Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP205543 | GII.2 | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5072
ORF2: 5053..6681
ORF3: 6681..7460
LOCUS OP205543 7460 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0059_R02-22 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205543
VERSION OP205543.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7460)
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JOURNAL Unpublished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 7460)
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..7460
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0059_R02-22"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-01-12"
/note="genotype: GII.2[P16]"
gene <1..5072
/gene="ORF1"
CDS <1..5072
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60930.1"
/translation="AVACNDNNDKEKSSGEGLFTNMSSTLRKALGARPKQPAPRDKPQ
KPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSV
PPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTP
LSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQ
RTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILN
ILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPV
VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANEL
AMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIV
GTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAREVARKVASTL
TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDR
IENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQ
PDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERM
DEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIR
NVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYV
KCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFI
ISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQD
RDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNP
DDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVI
PAGITEAFGVPTKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRP
TGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRG
NDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTK
TKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVL
EAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLA
DQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGRIKKRLLWGSDLSTMIRCARSF
GGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAT
ALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWL
LTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPD
KTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMI
PHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSD
LSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..968
/gene="ORF1"
/product="p48"
mat_peptide 969..2066
/gene="ORF1"
/product="NTPase"
mat_peptide 2067..2597
/gene="ORF1"
/product="p22"
mat_peptide 2598..2996
/gene="ORF1"
/product="VPg"
mat_peptide 2997..3539
/gene="ORF1"
/product="Pro"
mat_peptide 3540..5069
/gene="ORF1"
/product="RdRp"
gene 5053..6681
/gene="ORF2"
CDS 5053..6681
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60931.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQVQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6681..7460
/gene="ORF3"
CDS 6681..7460
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60932.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 ttgccgttgc ttgcaacgac aacaacgaca aagaaaaatc ttcaggtgaa ggcttattca
61 caaacatgtc ttccacctta aggaaagccc tcggggctag gcccaaacag cctgccccga
121 gagacaaacc acaaaagccc ccaagaccac caactcccga attggtcaag aggatacccc
181 ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgag gttaagagtg
241 ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgtggcc aatacagcat
301 tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggagccg ctaacagggg
361 caatattaga gatgtgggat ggagagatat accactatgg cctgtacgtg gagaaaggct
421 tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg gagctgacgc
481 cgttgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc cctgaaaccc
541 tcaggaggct caacggagag gcattccctt acaccgcctt tgacaacaac tgctatgcct
601 tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg gtacaaagaa
