLSSADAARAVAGAPVTRVVDWNG
TRVAAPNSSATTLRSGGFMSVPIPVQPKQKPPTTSGFNNPAYGETMSRVSSWVQSQNS
SRSMSPFHNSALRTVWVTPPGSTSSSSVSSVPIGVFNTDRLPLFANRK"
ORIGIN
1 atgatgatgg cgtcgaaaga cgtcgttgca gctactgctg ctagcaaaaa ttgtgctagt
61 gacaatagca atacaattaa gaatcgctta ttagcgaaac ttaagaatat aggcaataac
121 aaccagccta taaaaataga aaatactcac atggccttag ggctcattgg tagaggtccc
181 tcaccgaccc ctcccattga gccccccaaa cagcagcgcg accgtgcacc acggagtgct
241 gctgagaccc aacaggccat ggggtgggtt gaacaaccat tagatcagaa cctaccaacc
301 tgggaagaac tgagtgaagc tgaaaagcgc gacatcatgg ctaggaatga gaattggttt
361 gacgctggtg gtctggcgcc agcatccatc cctagtacgc atgagcgtgc ccataatgat
421 gagccaccag ggcaccaaat aagatggagc gccaatgctg gtgttgacct cggggttggg
481 gacctcacct ctgtttcagg ccccgcgtgg aatatgtgcc ccatgccacc aatggaccag
541 cgcaatgctg gtcctgcaaa agagccactc attggtgaca tgcttgagtt ttatgaggga
601 cgcatatatc actatgccat atacatcggg caaggcaagt ctattggagt ccattcaccg
661 caggcagcct tctctatagc taggataaca atacatccca ttgctgcttg gtggcgagtg
721 tgctacgtcc caagtactga acagagacta aattatgacc agctcaaaga acttgagaat
781 gagccgtggc cgtatgccgc agtcaccaac aactgctacg agttttgttg tcgagtcatg
841 ggtgtgcaag acacttggct tgagcgccgg ctcataaact cgggtcgttt caaccatccc
901 acacaagatt ggtctaagga caccccagac ttccaacaag atagtaaatt ggagatagtc
961 agggacgctg ttctggcagc cataaacggc ctggtttcaa aaccatttaa agacctttta
1021 gggaagttga aacccctaaa cgtcctcaat ctactctcca attgtgactg gacctttatg
1081 ggagtcgtgg agactgtgat tctcttgatg gaactttttg ggatattctg gaacccacct
1141 gatgtatcta gcttcattgc ctcactctta ccagacatgc acttacaggg ccctgaagat
1201 ttggctaaag acttgatacc cttaatactc ggtggcatcg ggcttgccat cgggttcacc
1261 aaggacaagg tcacaaaagt tatgaaaagt gcagtggagg gtcttcgggc cgcaacccag
1321 ctcggccagt atggtcttga gatctttgcc gtactaaaga agtatttctt tggaggtgac
1381 caaacagaga aaacactaaa agatattgag gcagcggtga tagacatgga agtcatttca
1441 accacagcca ttacacaact ggtcagagat aagcaatcag ccagaacgta tatggctatt
1501 ctggatgcag aggaggagaa agccagaaag ctctcagtga aacatgccga tcctcatgtg
1561 gtatccacca ccaatgctct cattgcacgc atatcgctag ctcgctctgc attggctaaa
1621 gcgcaagcag agatgaccaa tagagtcaaa cctgtggtca tcatgatgtg tggtccgcca
1681 ggcattggaa aaactaaggc agcagagtac ctggcaaagc ggttagccaa tgaaataaga
1741 ccaggaggta aagttggtct tgtaccgcgt gaggctgtgg atcattggga tgggtaccat
1801 ggtgaggaag tcatgttgtg ggatgactat gggatgtcga agattgctga tgactgcaac
1861 aagctgcagg caattgctga cacggcccct ttgacattga attgtgatag gatagaaaag
1921 aaaggactac aatttgtatc tgatgccata attataacca ccaacgcccc aggcccagca
1981 ccagtggatt ttgtcaacct tggtcctgtg tgccggcgag tggactttct tgtctattgt
2041 tcggctcccg atgtcgagca gactcgtcgc actaaccctg gtgatactgg ggccctcaag
2101 gactgcttca agagtgactt ctcacatcta aaaatggaac tcgctcccca aggtggattt
2161 gacaaccagg gtaacacccc gtttggcaag ggggtcatgc gcccaactac actcaatagg
2221 ttgttaatac aggcagttgc cctcaccatg gagcggcaag atgagttcca aatgcaagga
2281 ccaacttatg actttgatgc tgatagaatt gcagctttca ccagcttggc acgcgccaat
2341 ggccttggcc ttatcgacat ggctaaactt gggaagaaac tgcgaggtgt ggactccatc
2401 catggcctta agaatgcact taatgggtac accataacac cctgtagcat aaaatggcag
