Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP162341 | GI.5 | |
|
|---|---|---|---|
| GI.P4 |
ORF1: 1..5339
ORF2: 5323..6954
ORF3: 6954..7586
LOCUS OP162341 7586 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GI isolate RIVM-NOV-2019-0025_R04-15_major nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP162341
VERSION OP162341.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7586)
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JOURNAL Unpublished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 7586)
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..7586
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2019-0025_R04-15_major"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="Netherlands"
/collection_date="2018-12-12"
/note="genotype: GI.5[P4]"
gene <1..5339
/gene="ORF1"
CDS <1..5339
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUL90926.1"
/translation="VVAATAASAENTSDNSDSIKNRFFTRLKNLGSNNKPIKIENTHM
ALNLISRGPSPIPQDKPPKDQRDKPPRNVAETQQAMGWVDPPMDQNLPTWEELSQTEK
QEILKNNSNWFDAGGLAPASIPTGYVKNTEQQPPDHQVKWSASNGVDLGVGNLTTVPG
PVWNLCPMPPIDQRNNGPAKEPLIGDMIEFYEGHIYHYAIYIGQGKTVGVHSPQAAFS
IARITIHPIAAWWRVCYVPTPDQRLNYDQLKELENEPWPYAAVTNNCYEFCCRILNLQ
DSWLERRLVTSGRFNHPAQDWSRDTPDFQQDSKLEIVRDAVLAAINGLVSKPFKDLLN
KLKPLNVLSLLSNCDWTFMGVVETIILLMELFGIFWNPPDVSSFIASLLPDMHLQGPE
DLAKDLIPLVLGGVGLAIGFTKDKVTKVMKSAVEGLRAATQLGQYGLEIFAVLKKYFF
GGDQTEKTLKDIETAVIDMEVISTTAVTQLVRDKQAARTYMNILDAEEEKARKLSVRH
ADPHVVSTTNALISRISLARSALAKAQAEMTNRVKPVVIMMCGPPGIGKTKAAEYLAK
RLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMSKIADDCNKLQAIADTAPL
TLNCDRIEKKGLQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVYCTAPDVEQTR
RTNPGDTGALKDCFKSDFSHLKMELAPQGGFDNQGNTPFGKGTMRPTTLNRLLIQAVA
LTMERQDEFQMQGQVYDFDADRISAFTSLARANGLGLISMASLGKKLRGVDSVHGLKN
ALSGYAITPCSIKWQARVYDIESDGSNVRIKENTSAQTQRQQSIDTAALALTRLKAAR
AAAYAACIQSAITTILQMAGSAIVINRAVKRMFGAHSSTIALEGPPREHRCRAHLAKA
AGGGPIGHDDVIDKYGLCETEEEGTSEEINVELPTATSEGKNKGKTKKGRGRRANYNA
FSRRGLSDEEYEEYKKIREEKNGNYSIQEYLEDRQRYEEELAEVQAGGDGGIGETEME
IRHKIFYKSKKGRQNERRQLGLVTGSDIRKRKPIDWTPPKNDWADDNREVDYNEKLSF
EAPPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPSGAREFFGEPIESIAIHRAGEFTQ
FRFSHKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVH
GQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA
GEGETTLEGGDKGHYAGHEIIKHSKGPALSTKTKFWRSTPEPLPPGVYEPAYLGGRDP
RVKSGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSMLEQTMDTPIPWSFSDA
CQSLDKTTSSGHPYHKRKNDDWNGTSFVGELGEQAAHANNMYELGKSMKPLYTAALKD
ELVKPEKIYQKIKKRLLWGADLSTVIRAARAFGPFCDAIKSHVIKLPIKVGMNSIEDG
PMIYAEHAKYKNHFDADYSAWDSTQNRQIMTESFAIMCRLTASPELASVVAKDLLAPS
EMDVGDYIIRVKEGLPSGFPCTSQVNSINHWLITLCAMSEVTGLSPDVIQSQSYFSFY
