Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP205557 | GII.3 | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6709
ORF3: 6709..7473
LOCUS OP205557 7473 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0405_R03-12 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205557
VERSION OP205557.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7473)
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JOURNAL Unpublished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 7473)
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..7473
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0405_R03-12"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-10-19"
/note="genotype: GII.3[P16 ]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60972.1"
/translation="DATVAVACDNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYTGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKIGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVERVKNISVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSED
DEFVISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLNFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGYPHHARKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
THWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..2607
/gene="ORF1"
/product="p22"
mat_peptide 2608..3006
/gene="ORF1"
/product="VPg"
mat_peptide 3007..3549
/gene="ORF1"
/product="Pro"
mat_peptide 3550..5079
/gene="ORF1"
/product="RdRp"
gene 5063..6709
/gene="ORF2"
CDS 5063..6709
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60973.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPAPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDENQP
TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KSGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6709..7473
/gene="ORF3"
CDS 6709..7473
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60974.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVGAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESSV"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcgacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagacaaacc acaaaagccc ccaagaccac caactcccga gttggtcaag
181 aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgag
241 gttaagagtg ggatctctgg tctgcccgag ctcacaacag tccctcaacc ggacgtggcc
301 aacacagcat tcagtgttcc accactgagt ttgagagaaa acagggaggc caaagaaccg
361 ctaacagggg caatattaga gatgtgggat ggagagatat atcactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg
481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct taacggagag gcattccctt acaccgcttt tgataacaac
601 tgctatgcct tttgttgctg ggtgttagac ctcaacgact catggctcag caggaggatg
661 gtgcagagaa caacgggctt ctttagacct taccaagagt ggaacagaaa acccctacct
721 accatggatg actccaaaat taagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttatttacca gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaat
841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctaat attacttgct
901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccctactc
961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg
1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca
1081 gcagcatcaa cactcagagc ttgcaaagat cttggtgcct atggcttgga gatactcaaa
1141 ttggtcatga agtggttctt cccaaagaaa gaagaggcca atgagctagc catggtgagg
1201 gccatagagg atgctgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ttgaaagata aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccagaagat tgtccacaaa atctgcatcc cctgacatag ttgggacaat caatgccctg
1381 ctggctcgaa tagcagcggc caggtcacta gtccacaggg ctaaggaaga gctatctagc
1441 aggataaggc cagtagttgt tatgatatct ggtaaaccag gaataggcaa aactcatctg
1501 gccagggagg tggcaagaaa ggtggcatcc actctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtgga ccattgggat gcatacacag gtgagagagt cgtgctgtgg
1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat
1681 acgtgtcccc tcaccttaaa ttgtgacaga attgaaaata aaggaaaagt ttttgacagt
1741 gaagtcataa taatcacaac aaaccttgcc aatccagccc cacttgatta tgtcaacttt
1801 gaggcctgtt ccaggagaat tgacttcctg gtgtacgctg aggcaccaga agtagaaaag
1861 gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa gtcggacttt
1921 tcacacatca agttacagct tgcaccccag ggcggctttg acaagaatgg taacacccca
1981 catgggaaag gagtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc
2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ctacaatcac caccttcaat
2101 ttcgaccgga acagaatcac agcatttaga caattggctg cagaaaacaa gtatggactg
2161 gtggatacca tgaaaattgg caatcaatta aaaggagtga aaaccatgga agaacttaaa
2221 caagcaatca ggaatgtaac catcaagagg tgccggatca tctacggtgg ttccacatat
2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa gggtcaagaa catctctgta
2341 cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg gatcaggtac
2401 tatgtcaaat gtgtgcaaga agcagtctat tctatcatac aaattgccgg cgctgcattt
2461 gtcaccacgc gcatcgcacg ccgcatgaac atacaagagc tctggtcgaa gccacagtta
2521 gatcaaaatg aatcagagac taaggaagag gcccccaagt cggaagatga tgagttcgtc
2581 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaataaaac tggccgtggc
2641 aagaaacaca ctgcgttctc cagtaagggc ttgagcgatg aggagtacga cgagtacaag
