Typing tool
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Typing tool
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Complete norovirus genomes
| OP205551 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5094
ORF2: 5075..6697
ORF3: 6697..7503
LOCUS OP205551 7503 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0361_R03-06 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205551
VERSION OP205551.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7503)
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JOURNAL Unpublished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 7503)
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..7503
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0361_R03-06"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-09-18"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5094
/gene="ORF1"
CDS <1..5094
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60954.1"
/translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQ
PAPRDEPQKSPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPD
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
IAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK
HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2619
/gene="ORF1"
/product="p22"
mat_peptide 2620..3018
/gene="ORF1"
/product="VPg"
mat_peptide 3019..3561
/gene="ORF1"
/product="Pro"
mat_peptide 3562..5091
/gene="ORF1"
/product="RdRp"
gene 5075..6697
/gene="ORF2"
CDS 5075..6697
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60955.1"
/translation="MKMASSDANPSDGSAVNLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFAGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEVNQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6697..7503
/gene="ORF3"
CDS 6697..7503
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60956.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga caaggaaaaa
61 tcttcaggtg aaggcttatt tacaaatatg tcttccacct taaagaaagc cctcggggct
121 aggcccaaac agcctgcccc gagagacgaa ccacaaaagt ccccaagacc accaactccc
181 gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga agaaccagtc
241 attaggtatg aggttaagag tggaatctct ggcctgcccg agctcacaac agtcccccaa
301 ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga aaacagggag
361 gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggggagat ataccactat
421 ggcctatacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc
481 atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta cactccccaa
541 tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc ttacaccgcc
601 ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga ctcatggctt
661 agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga gtggaacaga
721 aaacccctgc ccaccatgga tgactccaaa ataaagaagg tagcaaatat attcctatgt
781 tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat taagccatta
841 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt ggagtctctg
901 atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatc
961 gctcccttac tcggggacta cgagttgcaa gggccagaag acatcgccgt tgaactcgta
1021 cctgtggtaa tgggagggat tggtctggtg ttgggattca ccaaagagaa aattggcaaa
1081 atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc ctatggctta
1141 gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc caatgagcta
1201 gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga aaacaaccac
1261 atgacaaccc tgttgaaaga caaagacagc ttagcaacgt acatgaaaac actggacatg
1321 gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat agttgggaca
1381 atcaacgccc tgctggctcg gatagcagca gccaggtcac tagtccacag ggccaaggaa
1441 gagctatcta gcaggataag accagtagtt gttatgatat ctggcaaacc aggaataggc
1501 aaaactcatc tggccaggga ggtggcaaga aaggtagcgt ccactctcac aggggatcaa
1561 agagtcggac ttataccaag aaacggtgtg gaccattggg atgcatataa aggtgagaga
1621 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgccct tcgcatacaa
1681 gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa taagggaaaa
1741 gtttttgata gtgaagtcat aataattaca acaaaccttg ccaacccagc cccacttgat
1801 tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc tgaggcacca
1861 gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa ggacgccttc
1921 aagccggact tttcacacat caagctacag cttgcacctc agggcggctt tgacaagaat
1981 ggcaacaccc cacatgggaa aggggtgatg aagaccctca ctaccggttc tctgattgcc
2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaatc
2101 accaccttca atttcgatcg gaacagaatc acagcattca gacaattggc tgcagaaaac
2161 aagtatggat tggtggatac catgaaagtt ggcaatcaac taaaaggagt gaaaaccatg
2221 gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat catctacggt
2281 ggctccacgt atgaccttga atctgatggc aagggcaaag tcttggtaga aaaggtcaag
2341 aacacctctg tacagaccaa caacgagttg gccggggccc tacaccatct caaacacgcc
2401 cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat acaaattgcc
2461 ggcgctgcgt ttgtcaccac gcgtattgca cgccgcatga acatacaaga actctggtcg
2521 aagccacaat tagatcaaaa tgaatcagag gctaaggaag aggcccccaa gtcagaagat
2581 gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg caaaaacaaa
2641 actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga tgaggagtat
2701 gacgagtaca agaggataag agaagagaga aatgggaagt actctataga ggagtatctt
2761 caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga agaagacttc
2821 tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag gaaacaaaga
2881 aaggaagaga gggccacatt ggggctggta acaggttcag aaatcagaaa aagaaaccct
2941 gatgacttca aacccaaagg taagctgtgg gccgatgaca acagaagtgt tgactacaat
