Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP205563 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS OP205563 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0461_R03-17 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205563
VERSION OP205563.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7491)
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JOURNAL Unpublished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 7491)
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..7491
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0461_R03-17"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-11-23"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60990.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQPGVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKIKNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEETPKSED
DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRRQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGVTEAFGVPIKQIQIHKSGEFCRLRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVFEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPNFVNEDGVE"
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..6685
/gene="ORF2"
CDS 5063..6685
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60991.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPAEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6685..7491
/gene="ORF3"
CDS 6685..7491
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60992.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARVTTYNAGHFSTPQPSRALPGRVNLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRDLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagatgaacc acaaaagccc ccaagaccac caactcccga gttggtcaag
181 aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgat
241 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc gggcgtggcc
301 aacacagcat tcagtgttcc accactgagc ttgagagaga acagagaggc caaggaaccg
361 ctaacagggg caatattaga gatgtgggac ggagagatat accactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg
481 gagctgacgc cactgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaacaac
601 tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg
661 gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa acccctgccc
721 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttattcacca gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaac
841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgct
901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc
961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtgatg
1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggaaaaat gttgtcctca
1081 gcagcatcaa cactcagggc ttgcaaagat cttggcgcct atggcttaga gatactcaaa
1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg
1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ctgaaagata aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg
1381 ctggctcgaa tagcagcagc caggtcatta gtccacaggg ccaaggaaga gctatctagc
1441 aggataagac cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg
1501 gccagggagg tggcaagaaa ggtagcatcc actctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg
1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat
1681 acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt
1741 gaagtcataa taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt
1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag
1861 gcaaaacggg attttcctgg tcagccagat atgtggaagg acgcctttaa gtcggacttt
1921 tcacacatca agctacagct tgcacctcag ggtggctttg acaagaatgg caacacccca
1981 catgggaaag gggtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc
2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac caccttcaat
2101 tttgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg
2161 gtggatacca tgaaagttgg caaccaacta aaaggagtga aaaccatgga agagctcaaa
2221 caagcaatca ggaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtat
2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa agatcaagaa cacctctgta
2341 cagaccaaca acgaattggc cggggccctg caccatctca aacacgcccg aatcaggtac
2401 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt
2461 gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2521 gatcaaaatg aatcagaggc taaggaagag acccccaagt cagaagatga cgagttcatc
2581 atatcttcca aggacatcaa ggaggaggga aagaagggca aaaacaaaac tggccgtggc
2641 aagaaacaca ctgcattctc tagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgtcagag aattttccgt cccaccagga gacaaagaaa ggaagagagg
2881 gccacattag ggctggtaac aggttcagaa atcagaaaaa gaaaccccga tgacttcaaa
2941 cccaaaggga aactgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac
3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3061 tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg cgtaacagaa
3121 gcatttggag tccccatcaa acaaattcag atccacaaat caggtgaatt ttgccgactc
3181 agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga aggtgcgcct
3241 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggtatggatt tgggaacaac tcctggtgac
3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacgc agggaagtga gggcgaggcg
3541 actcttgagg gtggagatga caaaggaaca tactgtgggg cacccatttt aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttctggaggt catcgaacac gccccttcca
3661 ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc
3721 tctttgcagc aggtgatgag agaccagttg aagccattca ctgaacccag gggcaaacct
3781 ccaagaccaa gtgtattgga agcagccaaa caaaccatta tcaatgtttt cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc
3901 tccagcggac atcctcacca cgtccgaaag aatgaattct ggaatggtga gaccttcact
3961 ggtaaattgg cagaccaagc gtcaaaagca aacctaatgt ttgaggaagg gaaacacatg
4021 acaccagtgt atacagcagc actcaaggac gagctagtta agactgagaa aatctatgga
4081 aaaatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg
4141 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtacgagtt
4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat
4261 cactatgatg cagactactc tcgttgggat tcaacacaac aaagggcagt actagcagca
4321 gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag
4381 gatctactgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg
4441 ctcccatctg gtgtgccatg cacttcccaa tggaactcca tcgcacactg gctgctaact
4501 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag
4621 ttgaccgcca agttgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgaggga
4681 cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaaactggac cagagttcaa ttttgaggca gatgtactgg
4801 actagaggac caaatcatga agaccccaat gagacaatga taccccattc tcaaagaccc
4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaga
4921 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5101 gtctgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg agcccgttgt
5161 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5221 aaataatttt gtacaagccc ctggtgggga gttcacagtg tcccctagaa acgctccagg
5281 tgaaatacta tggagcgcgc ccctaggccc tgatctaaat ccctacctat cccatttggc
5341 cagaatgtat aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc
5401 gttcaccgcc gggaagatta tatttgcagc agtcccacca aattttccag ctgaaggctt
5461 aagtcccagc caggtcacta tgttccccca tataatagta gatgttagac aattagaacc
5521 tgtgctgatt cccttacccg atgttaggaa taatttctat cattacaatc agtcaaatga
5581 ttccactatt aagttgatag caatgttgta cacaccactt agggctaata atgctggaga
5641 tgatgttttc acagtttcgt gccgagttct cacgaggcca tcccccgatt ttgatttcat
5701 atttttagtg ccccccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac
5761 tgttgaggag atgaccaatt caaggttccc catccctttg gaaaagttgt tcacaggccc
5821 cagtagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct
5881 aggcaccacc caactttctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat
5941 cacaggtagt cgcaactaca cgatgaattt ggcttcccaa aattggaaca actatgaccc
6001 aacagaagaa atcccagccc ctctagggac tccagatttt gtagggaaga ttcaaggcat
6061 gctcacccaa accacaagga cagacggttc aacacgcggc cacaaagcaa cagtgtacac
6121 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacagacca
6181 tgattttgaa gctaatcaaa acacaaaatt caccccagtc ggtgtcatcc aagatggtag
6241 caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaatac
6301 tcacaatgta catctggccc ctgctgtagc ccccaccttt ccgggtgagc aacttctctt
6361 tttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgcctgct
6421 cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat ccgatgtggc
6481 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcataa
6541 atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc cccccaatgg
6601 ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 gtccttggct ctggacttgg ttcccttatc aatgctggag ctggggccat caaccaaaaa
6781 gttgaatttg aaaataacag aaaattgcaa caagcatcct tccaatttag cagcaatctg
6841 caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga ggccactaaa
6901 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcttagaggg tgggttctct
6961 gagacagatg cagcccgcgg ggcaatcaat gcccccatga caaaagtttt ggattggagc
7021 gggacaaggt actgggctcc agatgctagg gttacaacat acaatgcagg ccacttttcc
7081 acccctcaac catcgagggc actgccagga agagttaatc ttagggatgc tgtccctgct
7141 cggggaccct ccaacaaatc ttctaactct tctactgcta cctctgtgta ctcaaatcaa
7201 actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagtctcccg
7261 tcaactgcaa ggactaggag ctgggttgag gatcaaaata gggatttgtc tcctttcatg
7321 aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc tagccaaggc
7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt taacacgcgc
7441 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta a
//