Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP205538 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 1..5099
ORF2: 5080..6702
ORF3: 6702..7508
LOCUS OP205538 7508 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2016-0128_R02-13_minor nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205538
VERSION OP205538.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7508)
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JOURNAL Unpublished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 7508)
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..7508
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0128_R02-13_minor"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2016-03-30"
/note="genotype: GII.4 Sydney[P31]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60915.1"
/translation="KMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPK
QPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEE
TNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISL
AKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSW
LSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKL
KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTK
SASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELA
KKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCP
LTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA
KRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS
GLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMS
DLKQALKNIAIKKCQIVYNGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRC
ARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGCP
KPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT
GSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPS
LFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGT
VATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGP
GSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWN
GESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLA
TMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDS
TQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKE
YGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPN
HEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..989
/gene="ORF1"
/product="p48"
mat_peptide 990..2087
/gene="ORF1"
/product="NTPase"
mat_peptide 2088..2624
/gene="ORF1"
/product="p22"
mat_peptide 2625..3023
/gene="ORF1"
/product="VPg"
mat_peptide 3024..3566
/gene="ORF1"
/product="Pro"
mat_peptide 3567..5096
/gene="ORF1"
/product="RdRp"
gene 5080..6702
/gene="ORF2"
CDS 5080..6702
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60916.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6702..7508
/gene="ORF3"
CDS 6702..7508
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60917.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSAATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRKRGESRA"
ORIGIN
1 tgaagatggc gtctaacgac gcttccgctg ccgctgttgc caacagcaac aacgacatcg
61 caaaatcttc aagtgacggt gtgttctcta acatggctgt cacttttaag cgggccctcg
121 gggcgcggcc taaacagccg cccccgaagg agataccacc caggcccccg cgaccaccca
181 caccagaatt ggtcaaaaag atccctcctc ccccacccaa cggggaggat gaactagtgg
241 tctcttacag cgccaaagat ggcgtttccg ggttgcctga gctcaccact gtcagacaac
301 cggaggaaac caacacggcg ttcagtgtcc ccccactcaa ccaaagggag aacagggacg
361 ccaaggagcc actaactgga acaattattg aaatgtggga tggagaaatc taccattacg
421 gcctgtacgt ggaacgaggt cttatacttg gtgtgcacaa gccaccggca gccatcagcc
481 ttgccaaggt cgagctaaca ccgctctctt tgttctggag acctgtatac accccccagt
541 atctcatctc tccagacact cttaggaggt tacatggaga gtcattcccc tacactgcat
601 ttgacaacaa ttgctacgcc ttttgttgtt gggtattaga cctaaacgac tcatggctaa
661 gcaggagaat gattcagaga acaacaggtt tcttcaggcc gtaccaggat tggaacagga
721 aacccctccc cactatggat gattccaaat taaagaaggt agccaatata ttcttgtgca
781 ctttgtcttc actattcact aggcccatca aggacataat agggaagttg aaacctctta
841 acatccttaa cattctggct acatgtgatt ggaccttcgc aggcatagtg gaatctttaa