661 caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgcct accatggatg
721 actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca ttattcacca
781 gacccataaa agacctcata ggaaaaatta aaccattgaa catattgaat atcctggcaa
841 cgtgtgactg gacttttgcc ggaatagtgg agtctctgat attacttgct gaactcttcg
901 gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc ggggactacg
961 agttgcaagg gccagaagac ctcgccgttg agctcgtacc tgtggtaatg ggggggattg
1021 gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca gcagcatcaa
1081 cactcagggc ttgcaaagat cttggtgcct atggcttaga gatactcaaa ttggtcatga
1141 agtggttctt cccaaagaaa gaggaggcca atgagctagc tatggtgagg gccatagagg
1201 atgcagtact agaccttgag gcaatagaaa ataaccacat gacaaccctg ttgaaagaca
1261 aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa gccaggaggt
1321 tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg ctggctcgaa
1381 tagcagcggc taggtcatta gtccacaggg ccaaagaaga gctatctagc aggatgaggc
1441 cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg gccagggagg
1501 tggcaagaaa agtggcatcc actctcacag gggatcaaag agtcggactc ataccacgaa
1561 acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg gacgactatg
1621 gcatgagtaa ccctattcat gatgctcttc gcatacaaga attggctgat acgtgtcccc
1681 ttaccttaaa ttgtgacaga atcgaaaata aaggaaaagt ttttgacagt gaagtcataa
1741 taattacaac aaaccttgcc aatccagccc cacttgatta tgtcaacttt gaggcctgtt
1801 ccaggaggat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag gcaaaacggg
1861 actttcctgg tcagccagat atgtggaagg acgctttcaa gtcggacttt tcacacatca
1921 agctacagct tgcaccccaa ggcggctttg acaagaatgg caacacccca catgggaaag
1981 gagtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc ctactgcatg
2041 agaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat ttcgaccgga
2101 acagaatcac ggcattcaga caattggctg cagaaaacaa gtatgggttg gtggatacca
2161 tgaaagttgg caatcaatta aaaggagtga aaaccatgga agaactcaaa caagcaatca
2221 ggaatgtgac catcaagagg tgccagatca tctacggtgg ttccacgtat gaccttgaat
2281 ctgacggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta cagaccaata
2341 acgagttggc tggggctctg caccatctca aacatgcccg aatcaggtac tatgtcaaat
2401 gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt gtcaccacgc
2461 gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaacta gatcaaaatg
2521 aatcagagac taaggaagag gcccccaagt cagaagatga cgagttcatt atatcttcta
2581 aggacatcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc aagaagcaca
2641 ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag aggataagag
2701 aagagagaaa cgggaagtac tctatagagg agtatcttca agacagagac aggtactatg
2761 aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag gagatcaaaa
2821 tccgtcagag aattttccgt cccaccagga aacaaagaaa ggaagagagg gccacattag
2881 ggctagtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa cccaaaggga
2941 agctgtgggc cgatgacaac aggagtgttg actacaatga gaaactggac tttgaggccc
3001 ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc tgggtgtcac
3061 caagcctttt cataacatca actcatgtaa tccccgcagg tataacagaa gcatttggag
3121 tccccaccaa acaaattcag atccacaaat caggcgaatt ttgccgattc agattcccaa
3181 aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct gagggcaccg
3241 tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca gccagaatgg
3301 gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg ggtatgttgc
3361 tcactggatc aaatgccaaa gggatggact taggaacaac tcctggtgat tgtggctgtc
3421 cttacatcta caaaaggggc aatgactatg tagtcattgg ggtgcacact gcagcagccc
3481 gtggtggaaa cactgtcatc tgtgccacac agggaagtga gggtgaggca actcttgagg
3541 gtggagatga caaaggaaca tactgtgggg cacccattct aggccctggg ggtgcaccaa
3601 aattgagcac caaaaccaaa ttttggagat catcaaacac gccccttcca ccagggacat
3661 atgagcctgc ctacctcggt ggccgcgatc cgcgtgttaa gggtgggcct tccctgcagc
3721 aggtaatgag agaccagttg aagccattca ctgaacccag gggcaaacct ccaagaccaa
3781 gtgtattgga agcagccaaa caaaccatca tcaatgtcct cgaacaaacc ctggaccctc
3841 cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc tccagcgggc
3901 acccccatca cgtccgaaag aatgaattct ggaatggtga gaccttcact ggcaaactgg
3961 cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg acaccagtgt
