Typing tool
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Typing tool
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Complete norovirus genomes
| OP205579 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS OP205579 7509 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0493_R04-11 nonstructural
polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP205579
VERSION OP205579.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7509)
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JOURNAL Unpublished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 7509)
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..7509
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0493_R04-11"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-12-05"
/note="genotype: GII.4 Sydney[P31]"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV61038.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDGLVVSYSAKDGVSGLPELTTVRQPE
ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLTTYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPERLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6703
/gene="ORF2"
CDS 5081..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV61039.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNNDFEANQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAL"
gene 6703..7509
/gene="ORF3"
CDS 6703..7509
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV61040.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTHNAGRFSIPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVLSFPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ccaacagcaa caacgacatc
61 gcaaaatctt caagtgacgg tgtgttttct aacatggctg tcacttttaa gcgggccctc
121 ggggcgcggc ccaaacagcc gcccccgaag gaaataccac ccagaccccc gcgaccaccc
181 acaccagaat tggtcaaaaa gattcctcct cccccaccca acggggagga tggactagtg
241 gtttcttata gcgccaaaga tggcgtttcc ggactgcctg agctcaccac tgtcagacaa
301 ccggaagaaa ccaacacggc gttcagtgtc cccccactca accagaggga gagcagggac
361 gccaaggaac cactaactgg aacaatcatt gaaatgtggg atggagaaat ctaccattac
421 ggcctgtacg tggaacgagg tcttatactc ggtgtgcaca agccaccagc agccattagc
481 ctcgccaagg tcgagctggc accgctctct ttgttctgga gacctgtgta caccccccag
541 taccttatct ctccagacac tcttaggaga ttacatggag agacattccc ctacactgca
601 tttgacaaca attgctacgc cttttgttgt tgggtattag acctaaacga ctcatggcta
661 agcaggagaa tgattcagag aacaacaggc ttcttcaggc cgtaccagga ttggaacagg
721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tggccaacat attcttgtgc
781 actttgtctt cactgttcac cagacccatt aaggacataa tagggaagtt gaaacctctc
841 aacatcctta atattctggc tacgtgtgat tggaccttcg caggcatagt ggaatcctta
901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatc
961 gcccccttgc taggtgatta tgaactgcaa ggacctgagg accttgcagt ggaactggtc
1021 ccaatagtga tgggggggat aggtttggtg ctaggattta ccaaagagaa aatcggaaag
1081 atgctgtcat ccgctgcatc cactttaaga gcttgtaaag accttggtgc atacggactg
1141 gaaatcttaa aattggtcat gaagtggttc ttcccaaaga aagaggaagc aaatgaactg
1201 gctatggtga gatccatcga ggatgcagta ctagacctcg aggcaattga aaacaaccac
1261 atgaccaccc tgctcaaaga caaagacagc ttgacaacct acatgagaac ccttgacctt
1321 gaggaggaga aagccagaaa actctcaacc aaatctgctt cacccgatat tgtgggcaca
1381 atcaactctc ttctggcaag aatcgctgct gcacgctccc tagtacatcg ggcgaaagaa
1441 gagctctcca gcaggccgag acctgtcgtt gtaatgatat cgggaagacc agggataggg