GDDEIVSTDIDFDPARLTQVLKEYGLRPTRPDKSEGPIILRRQVDGLVFLRRTISKDA
AGFQGRLDRGSIERQLWWTRGPNHDDPSETLIPHPQRKVQLISLLGEASLHGEKFYRK
ISSKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVNDDGV"
mat_peptide <1..1169
/gene="ORF1"
/product="p48"
mat_peptide 1170..2258
/gene="ORF1"
/product="NTPase"
mat_peptide 2259..2861
/gene="ORF1"
/product="p22"
mat_peptide 2862..3269
/gene="ORF1"
/product="VPg"
mat_peptide 3270..3812
/gene="ORF1"
/product="Pro"
mat_peptide 3813..5336
/gene="ORF1"
/product="RdRp"
gene 5323..6954
/gene="ORF2"
CDS 5323..6954
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUL90927.1"
/translation="MMMASKDAPPSADGANGAGQLVPEVNNAEPLPLDPVAGASTALA
TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLAQMYNG
WVGNMRVRLILAGNAFTAGKVIICCVPPGFQSRTLSIAQATLFPHVIADVRTLEPIEI
PLEDVRNTLYHNNDNQPTMRLLCMLYTPLRTGGGSGGTDAFVVAGRVLTCPSPDFNFL
FLVPPTVEQKTRPFSLPNIPLHLQSNSRVPNPIQSMVISPDQAQNTQFQNGRCTTDGQ
LLGTTPVSVSQILKFRGKVSPGSKVINLTELDGSPFLAFEAPAPTGFPDLGTCDWHIE
LSLNSNSQSSGNPIVQRDIQPNSSDFVPHLGSVAVTVAIETAGDYTGTIQWISQPSNV
SPVPNVNLWTIPNYGSSLAEASQLAPVVYPPGFGEAVVYFMSHIPGPNTEHKPNLVPC
LLPQEFITHFVSEQAPPMGEAALIHYVDPDTNRNLGEFKLYPEGVITCVPNGTGPQQL
PLNGVFVFASWVSRFYQLKPVGTASSARGRLGVRR"
gene 6954..7586
/gene="ORF3"
CDS 6954..7586
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUL90928.1"
/translation="MAQAIIGAIAASAAGSALGAGIQAGAEAALQSQRFQQDLTLQQN
SFKHDKEMMSYQVEMSNALLAKNLNTRYALLQSGGLSSADAARAVAGAPVTRIVDWNG
TRVAAPNSSATTLRSGGFMSVPIPIQPKQKPSTISGFNNPAYGETMSRVSSWVQSQNS
SVRSVPPFHSSALRTVWVTPPGSTSTSSSVSSMPMGVFNTDRLPLFANRR"
ORIGIN
1 acgtcgttgc agctactgct gctagtgctg aaaacactag tgacaatagt gattctataa
61 agaaccgttt cttcacaagg ttgaagaatt taggttctaa caacaagccc ataaaaattg
121 agaacaccca catggccctt aacttaatta gtaggggccc atccccaatt ccacaagaca
181 agcccccaaa agaccagagg gataaacccc caaggaatgt ggctgagacc cagcaggcaa
241 tgggctgggt cgaccccccc atggaccaga atctaccaac ctgggaggag ttgagccaaa
301 cagaaaaaca agagatactc aaaaacaatt caaattggtt tgatgctggt ggtttggcac
361 cagctagcat cccaactggt tatgtaaaga acacagaaca acaaccccct gaccaccaag
421 tcaaatggag tgccagtaat ggggttgatc ttggggtagg caatttgaca actgtgccag
481 gtccagtatg gaatctgtgc cccatgccac caattgatca acgcaacaat ggcccagcaa
541 aggagccact tattggtgac atgatagaat tctatgaggg gcacatttac cattatgcaa
601 tatacattgg acagggaaaa actgttgggg ttcactcacc ccaagcggcc ttttcaatag
661 ccaggataac tatacacccc atcgccgctt ggtggagggt ttgttatgtg ccaacacctg
721 atcagaggtt gaattatgac caactcaaag aacttgagaa tgagccatgg ccatatgctg
781 cagttactaa taattgttat gagttctgct gcaggattct taatcttcag gactcctggt
841 tggaacgtcg cttggtcaca tctggccgtt tcaaccaccc agcacaagac tggtccaggg
901 acacgcctga cttccagcaa gatagcaagt tagaaatagt cagggatgcc gtgcttgctg