901 tactcttagc agaactcttt ggagttttct ggacaccccc agatgtgtct gcgatgatcg
961 cccccttgct aggtgattat gaactgcaag gacctgagga ccttgcagtg gaactggtcc
1021 caatagtgat gggggggata ggtttggtgc taggatttac caaagagaaa attggaaaga
1081 tgctatcatc cgctgcatcc actttaagag cttgtaaaga ccttggtgca tacggactgg
1141 aaattttgaa actggtcatg aagtggttct tcccaaagaa agaggaagca aatgaactgg
1201 ctatggtgag atccatcgag gatgcagtac tagacctcga ggcaattgaa aacaaccaca
1261 tgaccaccct actcaaagac aaagacagct tggcaaccta catgagaacc cttgaccttg
1321 aagaggagaa agccagaaaa ctctcaacca aatctgcttc acccgatatt gtgggcacaa
1381 tcaattctct tctggcaaga atcgctgctg cacgctccct agtgcatcgg gcgaaagaag
1441 agctctccag caggccgaga cctgtcgttg tgatgatatc gggaagacca gggataggga
1501 aaactcacct tgccagggag ctggccaaga agatcgcggc ctccctcaca ggggaccagc
1561 gtgtgggtct tatcccacgc aatggtgtcg atcactggga cgcatataag ggcgaaagag
1621 ttgtcctatg ggacgactat ggaatgagca accccatcca tgatgccctc aggttgcagg
1681 agcttgctga cacctgcccc ctcacgctaa attgtgacag aattgagaat aaagggaaag
1741 tctttgacag tgatgctata attatcacca ccaatttggc caacccagca ccactggatt
1801 atgtcaactt tgaagcgtgc tcgagacgta ttgacttcct cgtgtacgca gaagcccctg
1861 aggtggagaa ggcaaagcgc gacttcccag gtcaacctga tatgtggaag aacgctttca
1921 gtcctgactt ctcacacata aaactgtcat tggccccaca gggtggtttc gacaagaacg
1981 gcaacacccc gcatggaaaa ggggtcatga agaccctcac cactggctcc ctcatcgccc
2041 gagcatcagg gttactccat gagaggctag atgaatatga actgcaaggc ccagccctca
2101 ccaccttcaa ctttgaccgc aacaagatac ttgcttttag acagcttgct gctgaaaaca
2161 agtatgggct gatggacaca atgagagttg gaaaacagct caaggatgtc aagaccatgt
2221 cagacctcaa acaggcactc aagaacatcg cgattaagaa gtgccagata gtgtacaatg
2281 gtagcaccta cacacttgag gccgatggca agggtagtgt gaaagttgac aaagtgcaaa
2341 gtgccactgt gcagaccaac aatgaactag ccggtgccct acaccaccta aggtgcgcta
2401 gaatcagata ctatgttaag tgcgtccagg aggcactgta ttccatcatc caaatcgctg
2461 gggctgcatt cgtcaccacg cgcatcgcta agcgcatgaa tatacagaat ctctggtcca
2521 agccacaggt ggaagacaca gaagagatga ccaacaaaga tggttgccca aaacccaaag
2581 atgatgaaga gtttgtcgtc tcatccgacg acatcaaaac tgagggcaag aaaggaaaga
2641 acaagtccgg ccgtggcaag aagcacacag ccttttcaag caaaggactc agtgatgagg
2701 agtacgatga gtacaagaga atcagagaag aaaggaatgg caaatactcc atagaagagt
2761 acctccagga cagagacagg tactacgagg aggtggccat tgccagggca accgaagagg
2821 acttctgtga agaagaagag gccaaaatcc ggcagagaat ttttagacca acaaggaaac
2881 aacgcaaaga agagagggcc tctctcggct tggtcacagg ctctgaaatt aggaagagaa
2941 acccagaaga cttcaaaccc aagggaaagc tgtgggctga tgatgacaga agtgttgact
3001 acaatgaaaa actcaacttt gaggccccac caagcatctg gtcgcggata gtcaactttg
3061 gttcaggctg gggcttctgg gtttccccta gtctatttat aacatcaacc catgtcatac
3121 ctcaaggtgc aaaagagttc ttcggagtcc ctatcaagca aatccagata cacaaatcag
3181 gtgaattctg ccggttgaga ttcccaaagc caatcagaac tgatgtgacg ggcatgattc
3241 tagaagaagg tgcgcccgag gggaccgtgg ccacactact catcaagaga ccaactggag
3301 agctcatgcc tctggcagcc agaatgggga cccatgcaac catgaaaatt caggggcgca
3361 cagttggagg gcaaatgggt atgctcctga caggatccaa cgccaagagt atggacctag
3421 gcacaacacc aggcgactgc ggctgcccct acatctacaa gagggggaat gactacgtgg
3481 tcataggggt ccatacggcc gctgcccgtg gaggaaacac tgtcatatgt gccacccagg
3541 ggagtgaggg agaagccaca cttgaaggag gtgacagtaa agggacatac tgtggcgcac
3601 caatcttggg cccagggagc gctccgaagc tcagcaccaa aactaagttt tggagatcat
3661 ccacaacacc actcccacct ggcacctacg aaccagccta cctcggtggc aaagacccca
3721 gagtcaaagg tggcccttca ttgcaacaag ttatgaggga ccagctaaag ccattcacag
3781 aacccagagg caaaccacca aggccaaatg tgttggaagc tgccaagaaa accatcatca
3841 atgtccttga gcagacaatt gatccacccc aaaaatggtc atttgcgcaa gcttgcgcat
3901 cccttgacaa aaccacctcc agcggccacc cgcaccacat gcggaaaaac gactgttgga
3961 atggggagtc ctttacagga aaattggctg atcaagcctc caaggccaac ctaatgtttg
4021 aagagggaaa gaacatgacc ccagtctaca caggtgcact taaagatgaa ttggtgaaaa
4081 ccgacaaagt ttatggtaag atcaagaaga ggcttctgtg gggttcagat ctggcgacca
4141 tgatacggtg cgcccgagct tttggaggcc tcatggatga actcaaggcg cactgtgtca