1501 aaaactcacc ttgccaggga gctggccaag aagatcgcgg cctccctcac aggggaccag
1561 cgtgtgggcc ttatcccacg caatggtgtc gaccactggg acgcatacaa gggtgaaaga
1621 gttgtcctat gggacgacta tggaatgagc aaccccatcc atgatgccct caggttgcag
1681 gagcttgctg acacttgccc cctcacgcta aattgtgaca gaattgagaa caaaggaaaa
1741 gtctttgaca gtgatgccat aattatcacc accaacctgg ccaacccagc accactggac
1801 tacgtcaact ttgaagcgtg ctcgagacgc attgatttcc tcgtgtacgc agaagcccct
1861 gaggtggaga aggcaaagcg cgacttccca ggtcaacctg acatgtggaa gaacgctttc
1921 agtcctgact tctcacacat aaaactgtca ttggctccac agggtggttt tgacaagaac
1981 ggcaacaccc cgcatggaaa aggggtcatg aagaccctta ccactggctc cctcatcgcc
2041 cgagcatcag ggttactcca tgagaggcta gatgaatatg aattgcaagg cccagccctc
2101 accactttca actttgaccg caacaagata cttgctttta gacagcttgc tgctgaaaac
2161 aagtatgggc tgatggacac aatgagagtt ggaaaacagc tcaaggatgt caagactatg
2221 tcagacctca aacaagcact caagaacatc gcgatcaaga agtgccagat agtgtacaat
2281 ggtggcacct acacacttga ggctgatggc aagggcagtg tgaaagttga caaagtgcaa
2341 agtgccactg tgcagaccaa caatgaacta gccggtgccc tacaccacct aagatgcgct
2401 agaatcagat actatgttaa gtgcgtccag gaggcactgt attccatcat ccaaatcgct
2461 ggggctgcat tcgtcaccac gcgcatcgct aagcgcatga atatacagaa tctctggtcc
2521 aagccacagg tggaagacac agaagagatg gccaacaaag atggttgcct aaaacccaaa
2581 gatgatgaag agtttgtcgt ctcatccgac gacatcaaaa ctgagggcaa gaaagggaag
2641 aacaagtccg gccgtggtaa gaagcacaca gccttttcaa gtaaagggct cagtgatgag
2701 gagtacgatg agtacaagag aatcagagag gaaaggaatg gtaagtactc catagaagag
2761 taccttcagg acagagacag gtactacgag gaggtggcca ttgctagggc aaccgaagag
2821 gacttctgtg aagaagaaga ggccaaaatc cggcagagga ttttcagacc aacaaggaaa
2881 caacgcaaag aagagagggc ctctctcggc ttggtcacag gctctgaaat caggaagaga
2941 aacccagaag acttcaaacc caagggaaag ctgtgggctg atgatgacag aagtgttgac
3001 tacaatgaga aactcaactt tgaggcccca ccaagcatct ggtcgcggat agtcaatttt
3061 ggttcaggct ggggcttctg ggtctccccc agtctgttta taacatcaac ccatgtcata
3121 ccccaaggtg caaaagagtt cttcggagtc cctatcaagc aaatccagat acacaagtca
3181 ggtgaattct gccgattgag attcccaaag ccaatcagaa ccgatgtgac gggcatgatt
3241 ctagaagaag gtgcgcccga ggggaccgtg gccacactgc tcatcaagag accaactgga
3301 gagctcatgc ctctggcagc cagaatgggg acccatgcaa ccatgaaaat tcaggggcgc
3361 acagttggag ggcaaatggg tatgctcctg acaggatcca acgccaagag tatggaccta
3421 ggcacaacac caggcgactg cggctgcccc tacatctaca agagggggaa tgactacgtg
3481 gtcatagggg tccatacggc cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag
3541 ggaagtgagg gagaggccac acttgaagga ggtgacagta aagggacata ctgtggcgcg
3601 ccaatcttgg gcccagggag cgctccgaag ctcagcacca agactaagtt ttggagatca
3661 tccacaacac cactcccacc tggcacttac gaaccagcct acctcggtgg caaagaccct
3721 agagtcaaag gtggcccttc attgcaacaa gttatgaggg accagctgaa gccattcaca
3781 gaacccagag gcaaaccacc aagaccaaat gtgttggaag ctgccaagaa aaccatcatc
3841 aatgtccttg agcaaacaat tgatccaccc caaaaatggt catttgcgca agcttgcgca
3901 tcccttgaca aaaccacctc cagcggccac ccgcaccaca tgcggaaaaa cgactgttgg
3961 aatggggagt ccttcacagg aaaattggct gaccaagcct ccaaggccaa cctaatgttt
4021 gaagagggaa agaacatgac tccagtctac acaggtgcac ttaaagatga gttggtaaag
4081 accgacaagg tttatggtaa ggtcaagaag aggcttctgt ggggttcaga tctggcgacc
4141 atgatacggt gcgcccgagc ttttggaggc ctcatggatg aactcaaggc acactgtgtc
4201 acactccctg tcagagttgg tatgaacatg aatgaggatg gccccatcat cttcgagaag
4261 cactccagat atagatatca ctatgatgct gactattccc ggtgggactc aacacaacaa
