Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP205549 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5087
ORF2: 5068..6690
ORF3: 6690..7496
LOCUS OP205549 7496 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0317_R03-04 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205549
VERSION OP205549.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7496)
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JOURNAL Unpublished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 7496)
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..7496
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0317_R03-04"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-07-28"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5087
/gene="ORF1"
CDS <1..5087
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60948.1"
/translation="NDATVAVARNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAP
RDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKGGISGLPELTTVPQPDVAN
TAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAR
VELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLS
RRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKP
LNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAV
ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKE
EANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSA
SPDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAREVARK
VASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLT
LNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKR
DFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGL
LHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEEL
KQAIRNVTIKRCRIIYGGSTYDLESDGRGKVLVEKVKNTSVQTNNELAGALHHLKHAR
IRYYVKCVQEAVYSIMQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSE
DDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDRYYEELAIAKATEEDFCEEEEVKIRQRIFRPTRKQRKEERATLGLVTGSEI
RKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFIT
STHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVAGMILEEGAPEGTVATV
LIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPY
IYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAP
KLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
RPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETF
TGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIR
CARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQR
AVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLK
PTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDP
NETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELREGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..983
/gene="ORF1"
/product="p48"
mat_peptide 984..2081
/gene="ORF1"
/product="NTPase"
mat_peptide 2082..2612
/gene="ORF1"
/product="p22"
mat_peptide 2613..3011
/gene="ORF1"
/product="VPg"
mat_peptide 3012..3554
/gene="ORF1"
/product="Pro"
mat_peptide 3555..5084
/gene="ORF1"
/product="RdRp"
gene 5068..6690
/gene="ORF2"
CDS 5068..6690
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60949.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6690..7496