2701 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgtcagag aattttccgc cctaccagga aacaaagaaa ggaagagagg
2881 gccacactag ggctagtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggga agctgtgggc cgatgacaac agaagcgttg attataatga gaaactgaac
3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3061 tgggtgtcac caagcctgtt cataacatca actcatgtga tccccgcagg cataacagaa
3121 gcatttggag tccccatcaa acaaattcag atccacaaat caggcgaatt ttgccgattc
3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct
3241 gagggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac acctggtgac
3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca
3541 actcttgagg gcggagatga caaaggaaca tactgtgggg cacccattct aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gcccctccca
3661 ccagggacat atgagcctgc ctacctcggc ggccgtgacc cgcgtgttaa gggtgggccc
3721 tccttgcagc aggtgatgag agaccagttg aagccattca ctgaacccag aggcaaacct
3781 ccaaaaccaa gtgtattgga agcagccaaa caaaccatca tcaatgtcct cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caagaccacc
3901 tccagcgggt acccccatca cgcccgaaag aatgaattct ggaatggtga gaccttcact
3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg
4021 acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa aatctatgga
4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgattcg gtgcgctagg
4141 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtccgagtt
4201 ggtatgaaca tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatac
4261 cactatgatg cagactactc tcgctgggat tcaacacaac agagggcagt actggcatca
4321 gccttggaaa ttatggtcag attctctgca gaaccacaac tggcacaaat agtcgctgag
4381 gacctgctgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg
4441 ctcccctctg gtgtgccatg cacttctcaa tggaactcca tcacacactg gctgctaact
4501 ctctgtgccc tgtctgaagt caccaaactt tcccctgaca ttgtacaggc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag
4621 ttaaccgcca aattgaagga gtacggcctg aaaccaaccc gcccagacaa aactgaggga
4681 cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaaactggac caaagctcaa ttttgaggca gatgtactgg
4801 actagaggac caaatcacga agaccccaat gagacaatga taccccattc tcaaagaccc
4861 atacagctta tggcattgct tggtgaagcc tctcttcacg ggccctcttt ctacagtaaa
4921 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggattttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccagttttgt gaatgaagat ggcgtcgaat gacgccgccc catctaatga
5101 tggtgccgcc ggcctcgttc cagagatcaa caatgaggca atggcgctag agccagtggc
5161 gggtgcagcg atagcagcac ccctcactgg tcagcaaaat ataattgatc cctggattat
5221 gaacaacttt gtgcaagcac ctggtggtga gtttacagtg tccccaagaa attcccctgg
5281 tgaagtcctt cttaatttgg aattgggccc agagataaac ccctacttgg cccatcttgc
5341 tagaatgtac aatggttatg caggtggatt tgaagtgcag gtggtcctag ctggaaatgc
5401 gtttacagca ggaaagataa tctttgcagc catcccccct aattttccaa ttgacaattt
5461 aagtgcagca cagatcacaa tgtgcccaca tgtaatcgtg gacgtcagac agttggaacc
5521 agtcaacctc ccgatgcctg acgttcgcaa taacttcttt cattataatc aagggtctga
5581 ttcgaggtta cgcctaattg caatgctata cacacctctt agggcaaaca attctgggga
5641 tgatgttttt actgtgtctt gtagagtgtt aactagacct agtcctgatt tctcgttcaa
5701 tttccttgtg cctcccactg tggagtcaaa gacaaaaccc ttttccctcc ccatcttgac
5761 tatctctgaa atgtccaact ctaggttccc agcaccaata gattccctac acaccagtcc
5821 tactgagaat attgttgttc agtgccaaaa tgggcgcgtc acccttgatg gtgagctgat
5881 gggcaccacc caactcttgc ccagccaaat ctgtgctttc aggggcgttc ttaccagatc
5941 aacaagcaga gccagtgacc aggccgatac agcaaccccc agattattta attactattg
6001 gcatatacaa ttggataatc taaatggaac cccttatgat cctgcagaag acataccagg
6061 ccccctaggg acaccagatt tccgtggcaa agtctttggc gtggccagcc agagaaatcc
6121 tgacaccacg actagagcac atgaagcaaa gatagacacc acatccggcc gtttcacccc
6181 aaagctaggc tcattagaga tatccactga atctagtgat tttgatgaaa accaaccaac
6241 aagattcacc ccagttggca ttggagttga ccatgaggca gactttcaac aatggaccct
6301 acccgactat gctggtcagt tcacacacaa catgaacttg gccccagctg ttgctcccaa
6361 cttccctggt gaacagctcc ttttcttccg ctcacatttg ccatcttctg gtgggcgatc
6421 taacgggatt ctagactgcc tggttcccca agaatgggta cagcacttct accaagagtc
6481 agccccctct cagactcaag tggccctggt taggtatgtt aatcctgaca ctggcagagt
6541 gttatttgag gccaagctac acaaattagg tttcatgact atagccaaga gtggtgattc
6601 cccaataact gtccccccaa atggatactt taggtttgaa tcttgggtga acccctttta
6661 cacacttgcc cccatgggaa ctgggaatgg gcgtagaagg attcaataat ggctggagct
6721 tttatagcag gattggctgg tgacatgctc acaaatactg taggatcttt agttggtgca
6781 ggagctaatg ctatcaatca aacaattgat tttgaaaata ataaatattt gcaaaatgct
6841 tcttttaacc atgataagga gatgttgaat gcacaaattg aggcaacaaa gaagttacag
6901 gctgacatga ttgctatcaa acaaggggtt ttgaccgctg gcggcttctc ccctactgat
6961 gcagcccgtg gggcaattaa tgcccccatg acaaaagtcc tagattggaa tggaacgaga
7021 tactgggcac caggtgccac ctccacaacc tcgatgtcgg gtggctttac acaccaaact
7081 gtgcacagat ccacaccaaa ttttaaaacg aatcaggccc ccaaatccac acctagtagt
7141 ggttcttcag tgaggtcaaa ctcaacccaa atcactagcc tgagctcaca ctcgtccggg
7201 tcgtctcgat ccagcgggtc tacagtcatc agctcaatac catcctctaa caggactagg
7261 gactgggtca accaacaaaa ttttaatttg gaaccacaca tgcctggatc tcttaggaca
7321 gcttttgtca ctccaccatc tagtacagcc tctagctcag gcacagtctc aactgtgccc
7381 aaaaatgttt tggactcctg gacatctgcg tttaacacgc gcagacagcc gctattcgca
7441 caccttcgca gaagggggga gtcaagtgtt tag
//