2461 gcaaggattt acaacataga atctgatggc acaacagtaa aaattaaaga ggacaccgca
2521 gcacagactc aacgccagca cacaattgac actgccgtgt tggccctaac ccgcttaaga
2581 gctgctaggg ctgcagcata tgcatcatgc ctacaaagtg caattacaac cattcttcag
2641 atggcgggct cagcacttgt tattaaccga gctgtcaaac gcatgtttgg cacccatacc
2701 aacaccattt cactagaagg cccccccaaa gaacaccgtt gcagggtcca cgtggccaaa
2761 gctaatgggg gcggcccaat tggacatgat gacgtaatag aaagatttgg cctgtgtgaa
2821 actgaggaag atgatgacag ccaagagctc aaagtcagcc tgcccactgc cacccatgaa
2881 ggtaagaaca agggtaagac gaagaaaggc agaggcaggc gtgccaatta taacgctttc
2941 tcaaggagag gcctcaatga tgaggaatat gaggagtaca agaagatcag agaagaaaag
3001 aatggcaatt atagtataca agagtacctt gaggacagac agcgttatga agaagagatg
3061 gccgaagttc aggccggagg ggatggtggc attggagaga ccgagatgga gatccggcac
3121 cgtgtctttt ataaatccaa aaccagaaag aaccggcagg aagagcgcca ccaattaggg
3181 cttgttactg ggagtgacat taggaagaga aaaccaattg attggacacc ccctaaaaat
3241 gagtgggctg atgataatag ggaggtggat tacaatgaga aaatcagctt tgaagcacca
3301 cccacactct ggagccgtgt cgtgaagttt ggttccggct ggggattctg ggtcagcccc
3361 acagtcttca tcaccacaac ccatgttatc ccaacaagtg tgagagaatt ctttggggag
3421 ccacttgaca ccatcgccat ccatcgggct ggtgaattta cacagctaag gttttccagg
3481 aaaataaggc ctgacctgac cggcatggtc cttgaggagg gttgcccaga aggtgtggtc
3541 tgttcaatcc tcataaaaag ggactctgga gagctcctcc cattggctgt tcggatgggc
3601 gccatagctt caatgaagat tcaagggcgc ttggtccatg gccaatcagg aatgttgttg
3661 acaggggcta atgctaaggg tatggacctt ggcactctcc ctggtgactg tggggcccca
3721 tatgtctaca aaaggaataa tgattgggta gtctgtggtg tccacgccgc agccacaaaa
3781 tctggaaata cagttgtgtg tgcagtgcaa gcaggtgaag gagagaccac actggaagga
3841 ggagacaagg gccattacgc cggacatgaa ataatcaagc atagtaaggg accagcacta
3901 tctagtaaaa ccaaattttg gcggtcaact actgaacctc taccaccagg agtgtatgag
3961 ccagcctacc ttggaggtcg cgaccctagg gttaaaggcg gcccatcact gcaacaggtg
4021 ttgagggacc agttgaagcc atttgctgag ccgcgcgggc gcatgcctga acctggctta
4081 ctagaggcag ctgttgaaac tgtcacatca gtgttagagc aagtcatgga taccccagtc
4141 ccctggactt atgctgacgc atgtcagtca ctggacaaaa ccactagttc cggccaccca
4201 taccacaaga ggaaaaatga tgactggaat gggactgcat ttattgggga attgggagaa
4261 caagcagccc atgcaaataa catgtatgaa cagggaaagc caatgaaacc cctatataca
4321 gctgcactca aggatgaact agttaaacct gagaaagtgt accagaagat taagaagcgg
4381 ctcctgtggg gtgctgacct ctcaacggtg atccgtgctg ccagagcctt tggcccattt
4441 tgtgatgcaa taaaacccca tgtcataaag ctccccatca aggttgggat gaattcaatt
4501 gaggatggcc caatgattta tgctgagcat gcaagattta agaatcactt tgatgctgac
4561 tattctgcat gggattcaac acagaacagg cagatcatga ctgaatcatt ctcaataatg
4621 tgccgcctca cggctacacc agagctagct tcagtggtgg ctaaagatct tctcgcacca
4681 tctgagatgg atgttgggga ctatatcata agggtcaaag aaggcctccc ttcaggcttc
4741 ccctgtactt cacaagtcaa tagcataaac cattggctaa ttaccctctg tgccctctct
4801 gaggttaccg ggctttctcc tgatgtaata caatcacaat catatttctc attttatggt
4861 gatgatgaaa ttgtgtccac tgatattgat tttgacccag cacgtctaac ccaagtgctt
4921 aaagaatatg gtcttcgccc cacacgccca gacaagagtg aagggccaat agtgttgaga
4981 aggcagattg atgggttggt gtttctcaga aggactatat caaaagatgc agctggtttt