961 ctatcaatgg cttggtatca aaacctttta aggacctcct aaataaactt aagccactca
1021 acgtgctcag cttactctct aactgtgatt ggacatttat gggggtggtt gagacgataa
1081 tattacttat ggagttgttt gggatcttct ggaatccccc tgatgtgtcc agtttcatag
1141 cctcactact acctgatatg cacttgcagg gaccagaaga tctggctaaa gacctgatac
1201 cgttggtgtt ggggggtgtg gggcttgcaa ttgggttcac caaggacaaa gttacaaaag
1261 tcatgaagag tgctgttgaa ggactcaggg cagccacaca attaggccag tatggcctag
1321 agatatttgc agttttaaag aaatatttct ttggtggaga tcaaacagag aagaccttaa
1381 aggacattga gacagccgtg attgacatgg aggttatctc aacaactgct gtaactcaac
1441 tagtcaggga caaacaggct gcccgaacct acatgaacat cttagatgct gaagaagaga
1501 aggcaagaaa gctttcagtt agacatgcag acccccatgt tgtgtccaca accaatgccc
1561 tgatctcacg tatttcattg gctcgttccg cacttgctaa ggcacaagct gagatgacta
1621 atagggttaa accagtagtg ataatgatgt gtggtccccc aggtataggc aaaacaaagg
1681 cagccgagta ccttgctaag agactggcta atgagatacg acctggagga aaagtgggcc
1741 ttgtgccaag ggaggctgtg gaccactggg atggatatca tggtgaagag gtaatgctat
1801 gggatgacta tggtatgtca aaaatagctg atgactgcaa taaattacag gctatagccg
1861 acacagctcc actcactttg aattgtgacc ggattgagaa gaaagggtta caatttgtct
1921 ctgatgccat agtgataaca acaaatgccc caggaccagc cccagttgac tttgtcaatc
1981 ttggcccagt gtgtcggcgg gtagatttcc tggtttattg cactgcaccc gatgttgaac
2041 agacacgtcg cactaaccca ggagacaccg gagccctcaa ggattgtttt aaaagtgact
2101 tctctcattt aaaaatggag ttggctccac agggcgggtt cgacaaccaa ggaaacactc
2161 catttggcaa agggaccatg cggcctacca cattaaaccg cctccttata caggccgtgg
2221 cactaaccat ggagcgtcag gatgagttcc agatgcaagg tcaggtgtac gactttgatg
2281 ctgataggat ctctgccttc accagcttag cgagagccaa tggtttgggt ctcattagca
2341 tggcctccct aggaaagaaa ctgaggggtg tggactcggt tcatggcctc aagaatgcac
2401 tatcaggcta tgccataacc ccctgtagca taaagtggca agctagagtg tatgacattg
2461 aatcagatgg ctccaatgtg cgcataaaag aaaacacctc agcccagaca caacgccagc
2521 aatcaattga tacagcagcc ctggcactta ccagacttaa agcagcacgg gcagcagcat
2581 atgcagcttg catacaaagc gcaataacaa ctatcctgca gatggctggg tcagccatcg
2641 ttataaatcg tgctgttaag aggatgttcg gtgcacattc gagcactata gcccttgaag
2701 gacctccaag agaacatcgg tgcagggctc atttagccaa ggctgcagga ggtgggccaa
2761 taggccatga tgatgtcatt gataaatatg gcctatgtga gactgaagaa gagggtacca
2821 gtgaggagat aaatgtggag ctacccaccg ccacttccga aggcaagaac aaaggaaaga
2881 ccaagaaagg aagaggcaga agggccaact acaatgcttt ttcacggcgc ggcctgagtg
2941 atgaggagta tgaggaatat aagaaaatca gggaagaaaa gaatggcaac tacagcattc
3001 aggagtacct tgaagacagg caacgctatg aagaagaact cgcagaagta caagctggtg
3061 gtgatggagg cattggtgag acagaaatgg agatccgaca taaaatcttt tacaagtcta
3121 aaaagggccg ccagaatgaa cgccgccaac tagggctagt cactggtagt gatattagaa