/gene="ORF3"
CDS 6690..7496
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60950.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAAPARGPSNKSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 ctaacgacgc taccgttgcc gttgctcgca acaacaacaa cgacaaggaa aaatcttcag
61 gtgaaggctt attcacaaat atgtcttcca ccttaaagaa agccctcggg gctaggccca
121 aacagcctgc cccgagagac gaaccacaaa agcccccaag accaccaact cccgagttgg
181 tcaagaggat accccctcct ccacctaatg gcgaaggaga agaagagcca gtcattaggt
241 atgaggttaa gggtgggatc tctggcctgc ccgagctcac aacagtcccc caaccggacg
301 tggccaacac agcattcagt gttccaccac tgagcttgag agaaaacagg gaggccaagg
361 aaccgctaac aggggcgata ttagagatgt gggatggaga gatataccac tatggcctgt
421 acgtggagaa aggtttagtg ttgggtgtgc acaaaccacc tgcagccata agcatggcaa
481 gagtggagct gacgccgctg tcattgtact ggcgtgtggt gtacactccc caatacctca
541 tctcccctga aactctcagg aggctcaacg gagaggcgtt cccttacacc gccttcgaca
601 acaactgcta tgccttttgc tgctgggtgt tagacctcaa tgactcatgg cttagcagga
661 ggatggtgca aagaacaacg ggcttcttca gaccttacca agagtggaac agaaagcccc
721 tgcctaccat ggatgactcc aaaattaaga aggtagcaaa tatattccta tgttcattgt
781 ccacattatt caccagaccc ataaaagacc tcataggaaa aattaaacca ttaaacatat
841 taaacatcct ggcaacgtgt gactggacgt ttgccggaat agtggagtct ctgatattac
901 ttgctgaact cttcggagtt ttctggacgc ccccagatgt gtctgctatg atcgctccct
961 tactcgggga ctacgagttg caagggccag aagacctcgc cgttgaactc gtacccgtgg
1021 taatgggagg gattggtttg gtgttgggat tcaccaaaga gaaaattggc aaaatgttgt
1081 cctcagcagc atcaacactc agggcttgca aagatcttgg tgcctatggc ttagagatac
1141 tcaaattggt catgaagtgg ttcttcccaa agaaagagga ggccaatgag ctagccatgg
1201 tgagggccat agaggatgcc gtactagatc ttgaggcaat agaaaataac cacatgacaa
1261 ccctgttgaa agacaaagac agcttagcaa catacatgaa aacactggac atggaggagg
1321 agaaagccag aaggttgtcc acaaagtctg catcccctga catagttggg acaatcaacg
1381 ccctgctggc tcgaatagca gcggccaggt cattagttca cagggccaag gaagagttat
1441 ctagcaggat gagaccagta gttgttatga tatctggtaa accaggaata ggtaaaactc
1501 atctggccag ggaggtggca agaaaggtgg catccaccct cacaggggac caaagagtcg
1561 gactcatacc aagaaacggt gtggaccatt gggatgcata caaaggtgag agagtcgtgc
1621 tgtgggacga ctatggcatg agtaacccca ttcatgatgc tcttcgcata caagaattgg
1681 ctgatacgtg tccccttacc ttaaattgtg acagaattga aaacaagggg aaagtttttg
1741 acagtgaagt cataataatt acaacaaacc ttgccaaccc agccccactc gattatgtca
1801 actttgaggc ctgttccagg agaattgatt tcctggtgta cgctgaggca ccagaagtag
1861 aaaaggcaaa acgggatttt cctggtcagc cagatatgtg gaaggacgcc ttcaagccgg
1921 acttttcaca catcaagcta cagcttgcac ctcagggcgg ctttgacaag aatggcaaca
1981 ccccacatgg gaaaggagtg atgaagaccc tcactaccgg ttctctgatt gcccgtgcat
2041 caggcctact gcatgagagg atggatgagt ttgagctcca aggtcccaca accaccacct
2101 tcaatttcga ccggaacaga atcacagcat tcagacaact ggctgcagaa aacaagtatg
2161 gattggtgga tactatgaaa gttggcaatc aactaaaagg agtgaaaacc atggaagaac
2221 tcaaacaagc aatcagaaat gtgaccatca agaggtgccg gatcatctac ggtggctcca
2281 cgtatgacct tgaatctgat ggcaggggca aagttttggt ggaaaaggtc aagaatacct
2341 ctgtacagac caacaacgag ttggccgggg ccctgcacca tcttaaacac gcccgaatca