5041 caaggccgat tggacagagg ttctattgag aggcaacttt ggtggacccg tgggccaaac
5101 cacgatgatc ccaatgagac cctgataccc cacccccaga gaaaggtgca actcatatca
5161 ctgcttggtg aggcctcact ccatggtgaa aaattctaca gaaaaatcgc cgctaaggtc
5221 atccaagaaa tcaagactgg tggcttagaa atgtatgtgc caggctggca ggccatgttc
5281 cgttggatgc gcttccacga cctcggattg tggacaggag atcgcaatct cctgcccgaa
5341 ttcgtaaatg atgatggcgt ctaaggacgc ctcaccaagc gcagatggcg cgaatggcgc
5401 cggtcagctt gtgccggagg ttaataatgc tgaaccactg ccacttgatc cagtggcggg
5461 ggcttccacc gccctcgcca ctgctggaca agttaatatg attgacccat ggatcttcaa
5521 taactttgtc caggcccctc agggtgaatt tactatttcc ccaaataata cccccggtga
5581 tattttgttt gatttgcaat taggcccaca tctaaatcct tttctagcac atttatctca
5641 gatgtataat ggctgggttg gcaatatgcg ggtcagggtt atcttggccg gcaatgcctt
5701 cactgctggt aaagttataa tttgttgtgt tccccctggc tttcaatcta gaaccctttc
5761 tatagcccag gctacactct ttccccacgt catagctgat gtacgaactc tggagccaat
5821 tgagatccct ctagaggatg ttaggaacac tctttatcat actaatgata atcaaccaac
5881 aatgcgctta ctgtgcatgc tttacactcc actgcgcacc ggtggcggtt ctggtggcac
5941 ggatgcgttc gttgtggcag gccgagtatt aacttgtccc agctctgatt ttaatttctt
6001 gtttttagtc cctcccactg tagagcagaa aacacgcccc tttagtgtac ctaacatacc
6061 cttgcaattg ctgtctaatt cccgcgttcc caatctcata caaagcatgg ttctttcgcc
6121 tgatcaggct cagaatgtcc aatttcagaa tggccgctgc accaccgatg ggcagctctt
6181 gggtacaaca cctgtctcag ttagtcagat tttaaagttt agaggaaagg tgtcagctgg
6241 ctctaaagtc atcaatctta ctgaactgga tggctccccc tttctagctt ttgaggcccc
6301 agcacccacg ggtttccctg acctggggac tagcgattgg catgttgaga tgagtcttaa
6361 ctcaaatagc caaagttctg gcaatccaat tttgttgagg gacatacaac caaattcctc
6421 agactttgta ccgcatttgg gcagtgtgtc tgtcaccgct gcaattgaag tggccgggga
6481 ttacactggc acaattcaat ggacctctca accatccaat gtcactccag ttcccgatgt
6541 caacttctgg accatccccc attatggatc aaatttggca gaagcctccc agttggcccc
6601 tgtggtgtat cccccaggat ttggtgaagc tatagtgtat tttatgtccc ccataccagg
6661 cccaaacact gcacacaaac ccaatttggt accttgccta ctcccacaag aatttgtaac
6721 acattttgtc agtgaacaag ctccatccat gggtgaggca gctcttgtcc attatgttga
6781 cccagacacc aatcgcaact tgggcgagtt caaattgtac cctgaaggtt ttatcacgtg
6841 tgtgccgaat ggcactggcc cacaacaact ccctcttaat ggagtttttg tatttgcttc
6901 ctgggtatcc agattttatc agttaaagcc tgtgggaacg gccagctcgg ccagaggtag
6961 gcttggggtt agaagataat ggctcaagcc atcattggag ccattgctgc atcagcggct
7021 ggaagtgccc ttggagctgg tatccaagca ggtgctgagg ccgcccttca gagccagagg
7081 tttcagcagg acctcaccct ccaacaaaat tcttttaaac atgataagga gatgatgtca
7141 tatcaagttg aaatgtctaa tgttttgtta gctaaaaatc ttaacactcg ctatgctttg
7201 cttcaatctg gtggtctatc tagtgctgat gctgctcgtg ctgtggctgg tgcgcctgtc
7261 acaagggttg ttgattggaa cggcacaaga gtagcagccc caaattcctc tgcaacaact
7321 cttaggtctg gtggatttat gtctgttcct atacctgttc aacccaaaca gaagccccct
7381 accacctcag ggtttaacaa tccagcatat ggagaaacta tgtcaagggt ttcctcctgg
7441 gttcagtccc agaattcaag tagaagtatg tccccttttc acaattctgc ccttaggact
7501 gtttgggtca caccaccagg ctcaacttct tcttcgtctg tttcatctgt gcctataggt
7561 gtgttcaaca ccgataggct tcccctattc gcaaatagga aataa
//