4321 agggatgtgc tagcagcagc actagaaatc atggttaagt tctctccaga accacacctg
4381 gcccagatag ttgcagaaga cctcctctcc cctagcgtga tggatgtggg tgactttcaa
4441 atatcaataa gtgagggtct cccctctggg gtgccttgta cctcccagtg gaattccatc
4501 gcccactggc tcctcactct gtgtgcactc tctgaagtca cggacctgtc ccctgatatc
4561 attcaggcca actccctttt ctccttctat ggtgatgacg agattgtaag cacagacata
4621 aagttggacc cagagaggct gacagcaaaa ctcaaggagt acgggctgaa accaacccgc
4681 cccgacaaaa ctgaaggacc ccttgttatc tctgaagacc tggatggtct gacattcctc
4741 cggagaactg tgacccgtga tccagctggc tggtttggaa aattggaaca aagctcaatt
4801 cttaggcaaa tgtactggac caggggtccc aaccatgaag atccatttga aacaatgata
4861 ccacactccc aaagacccat acaattgatg tccttgctgg gcgaggctgc actccacggc
4921 ccggcattct acagcaaaat tagcaaattg gtcattgcag agttgaagga aggtggcatg
4981 gatttttacg tacccagaca agagccaatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctctggag cccgttgttg gtgccgccat tgcggcacct gtggcgggcc aacaaaatgt
5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt ttacagtgtc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttgggccctg atctaaatcc
5341 ctacttatct cacttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcttga gccccagcca ggtcactatg ttcccccata tagtagtaga
5521 tgttaggcaa ttagaacctg tgttgattcc cttacccgat gttaggaata atttctatca
5581 ttacaatcaa tcaaatgacc ccaccattaa gttgatagca atgttgtata caccacttag
5641 ggctaataat gctggggatg atgtctttac agtttcttgc cgagttctca cgagaccatc
5701 ccccgacttt gatttcatat ttctagtgcc acccacagtt gagtcaagaa ctaaaccatt
5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca ttcctttgga
5821 aaagttgttc acgggtccca gcagtgcctt tgttgtccaa ccacaaaacg gtaggtgcac
5881 gactgatggc gtgctcctag gcaccaccca actgtctcct gtcaacatct gcaccttcag
5941 aggagatgtc acccatatca caggtagtca taactacaca atgaatttgg cttctcaaaa
6001 ttggaacaat tacgacccaa cagaagaaat cccagcccct ctagggactc cagactttgt
6061 ggggaagatt caaggcatgc ttacccaaac cacaaggaca gatggctcaa cacgcggcca
6121 caaagccaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt
6181 tgaaactgac acaaacaatg attttgaagc taaccaaaac acaaagttca ccccagttgg
6241 tgtcatccaa gatggtggca ccacccaccg aaatgaaccc caacagtggg tgctcccaag
6301 ttactcaggc aggaacactc ctaacgtgca tctggccccc gctgtagccc ccacttttcc
6361 gggtgagcaa ctcctcttct tcagatccac catgcccgga tgcagcgggt accccaacat
6421 ggatttggat tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
6541 tgagtgtaag cttcataaat caggctatgt tacagtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tttacacgct
6661 tgcccccatg ggaaatggag cggggcgtag acgtgcacta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct
6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagca gtaatctaca acaggcttcc tttcaacatg acaaagagat gctccaagca
6901 caaattgagg ctaccaaaaa gttacaacag gaaatgatga aagttaagca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caatcaacgc ccctatgaca
7021 aaagctttgg actggagcgg gacaaggtac tgggctcctg atgctaggac tacaacacac
7081 aatgcaggcc gcttttccat cccccaacca tcgggggcgc tgccaggaag agctaatctt
7141 agggatgctg tccctgctcg gggttcctct agtaagtctt ctaattcttc tactgctact
7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggtacc
7261 agtgtcttga gcttcccgtc aactgcaagg actaggagct gggttgagga tcaaagtagg
7321 aatttgtcac ctttcatgag gggggcccat aacatatcgt ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagccactc ttcgctcaca ttcgtaagcg aggggagtca
7501 cgggtgtaa
//