3181 agagaaagcc aattgattgg acccccccca aaaatgattg ggcagatgat aatagggaag
3241 tggactacaa tgaaaaactc agttttgaag ccccaccaac cctttggagc cgcgttgtga
3301 gatttggctc tgggtggggc ttttgggtga gcccgactgt ttttatcacc accactcatg
3361 tcataccatc tggggcgcgt gaattctttg gggaacccat cgagtccatt gcaatccatc
3421 gtgctggtga attcacacaa ttcagatttt cacacaaggt ccgcccggat ttgactggaa
3481 tggtgctgga ggaaggttgt cctgagggtg ttgtgtgttc tattctcata aagcgtgact
3541 ctggtgagct gctgcccctt gctgtccgaa tgggcgctat agcgtccatg aagattcagg
3601 gaaggctagt gcatggccag tctgggatgc tgctcactgg agctaacgct aaggggatgg
3661 atttaggtac cctaccaggt gattgtggtg ccccttatgt gtacaaaagg aataacgact
3721 gggtagtctg tggtgtacac gcagccgcta caaagtcagg caacactgtg gtgtgtgctg
3781 tccaggctgg agagggtgaa accaccctag agggtggtga caaaggccac tatgcaggcc
3841 atgaaataat caagcatagt aagggcccag ctctatctac taagaccaag ttttggaggt
3901 caacccctga accattacca ccaggcgttt atgaaccagc atatcttggg ggtcgagatc
3961 ccagggtgaa aagtgggccc tctctacagc aagtcttgcg tgatcagttg aaaccatttg
4021 ctgagccgcg aggtcgaatg ccagagcctg gtctacttga ggcagctgtt gaaactgtca
4081 catccatgct tgagcaaaca atggatacac caatcccctg gtctttctct gatgcatgtc
4141 aatcacttga caagaccaca agttcaggac acccgtatca caaaagaaag aatgatgatt
4201 ggaatggaac ttcattcgtt ggagagcttg gagaacaggc agcacatgcc aacaacatgt
4261 atgaattagg caaatctatg aaaccactat acactgcagc ccttaaagac gagttagtca
4321 agcccgagaa aatttatcaa aagatcaaga agaggcttct ctggggtgct gacctctcaa
4381 cagtcataag ggctgccagg gcctttggac ctttttgtga tgctataaag tctcatgtca
4441 ttaaactccc catcaaagtt ggtatgaact ccatagaaga tggcccaatg atttatgcag
4501 agcatgcaaa gtacaagaac cattttgatg cagattattc ggcctgggat tccacgcaaa
4561 atagacagat catgactgaa tcctttgcaa tcatgtgccg tctcacagct tcaccggagt
4621 tggcttctgt tgtagctaaa gatttactag ccccttcaga aatggatgtt ggtgattaca
4681 tcatccgtgt aaaagagggc ttgccatcag gattcccttg cacatcacag gtgaacagca
4741 taaaccactg gctgatcaca ctgtgtgcca tgtctgaagt cacgggtttg tcaccagatg
4801 tcatacaatc ccagtcttac ttttctttct atggtgatga tgagatagtc tctacagaca
4861 ttgattttga ccctgctcgc ctcactcaag tgctcaagga atatgggttg agacccacca
4921 ggccagacaa gtcagaaggg cccatcatac tcagaagaca ggtggatggt cttgttttct
4981 tgaggaggac aatctctaaa gatgctgcgg gcttccaggg aaggctagat agaggttcaa
5041 ttgaaagaca gctctggtgg actcgaggcc ctaaccatga tgaccctagt gagactctaa
5101 tcccacaccc ccagaggaaa gttcagctta tatccctcct tggtgaggct tccctccatg
5161 gtgagaagtt ttacaggaag atctccagta aagttataca ggagataaaa actggtggtt
5221 tggaaatgta tgtgccaggc tggcaggcca tgttccgctg gatgcgcttc catgacctcg
5281 gattgtggac aggagatcgc aatctcctgc ccgaattcgt aaatgatgat ggcgtctaag
5341 gacgccccac caagcgcaga tggcgcgaat ggcgccggtc agcttgtgcc ggaggttaat
