Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP205553 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5083
ORF2: 5064..6686
ORF3: 6686..7492
LOCUS OP205553 7492 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0376_R03-08 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205553
VERSION OP205553.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7492)
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JOURNAL Unpublished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 7492)
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..7492
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0376_R03-08"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-09-28"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5083
/gene="ORF1"
CDS <1..5083
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="UUV60960.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DEPQKPPRPPTPELVKRIPPPPPNGEEGEEPVIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKERIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEAPKSED
DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..979
/gene="ORF1"
/product="p48"
mat_peptide 980..2077
/gene="ORF1"
/product="NTPase"
mat_peptide 2078..2608
/gene="ORF1"
/product="p22"
mat_peptide 2609..3007
/gene="ORF1"
/product="VPg"
mat_peptide 3008..3550
/gene="ORF1"
/product="Pro"
mat_peptide 3551..5080
/gene="ORF1"
/product="RdRp"
gene 5064..6686
/gene="ORF2"
CDS 5064..6686
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60961.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6686..7492
/gene="ORF3"
CDS 6686..7492
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60962.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPPRALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGPTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgacgctact gttgccgttg cttgcaacaa caacaacgac aaggaaaaat cttcaggtga
61 aggcttattc acaaatatgt cttccacctt aaagaaagcc ctcggggcta gacccaaaca
121 gcctgccccg agagacgaac cacaaaagcc cccaagaccg ccaactcccg agttggtcaa
181 gaggataccc ccccctccac ctaatggcga agaaggagaa gaaccagtca ttaggtatga
241 ggttaagagt gggatctctg gcttgcccga gctcacaaca gtcccccaac cggacgtggc
301 caacacagca ttcagtgttc caccactgag cttgagagaa aacagggagg ccaaggaacc
361 gctaacaggg gcaatattag agatgtggga cggagagata taccactatg gcctgtacgt
421 ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca gccataagca tggcaagagt
481 ggagctgacg ccgctgtcat tgtactggcg tgtggtgtac actccccaat acctcatctc
541 ccctgaaact ctcaggaggc tcaacggaga ggcgttccct tacaccgcct tcgacaacaa
601 ctgctatgcc ttttgctgct gggtgttaga cctcaatgac tcatggctta gcaggaggat
661 ggtgcaaaga acaacgggct tcttcagacc ttaccaagag tggaacagaa aacccctgcc
721 caccatggat gactccaaaa taaagaaggt agcaaatata ttcctatgtt cattgtccac
781 attattcacc agacccataa aagacctcat aggaaaaatt aaaccattaa acatattgaa
841 catcctggca acgtgtgact ggacgtttgc cggaatagtg gagtctctga tattgcttgc
901 tgaactcttc ggagttttct ggacaccccc agatgtgtct gctatgatcg ctcccttact
961 cggggactac gagttgcagg ggccagaaga cctcgccgta gaactcgtac ctgtggtaat
1021 gggagggatt ggtttggtgt tgggattcac caaagagaga attggcaaaa tgttgtcctc
1081 agcagcatca acactcaggg cttgcaaaga tcttggtgcc tatggcttag agatactcaa
1141 attggtcatg aagtggttct tcccaaagaa agaggaggcc aatgagctag ccatggtgag
1201 ggccatagag gatgccgtac tagatcttga ggcgatagaa aataaccaca tgacaaccct
1261 gttgaaagac aaagacagct tggcaacata tatgaaaaca ctggacatgg aggaggagaa
1321 agccagaagg ttgtccacaa aatctgcatc ccctgacata gttgggacaa tcaacgccct
1381 gctggctcga atagcagcag ccagatcatt agtccacagg gccaaggaag agctatctag
1441 caggataaga ccagtagttg ttatgatatc tggcaaacca ggaataggca aaactcatct