4201 cacttcctgt cagagttggt atgaacatga atgaggatgg ccccatcatc tttgaaaagc
4261 actccagata cagatatcac tatgatgctg attattcccg gtgggactca acacaacaaa
4321 gggatgtgct agcagcagca ctagaaatca tggttaagtt ctctccagaa ccacacctag
4381 cccaggtagt tgcagaagac ctcctttccc ctagcgtaat ggatgtaggt gactttcaaa
4441 tatcaataag tgagggtctt ccctctgggg tgccttgtac ctcccagtgg aattccatcg
4501 cccactggct cctcactctt tgtgcactct ctgaagtcac ggacctgtcc cctgacatca
4561 ttcaggccaa ctcccttttc tccttctatg gtgatgatga gattgtaagc acagacataa
4621 agttggaccc agagaagctg acagcaaaac tcaaggagta cgggctgaaa ccaacccgcc
4681 ccgacaaaac tgaaggaccc cttgttatct ctgaagatct ggatggcttg acattccttc
4741 ggagaactgt gactcgtgat ccagctggct ggtttggaaa attggaacaa agttcaattc
4801 tcagacaaat gtactggacc aggggtccta accatgaaga tccatttgaa acaatgatac
4861 cacactccca aagacccata caattgatgt ccttgctggg tgaggctgcg ctccacggcc
4921 cggcatttta tagcaaaatt agcaaattag tcattgcaga gttgaaggaa ggtggcatgg
4981 atttttacgt gcccaggcaa gagcctatgt tcagatggat gagattctca gacctgagca
5041 cgtgggaggg cgatcgcaat ctggctccca gctttgtgaa tgaagatggc gtcgagtgac
5101 gccaacccat ctgatgggtc cgcagccaac ctcgtcccag aggtcaacaa tgaggttatg
5161 gctctggagc ccgttgttgg tgccgctatt gcggcacctg tagcgggcca acaaaatgta
5221 attgacccct ggattagaaa caattttgta caagcccctg gtggagagtt tacagtgtcc
5281 cctagaaacg ctccaggtga aatactatgg agcgcgccct tgggccctga tctaaatccc
5341 tacctatccc atttggccag aatgtacaat ggttatgcag gtggttttga agtgcaggta
5401 attctcgcgg ggaacgcgtt caccgccggg aaggtcatat ttgcagcagt cccaccaaac
5461 tttccaactg aaggcttgag ccccagccag gtcactatgt tcccccatat agtagtagat
5521 gttaggcaac tagaacctgt gttgattccc ttacccgatg ttaggaataa tttctatcat
5581 tataatcaat caaatgaccc caccattaaa ttgatagcaa tgttgtatac accacttagg
5641 gctaataatg ctggagatga tgtctttacg gtttcttgcc gagttctcac gagaccatcc
5701 cccgactttg atttcatatt tctagtgcca cccacagttg agtcaagaac taaaccattc
5761 tctgtcccag ttttaactgt tgaggagatg accaattcaa gattccccat tcctttggaa
5821 aagttgttca cgggtcccag cagtgccttt gttgtccaac cacaaaacgg caggtgcacg
5881 actgatggcg tgctcctagg caccacccaa ctgtctcctg tcaacatctg caccttcaga
5941 ggagatgtca cccacatcac aggtagccgt aactacacaa tgaatttggc ttctcagaat
6001 tggaacaatt atgacccaac agaagaaatc ccagcccctc taggaactcc agactttgtg
6061 gggaagattc aaggcgtgct cacccagacc acaaggacag atggctcaac acgcggccac
6121 aaagccacag tgtacactgg gagcgccgac tttgctccaa aactgggtag agttcaattt
6181 gaaactgaca cggaccatga ttttgaagct aaccaaaaca caaagttcac cccagtcggt
6241 gtcatccaag atggtagcac cacccaccga aatgaacccc aacagtgggt gctcccaagt
6301 tactcaggca gaaatactca taatgtgcac ctggcccccg ctgtagcccc cacttttccg
6361 ggtgagcaac ttcttttctt cagatccacc atgcccggat gcagcgggta ccccaacatg
6421 gatttggact gtctgctccc ccaggaatgg gtgcagtact tctaccaaga ggcagcccca
6481 gcacaatctg atgtggctct gctaaggttt gtgaatccag acacaggtag ggttttgttt
6541 gagtgtaagc ttcataaatc aggctatgtt acagtggctc acactggcca acatgatttg
6601 gtcatccccc ccaatggtta tttcagattt gattcctggg tcaaccagtt ctacacgctt
6661 gcccccatgg gaaatggaac ggggcgtaga cgtgcagtat aatggctgga gctttctttg
6721 ctggattggc atctgatgta cttggctctg gacttggttc ccttatcaat gctggggctg
6781 gggccatcaa ccaaaaagtt gagtttgaaa acaatagaaa attgcaacaa gcatccttcc
6841 aatttagcag caatctacaa caggcttcct ttcaacatga caaagagatg ctccaagcac
6901 aaattgaggc caccaaaaag ctacaacagg aaatgatgaa agttaagcag gcaatgctcc
6961 tggagggtgg gttctctgag acagatgcag cccgcggggc aatcaacgcc cccatgacaa
7021 aagctttgga ctggagcggg acaaggtact gggctcccga tgctaggact acaacataca
7081 atgcaggccg cttttccacc cctcaaccat cgggggcact gccaggaaga gctaatctta
7141 gggatgctgt ccctgctcgg ggttcctcca gtaaatcttc taactcttct gctgctactt
7201 ctgtgtactc aaatcaaacc atttcaacga gacttggttc tacagctggt tctggcacca
7261 gtgtctcgag cctcccgtca actgcaagga ctaggagctg ggttgaggat caaagtagga
7321 atttgtcacc tttcatgagg ggggcccaca acatatcgtt tgtcacccca ccatctagca
7381 gatcctctag ccaaggcaca gtctcaaccg tgcctaaaga ggttttggac tcctggactg
7441 gtgctttcaa cacgcacagg cagccactct tcgctcacat tcgtaagcga ggggagtcac
7501 gggcgtaa
//