2401 ggtactatgt caaatgtgtg caagaagcag tctattccat catgcaaatt gccggcgctg
2461 cgtttgtcac cacgcgcatt gcacgccgca tgaacataca agaactctgg tcgaagccac
2521 aattagatca aaatgaatca gagactaagg aggaggcccc taaatcagaa gatgacgagt
2581 tcatcatatc ttctaaggac atcaaggagg aaggaaagaa gggcaaaaac aagactggcc
2641 gtggcaagaa acacactgca ttttccagca agggcttgag cgatgaggag tatgacgagt
2701 acaagaggat aagagaagag agaaatggga agtactctat agaggagtat cttcaagaca
2761 gagacaggta ctatgaggag cttgccattg ccaaggccac ggaagaagac ttctgtgaag
2821 aggaggaggt caaaatccgt cagagaattt tccgtcccac caggaaacaa aggaaggaag
2881 agagggccac attaggactg gtgacaggtt cagaaatcag aaaaagaaac cctgatgact
2941 tcaaacccaa agggaagctg tgggccgatg acaacagaag tgttgactat aatgagaaac
3001 tggactttga ggccccccca agcatatggt ctaggattgt gagctttggt tctggctggg
3061 gcttctgggt atcaccaagc ctgttcataa catcaactca tgtaatcccc gcaggcataa
3121 cagaagcatt tggagtcccc atcaaacaaa ttcagatcca caaatcaggt gaattttgcc
3181 gattcagatt cccaaaacca attaggccag acgtggcagg aatgatcttg gaagaaggtg
3241 cgcctgaagg caccgtggca actgtgctca tcaaacgccc caccggagag ctcatgcctc
3301 tcgcagccag aatgggaaca cacgcaacca tgaaaattca aggccgcatg gttggcggac
3361 agatgggtat gttgctcact ggatcaaatg ctaaaggaat ggatttggga acaactcctg
3421 gtgactgtgg ctgtccctac atctacaaaa ggggcaatga ctatatagtc attggggtgc
3481 acactgcagc agcccgtggt ggaaacaccg tcatctgtgc cacacaggga agtgagggtg
3541 aggcaactct tgagggtgga gatgacaaag gaacatactg tggggcaccc attctaggcc
3601 ctgggggtgc accaaagttg agcaccaaaa ccaaattttg gaggtcatcg aacacgcccc
3661 ttccaccagg gacatatgag cctgcctacc tcggtggccg tgatccgcgt gttaagggtg
3721 ggccttcctt gcagcaggta atgagagacc agttgaagcc attcactgaa cccaggggca
3781 agcctccaag accaagtgta ttggaagcag ccaaacaaac cattatcaat gtcctcgaac
3841 aaaccctgga tcctccacaa aaatggacat acgcacaggc gtgtgcctca cttgacaaaa
3901 ccacttccag cgggcatccc catcacgtcc gaaagaatga attctggaat ggtgagacct
3961 tcactggcaa attggcagac caagcatcaa aagcaaacct aatgtttgag gaagggaaac
4021 acatgacacc agtgtataca gcagcactca aggacgagct agtcaagact gagaaaatct
4081 atggaaagat caagaagaga ctgctctggg gctccgactt gtccaccatg atccggtgcg
4141 ctaggtcatt tggtgggctc atggacgaga tgaaggcaca ctgcatatca ctcccagtac
4201 gagttggcat gaatatgaat gaggatggcc caataatatt tgagaaacat tccagataca
4261 aataccacta tgatgcagac tactctcgtt gggactcaac acaacagagg gcagtactag
4321 cagcagcctt ggaaatcatg gtcagattct ctgcagaacc acaattggca caaatagtcg
4381 ctgaggatct gctggcccct agcgtagtgg atgtgggaga ctttaaaatc acaataaatg
4441 aagggctccc atctggtgtg ccatgcactt ctcaatggaa ctccatcgca cactggctgc
4501 taaccctctg tgccttgtct gaagtcacca aactgtcccc tgacattata caagcaaatt
4561 ccatgttctc attttacggt gatgacgaga ttgtcagcac cgacataaaa ttggaccctg
4621 aacagttaac cgctaagttg aaggagtacg gcctgaaacc aacccgccca gacaagaccg
4681 agggacccct gatcatcagt gaagatttga acggactcac tttcctccga aggacggtga
4741 ctcgtgaccc agctggctgg tttggaaaac tggaccaaag ttcaattttg aggcagatgt
4801 actggactag aggaccaaat catgaagatc ccaatgagac aatgataccc cattctcaaa
4861 gacccataca gctcatggca ctgcttggtg aagcctctct tcacggaccc tctttctaca
4921 gtagaatcag taaattggtc ataactgaac tcagagaagg cgggatggac ttttacgtgc