1501 ggccagggag gtggcaagaa aggtagcgtc cacactcaca ggggatcaaa gagtcggact
1561 cataccaaga aacggtgtgg accattggga tgcatacaaa ggtgagagag tcgtgctgtg
1621 ggatgactat ggcatgagta accccattca tgatgctctt cgcatacaag aattggctga
1681 tacgtgcccc cttaccttaa attgtgacag aattgaaaat aaggggaaag tttttgacag
1741 tgaagtcata ataattacaa caaaccttgc caacccagcc ccacttgatt atgtcaactt
1801 tgaggcctgt tccaggagaa ttgatttcct ggtgtacgct gaggcgccag aagtagaaaa
1861 ggcaaaacgg gattttcctg gtcagccaga tatgtggaag gacgccttca agccggactt
1921 ttcacacatc aagctacagc ttgcacctca gggcggcttt gacaagaatg gcaacacccc
1981 acatgggaaa ggggtgatga agaccctcac taccggttct ctgattgccc gtgcatcagg
2041 cctactgcat gagaggatgg atgaatttga actccaaggt cccacaatca ccaccttcaa
2101 tttcgaccgg aacagaatca cagcattcag acagttggct gcagaaaata agtatggatt
2161 ggtggatacc atgaaagttg gcaatcaact aaaaggagtg aaaaccatgg aagaactcaa
2221 acaagcaatc aggaatgtga ccatcaagag gtgccggatc atctacggtg gctccacgta
2281 tgaccttgaa tctgatggca agggcaaagt tttggtggaa aaggtcaaga acacctctgt
2341 acagaccaac aacgagttgg ccggggccct gcaccatctc aaacacgccc gaatcaggta
2401 ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata caaattgccg gcgctgcgtt
2461 tgtcaccacg cgcattgcac gccgcatgaa catacaagaa ctctggtcga agccacaatt
2521 agatcaaaat gaatcagaag ctaaggaaga ggcccccaag tcagaagatg acgaattcat
2581 catatcttct aaggacatca aggaggaagg aaagaagggc aaaaacaaaa ctggccgtgg
2641 caagaaacac actgcattct ccagcaaggg cttgagcgat gaggagtatg acgagtacaa
2701 gaggataaga gaagagagaa acgggaagta ctctatagag gagtatcttc aagacagaga
2761 caggtactat gaggagctcg ccattgccaa ggccacggaa gaagacttct gtgaagagga
2821 ggagatcaaa atccgtcaga gaattttccg tcccaccagg aaacaaagaa aggaagagag
2881 ggccacatta ggactggtaa caggttcaga aatcagaaaa agaaaccctg atgacttcaa
2941 acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt gactacaatg agaaactgga
3001 ctttgaggcc cccccaagta tatggtctag gattgtgagc tttggttctg gctggggctt
3061 ctgggtatca ccaagcctgt tcataacatc aactcatgta atccccgcag gcataacaga
3121 agcttttgga gtccccatca aacaaattca gatccacaaa tcaggtgaat tttgccgatt
3181 cagattccca aaaccaatta gaccagatgt gacaggaatg atcttggaag aaggtgcgcc
3241 tgaaggcacc gtggcgactg tgctcatcaa acgccccacc ggagagctca tgcctcttgc
3301 agccagaatg gggacacacg caaccatgaa aattcaaggc cgcatggttg gcggacagat
3361 gggtatgttg ctcaccggat caaatgctaa aggaatggat ctgggaacaa ctcctggtga
3421 ctgtggctgt ccttatatct ataaaagggg caatgactat atagtcattg gggtgcacac
3481 tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca cagggaagtg agggtgaggc
3541 aactcttgag ggtggagatg acaaaggaac atactgtggg gcacccattt taggccctgg
3601 gggtgcacca aaattgagca ccaaaaccaa attttggagg tcatcgaaca cgccccttcc
3661 accagggaca tatgagcctg cctacctcgg tggccgtgat ccgcgtgtta agggtgggcc
3721 ctccttgcag caggtaatga gagaccagtt gaagccattc actgaaccca ggggcaaacc
3781 tccaagacca agtgtattgg aagcagccaa acaaaccatt atcaatgttc tcgaacaaac
3841 cctggaccct ccacaaaaat ggacatacgc acaggcgtgt gcctcacttg acaaaaccac
3901 ctccagcggg catccccatc acgtccgaaa gaatgaattc tggaatggtg agaccttcac
3961 tggtaaattg gcagaccaag catcaaaagc aaacctaatg tttgaggaag ggaaacacat
4021 gacaccagtg tatacagcag cactcaagga cgagctagtt aagactgaga aaatctatgg
4081 aaagatcaag aagagactgc tctggggatc tgacttgtcc accatgatcc ggtgcgctag
4141 gtcatttggt gggctcatgg acgagatgaa ggcgcactgc atatcactcc cagtacgagt
4201 tggcatgaat atgaatgaag atggcccaat aatatttgag aaacattcca gatacaaata
4261 ccattatgat gcagactact ctcgttggga ttcaacgcaa cagagggcag tactagcagc
4321 agccttggaa atcatggtaa gattttctgc agaaccacaa ttggcacaaa tagtcgctga
4381 ggatctactg gcccctagtg tagtagatgt aggagacttt aaaatcacaa taaatgaagg
4441 gctcccatct ggtgtgccat gcacttctca atggaactcc atcgcacact ggctgctaac