3001 gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag ctttggttct
3061 ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt aatccccgca
3121 ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa atcaggtgaa
3181 ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat gatcttggaa
3241 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc
3301 atgcctcttg cagccagaat ggggacacac gcaaccatga aaattcaagg ccgcatggtt
3361 ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga tttgggaaca
3421 actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta tatagtcatt
3481 ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3541 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatt
3601 ttaggccctg ggggtgcacc aaaattgagc accaaaacca agttttggag gtcatcgaac
3661 acgccccttc caccagggac atatgagcct gcctacctcg gtggtcgtga tccgcgcgtt
3721 aagggtgggc cctccttgca gcaggtaatg agagaccagt tgaagccatt cactgaaccc
3781 aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat tatcaatgtt
3841 ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcgtg tgcctcactt
3901 gacaaaacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt ctggaatggt
3961 gagaccttca caggtaaatt ggcagaccaa gcatcaaaag caaacctaat gtttgaggaa
4021 gggaaacaca tgacaccagt gtatacagca gcgctcaagg acgagctagt taagactgag
4081 aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc caccatgatc
4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg catatcactc
4201 ccagtacgag ttggcatgaa catgaatgaa gatggcccaa taatatttga gaaacattcc
4261 agatacaaat accactatga tgcagactac tctcgttggg attcaacaca acagagggca
4321 gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca attggcacaa
4381 atagtcgctg aagatctact ggcccctagt gtagtagatg taggagactt taaaatcaca
4441 ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc catcgcacac
4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga cattatacaa
4561 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaattg
4621 gaccctgaac agctaaccgc caagttgaag gagtacggcc tgaaaccaac ccgcccagac
4681 aagaccgagg ggcccctgat catcagtgaa gatttgaacg gactcacttt cctccgaagg
4741 acggtgactc gtgacccagc tggctggttt ggaaagctgg accaaagttc aattttgagg
4801 cagatgtact ggactagagg accaaaccat gaagacccca atgagacaat gataccccat
4861 tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4921 ttctacagta gaattagtaa attggtcata actgaactca aagaaggtgg gatggacttt
4981 tacgtgccaa ggcaggaacc catgttcagg tggatgagat tttctgactt gagcacgtgg
5041 gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga gtgacgccaa
5101 cccatctgat gggtccgcag tcaacctcgt accagaggtc aacaatgagg ttatggcttt
5161 ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa atgtaattga
5221 cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag tgtcccctag
5281 aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa atccctacct
5341 atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc aggtaattct
5401 cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac caaattttcc
5461 aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag tagatgttag
5521 acaattagaa cctgtgctga ttcccttacc cgatgttagg aataatttct atcattacaa
5581 tcagtcaaat gattccacta ttaagttgat agcaatgttg tacacaccac ttagggctaa
5641 taatgctgga gatgatgttt tcacagtttc gtgccgagtt ctcacgagac catcccccga
5701 ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac cattctctgt
5761 cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt tggaaaagtt
5821 gttcacaggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt gcacaactga
5881 tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct tcagagggga
5941 tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc aaaattggaa
6001 caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt tcgcagggaa
6061 gattcaaggc atgctcaccc aaaccacaag gacagacggt tcaacacgcg gccacaaagc
6121 tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc aatttgcaac
6181 tgacacagac catgattttg aagttaatca aaacacaaag ttcaccccag tcggtgtcat
6241 ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc caagttactc
6301 gggcagaaat actcacaatg tacatttggc ccccgctgta gcccccacct ttccgggtga
6361 gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca acatggattt
6421 ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag ccccagcaca
6481 atctgatgtg gctctgctaa gatttgtgaa cccagacaca ggtagggttt tgtttgagtg
6541 caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg acttggttat
6601 cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca cgcttgcccc
6661 catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt ctttgctgga
6721 ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg ggctggggcc
6781 atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcatc cttccaattt
6841 agcagcaatc tgcaacaggc ttcctttcaa catgataaag agatgctcca agcacaaatt
6901 gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat gctcctagag
6961 ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat gacaaaagct
7021 ttggactgga gcgggacaag gtactgggct ccagatgcta ggattacaac atacaatgca
7081 ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa tcttagggat
7141 gctgtccctg ctcggggacc ctccaataaa tcttctaact cttctactgc cacctctgtg
7201 tattcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg aaccagtgtc
7261 tcgagcctcc cgtcaactgc aaggactagg agttgggttg aggatcaaaa taggaatttg
7321 tcacctttca tgaggggggc ccacaacata tcatttgtta ccccaccatc tagcagatcc
7381 tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg gactggcgct
7441 ttcaacacgc gcaggcagcc tctcttcgct cacattcgta ggcgagggga gtcacgggtg
7501 taa
//