5401 aatgctgaac cactgccact tgatccagtg gcgggggctt ccaccgccct tgccactgct
5461 ggacaagtta atatgattga cccatggatc tttaataatt ttgtccaggc cccccaaggt
5521 gaatttacta tttccccaaa taataccccc ggcgatatcc tgtttgattt acaattaggt
5581 ccacatctaa atccttttct agcacatttg gctcagatgt acaatggctg ggttggcaac
5641 atgcgggtca ggctcatctt ggccggtaat gctttcactg ctggtaaagt tataatttgt
5701 tgtgttcccc ctggttttca atctagaacc ctttccatag cccaggctac actctttccc
5761 catgtgatcg ctgacgtgag aactctggaa ccaattgaga tccctttaga agatgttagg
5821 aatactcttt atcataataa tgacaatcaa ccaacaatgc gcttactgtg catgctctac
5881 acgccattac gcaccggtgg cggttctggt ggtacagatg cgtttgttgt agcaggtcga
5941 gttctaactt gccctagccc tgatttcaat ttcttgttct tggtcccacc cactgtggag
6001 cagaagacac gtccctttag tctgcccaat atacccttgc acttgcagtc taactcccgt
6061 gtccccaacc ccatacagag tatggtcatt tcgcctgatc aggcccagaa tacccaattt
6121 cagaatggcc gctgcaccac cgatgggcag ctcttgggta caacacctgt ctcagttagt
6181 cagatcttaa agtttagagg aaaggtgtca cctggttcta aggttatcaa tctcactgag
6241 ttagatggtt ccccctttct ggcttttgag gcccctgcgc ccacgggctt tcctgacttg
6301 ggaacttgtg attggcatat tgaattaagc cttaactcaa atagtcaaag ttctggcaac
6361 ccaattgtac aaagggacat acaaccaaat tcttcagatt ttgtgccaca cttgggcagt
6421 gtggctgtca ccgttgcaat tgaaacagct ggggattata ctggtacaat acaatggatc
6481 tctcagccat ccaatgtctc cccagttccc aatgtcaacc tatggactat tcccaactat
6541 ggatcaagtt tggcagaagc ctcccaactg gcccctgtag tgtacccccc ggggtttggt
6601 gaagctgtag tgtactttat gtctcacata ccaggcccaa acactgaaca caaacccaat
6661 ttggtaccct gcctacttcc acaagaattt ataactcatt ttgtcagtga acaagcccca
6721 cccatgggtg aggcagctct tatccattat gtggacccag ataccaaccg taatctaggt
6781 gagttcaaac tgtatcctga aggtgttatc acttgtgtgc caaatggcac tggtccacaa
6841 caactccccc tcaatggggt ctttgtcttt gcttcctggg tttctagatt ttatcaatta
6901 aagcctgtgg gaacggccag ttcggccaga ggtaggcttg gagttagaag ataatggctc
6961 aagccatcat tggagccatt gctgcatcag cggctggaag tgcccttgga gctggtatcc
7021 aagcaggtgc tgaggccgcc ctccagagcc agaggttcca gcaggacctt acccttcaac
7081 aaaattcttt taaacatgat aaggaaatga tgtcatatca agttgaaatg tctaatgctt
7141 tgctagctaa aaatcttaat actcgctatg ctttgctcca atctggaggt ctatctagtg
7201 ctgatgctgc tcgtgctgtg gcaggtgcgc ctgttacaag gattgttgat tggaatggca
7261 cgagagtggc agccccaaat tcttctgcaa caactctcag atctggtgga tttatgtctg
7321 ttcctatacc tattcaaccc aaacaaaagc cctctaccat ctcagggttt aataatccag
7381 catatggaga aactatgtca agagtttcct cctgggtcca atcccagaat tcaagtgtta
7441 gaagtgtgcc tccttttcat agttctgccc tcaggactgt ttgggttaca ccaccaggtt
7501 caacttctac ttcttcatct gtttcatcca tgcctatggg cgtgtttaac accgataggc
7561 ttcccctatt cgcaaatagg agatga
//