4501 tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac atcatacaag caaattccat
4561 gttctcattt tacggtgatg acgagattgt cagcaccgac ataaaattgg accctgaaca
4621 gttaaccgcc aagttgaagg agtacggcct gaaaccaacc cgcccagaca agaccgaggg
4681 acccctgatc atcagtgaag atttgaacgg actcactttc ctccgaagga cggtgactcg
4741 tgacccagct ggctggtttg gaaaactgga ccaaagttca attttgaggc agatgtactg
4801 gactagagga ccaaatcatg aagaccccaa tgaaacaatg ataccccatt ctcaaagacc
4861 catacagctc atggcactgc ttggtgaggc ctctcttcac ggaccctctt tctacagtag
4921 aattagtaaa ttggtcataa ctgaactcaa agaaggtggg atggactttt acgtgccaag
4981 gcaggaaccc atgttcaggt ggatgaggtt ttctgacttg agcacgtggg agggcgatcg
5041 caatctggct cccaattttg tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg
5101 ggtccgcagc caacctcgta ccagaggtca acaatgaggt tatggctttg gagcccgttg
5161 ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta
5221 gaaataattt tgtacaagcc cccggtgggg agtttacagt gtcccctaga aacgctccag
5281 gtgaaatact atggagcgcg cccctaggcc ctgacctgaa tccctaccta tcccatttgg
5341 ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtgattctc gcggggaacg
5401 cgttcaccgc cgggaagata atatttgcag cagtcccacc aaattttcca actgaaggct
5461 taagtcctag ccaggtcact atgttccccc acataatagt agatgttaga caattagaac
5521 ctgtgctgat tcccttaccc gatgttagga ataatttcta tcattacaat cagtcaaatg
5581 actccactat taagttgata gcaatgttgt atacaccact tagggctaat aatgctggag
5641 atgatgtttt cacagtttcg tgccgagttc tcacgagacc atcccccgat tttgatttca
5701 tatttttagt gccacccaca gttgagtcaa ggactaaacc attctctgtc ccagttttaa
5761 ccgttgagga gatgaccaat tcaagattcc ccatcccttt ggaaaagttg ttcacaggcc
5821 ccagcagtgc ctttgttgtt caaccacaaa atggcaggtg cacaactgat ggcgtgctcc
5881 taggcaccac ccaactttct cctgtcaaca tctgcacctt cagaggggat gtcacccaca
5941 tcacaggtag tcgcaactac acaatgaatt tggcttctca aaattggaac aactatgacc
6001 caacagaaga aatcccagcc cctctaggaa ctccagattt tgtggggaag attcaaggca
6061 tgctcaccca aaccacaagg gcagatggtt caacacgcgg ccacaaagct acagtgtaca
6121 ctgggagcgc cgactttgct ccaaaactgg gtagagttca atttgaaact gacacagacc
6181 atgattttga agctaatcaa aacacaaagt tcaccccagt cggtgtcatc caagatggca
6241 gcaccaccca ccgaaacgaa ccccaacagt gggtgctccc aagttactca ggcagaaata
6301 ctcacaatgt acatttggcc cccgctgtag cccccacctt tccgggtgag caactcctct
6361 tcttcagatc caccatgccc ggatgcagcg ggtaccccaa catggatttg gactgtctgc
6421 tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa tctgatgtgg
6481 ctctgctaag atttgtgaat ccagacacag gtagagtctt gtttgagtgc aagcttcaca
6541 aatcaggcta tgtcacagtg gctcacactg gccaacatga tttggttatc ccccccaatg
6601 gttactttag gtttgattcc tgggtcaacc agttctacac gcttgccccc atgggaaatg
6661 gaacggggcg tagacgtgta gtataatggc tggagctttc tttgctggat tggcatctga
6721 tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca tcaaccaaaa
6781 agttgaattc gaaaataaca gaaaattgca acaagcatcc ttccaattta gcagcaatct
6841 gcaacaggct tccttccaac atgataaaga gatgctccaa gcacaaattg aggccaccaa
6901 aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg gtgggttctc
6961 tgagacagat gcagcccgcg gggcaattaa cgcccctatg acaaaagctt tggactggag
7021 cgggacaagg tactgggctc cagatgctag gattacaaca tacaatgcag gccacttttc
7081 cacccctcaa ccaccgaggg cactgccagg aagagctaat cttagggatg ctgtccctgc
7141 tcggggaccc tccaacaaat cttctaactc ttctactgcc acctctgtgt attcaaatca
7201 aactatttca acgaggcttg gtcctacagc tggttctggg accagtgtct cgagcctccc
7261 gtcaactgca aggactagga gctgggttga ggatcaaaat aggaatttgt cacctttcat
7321 gaggggggcc cacaacatat catttgtcac cccaccatct agcagatcct ccagtcaagg
7381 cacagtctca accgtgccta aagagatttt ggactcctgg actggcgctt tcaacacgcg
7441 caggcagcct ctcttcgctc acattcgtaa gcgaggggag tcacgggtgt aa
//