4021 acacagcagc actcaaggac gagctagtca agactgagaa aatctatgga aggatcaaga
4081 agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg tcatttggtg
4141 ggcttatgga cgagatgaag gcacactgca tatcactccc agtccgagtt ggcatgaata
4201 tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat cactatgatg
4261 cagactactc tcgttgggat tcaacacaac agagggcagt actagcaaca gccttggaaa
4321 tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag gatctgctgg
4381 cccctagtgt agtagatgta ggagacttta aaattacaat aaatgaaggg cttccttctg
4441 gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact ctctgtgcct
4501 tgtctgaagt caccaaactg tcccctgata tcatacaggc aaactccatg ttctcatttt
4561 acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag ttaaccgcca
4621 aattgaagga gtacggccta aaaccaaccc gcccagacaa aaccgaggga cccctgatta
4681 tcagtgaaga tttgaatggt ctcactttcc tccgaaggac ggtgactcgt gacccagctg
4741 gctggtttgg aaaactggac caaagctcaa ttttgaggca gatgtactgg actagaggac
4801 caaatcatga agaccccaac gagacaatga taccccattc tcaaagaccc atacagctca
4861 tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaaa atcagtaaat
4921 tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg caggaaccca
4981 tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc aatctggctc
5041 ccaatttcgt gaatgaagat ggcgtcgaat gacgccgctc catctactga tggtgcagcc
5101 ggcctcgtgc cagaaagtaa caatgaggtc atggctcttg aacccgtggc tggtgccgcc
5161 ttggcagccc cggtcaccgg tcaaacaaat attatagacc cttggattag agcaaatttt
5221 gtccaggccc ccaatggtga atttacagtc tctccccgaa acgcccctgg tgaagtgcta
5281 ctgaatctag agttgggtcc agaattaaat ccttatctgg cacatttagc aagaatgtac
5341 aatgggtatg ccggtgggat ggaggtgcag gtcatgttgg ctgggaacgc gttcacagcc
5401 ggcaagttgg tcttcgccgc cgtgccaccc cacttcccgg ttgaaaacct tagcccacag
5461 caaataacca tgttccctca tgtgatcata gatgtgagaa ccctggaacc tgttttgtta
5521 ccactccctg atgttaggaa taacttcttc cattataacc agaaagatga tcccaagatg
5581 agaattgtgg ctatgcttta tacccccctc aggtctaatg gttcaggtga tgatgtgttt
5641 acagtctcct gtagagtgtt gactagacct tcccctgact ttgacttcac atacctggtg
5701 ccaccaacag tggagtctaa aacaaagcca ttcaccctcc caatcctcac acttggggaa
5761 ctttccaatt ctaggttccc agtgtccata gaccagatgt acaccagccc taatgaaatt
5821 atatcagtgc agtgtcaaaa tggtaggtgc acactggacg gggagctcca agggacaaca
5881 caactccaag tcagtggcat ttgtgctttc aaaggtgaag tgaccgccca cttgcatgac
5941 aatgatcacc tatataatgt caccatcaca aacttgaatg ggtccccttt tgatccctct
6001 gaggatatcc ctgcccctct gggtgtgcct gacttccagg gaagggtttt tggtatcatc
6061 tcccaaagag ataaacacaa tagtcctggg cataatgaac cagcaaacag gggacacgac
6121 gctgtggtcc ctacttacac agcacagtac actccaaaac ttggacaagt tcaaattggc
6181 acatggcaaa ctgacgacct tacagtcaac caaccagtta aattcacccc agttggactc
6241 aatgacactg aacacttcaa ccaatgggtg gtccctaggt atgctggtgc cctaaacctc
6301 aatacaaacc ttgccccttc tgttgctcca gtattcccag gagagcgcct gctcttcttc
6361 agatcataca ttcccctcaa gggcggttat ggaaacccag ccattgattg cctactacca
6421 caagagtggg tgcaacactt ctatcaagaa gcagcccctt caatgagtga ggtggccctc
6481 gtcagataca tcaacccgga cactggtcgg gcactgtttg aggccaagct ccacagagct
6541 ggtttcatga cagtctcgag caacaccagt gccccggtgg ttgtgcctgc caacgggtac
6601 ttcagatttg attcttgggt gaaccaattt tattctctcg cccccatggg aactgggaat
6661 gggcgtagaa gggttcaata atggctggag cttttgtagc tggtcttgca ggggacgtgc
6721 tcagcaatgg gcttagttca ttaatcaatg caggtgctaa tgcaataaat cagagggcag
6781 aatttgattt taatcagaaa ttgcagcaaa attcttttaa tcatgataag gagatgttgc
6841 aggctcagat tcaggcaact aagcagctgc aggcagacat gatggctata aaacaagggg
6901 tcttgaccgc tggcggtttt tcccctgctg atgcagccag aggtgctgtg aacgcgccca
6961 tgacacaggc gctggattgg aatggcacaa ggtattgggc accaaactcc atgaggacca
7021 catcttattc tggaaaattc acatcaaccg ccccagtgag gcaggctgac ttccagcaca
7081 cccaaagccg gccttcgagt ggctcctctg tgtcttcctt tgccactcag tcttcaaggc
7141 caactctgac cacaaccact ggttcctcac atggcacagc ctcatcaaat tcaactcgca
7201 gcacaagcct ctcccaatca acggtctcca gagctacatc taggactggt gagtgggtta
7261 gagatcaaaa tagaaatttg gaaccctaca tgcatggtgc cttacagaca gcctttgtca
7321 ccccaccttc cagcagggca tctgacggga cagtctcgac cgtccctaaa ggtgttttgg
7381 actcctggac acctgcgttt aacacccgca ggcagccgct ttttgcacac ctccgtaaga
7441 ggggggagtc acaagcttag
//