4981 caaggcagga acccatgttc aggtggatga ggttttctga cttgagcacg tgggagggcg
5041 atcgcaatct ggctcccaat tttgtgaatg aagatggcgt cgagtgacgc caacccatct
5101 gatgggtccg cagccaacct cgtaccagag gtcaacaatg aggttatggc tttggagccc
5161 gttgttggtg ccgctattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg
5221 attagaaata attttgtaca agcccctggt ggggagttta cagtatcccc tagaaacgct
5281 ccaggtgaaa tactatggag cgcgccccta ggccctgacc taaatcccta cctatcccat
5341 ttggccagaa tgtacaatgg ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg
5401 aacgcgttca ccgccgggaa gatcatattt gcagcagtcc caccaaattt cccaactgaa
5461 ggcttaagtc ctagccaggt cactatgttc ccccatataa tagtagatgt tagacaatta
5521 gaacctgtgc tgattccctt acccgatgtt aggaataatt tctatcatta caatcagtca
5581 aatgattcca ctattaagtt gatagcaatg ttgtacacac cacttagggc taataatgct
5641 ggggatgatg ttttcacagt ttcgtgccga gttctcacga gaccatcccc cgattttgat
5701 ttcatatttt tagtgccacc cacggttgag tcaagaacta aaccattctc tgtcccagtt
5761 ttaactgttg aggagatgac caattcaaga ttccccatcc ctttggaaaa gttgttcaca
5821 ggccccagca gtgcctttgt tgttcaacca caaaacggca ggtgcacaac tgatggcgtg
5881 ctcctaggca ccacccaact ttctcctgtc aacatctgca ctttcagagg ggatgtcacc
5941 cacatcacag gtagtcacaa ctacacaatg aatttggctt ctcaaaattg gaacaactat
6001 gacccaacag aagaaatccc agcccctcta ggaactccag attttgtagg gaagattcaa
6061 ggcatgctca cccaaaccac aaggacagat ggttcaacac gcggccacaa agctacagtg
6121 tacactggga gcgccgactt tgctccaaaa ctgggtagag ttcaatttga aactgacaca
6181 aaccatgact ttgaagctaa tcaaaacaca aagttcaccc cagtcggtgt catccaagat
6241 ggtagcacca cccatcgaaa cgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga
6301 aatactcaca atgtacatct ggcccccgct gtagccccca cctttccggg tgagcagctt
6361 ctcttcttca gatccaccat gcccggatgc agcgggtacc ccaacatgga tttggactgt
6421 ctgctccccc aggaatgggt gcagtacttc taccaagagg cagccccagc acaatctgat
6481 gtggctctgt taagatttgt gaatccagac acaggtaggg ttttgtttga gtgcaagctt
6541 cacaaatcag gttatgttac agtggctcac actggccagc atgatttggt tatccccccc
6601 aatggctact ttaggtttga ttcctgggtc aaccagttct atacgcttgc ccccatggga
6661 aatggaacgg ggcgtagacg tgtagtataa tggctggagc tttctttgct ggattggcat
6721 ctgatgtcct tggctctgga cttggttccc ttatcaatgc tggtgctggg gccatcaacc
6781 aaaaagttga gtttgaaaac aatagaaaat tgcaacaagc atccttccaa tttagcagca
6841 atctgcaaca ggcttccttc caacatgata aagagatgct ccaagcacaa attgaggcca
6901 ccaaaaagct acaacaggaa atgatgaaag ttaagcaggc aatgctccta gagggtgggt
6961 tctctgagac agatgcagcc cgcggggcaa ttaacgcccc catgacaaaa gctttggact
7021 ggagcgggac aaggtactgg gctcccgatg ctaggactac aacatacaat gcaggccgct
7081 tttccacccc tcaaccatcg ggggcactgc caggaagagc taatcttagg gatgctgccc
7141 ctgctcgggg accctccaac aaatcttcta actcttctat tgcgacctct gtgtattcaa
7201 atcaaactac ttcaacgaga cttggttcta cagctggttc tggaaccagt gtctcgagcc
7261 tcccgtcaac tgcaaggact aggagctggg ttgaggatca aaataggaat ttgtcacctt
7321 tcatgagggg ggcccacaac atatcatttg tcaccccacc atctagcaga tcctctagcc
7381 aaggcacagt ctcaaccgtg cctaaagaga ttttggactc ctggactggc gctttcaaca
7441 cgcgcaggca gcctctcttc gctcacattc gtaagcgagg ggagtcacgg gtgtaa
//