Typing tool
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Typing tool
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Complete norovirus genomes
| MF140633 | GII.4 Den Haag | |
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| GII.P4 Hunter |
ORF1: 1..5085
ORF2: 5066..6688
ORF3: 6688..7494
LOCUS MF140633 7539 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2009/GII.P4-GII.4/Rotterdam/E7800007_p1_d0 ORF1
gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140633
VERSION MF140633.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7539)
AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E.,
Verjans,G.M.G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T.,
Cotten,M.L. and Koopmans,M.P.G.
TITLE Whole genome next generation sequencing to study within-host
evolution of chronic norovirus infection among immunocompromised
patients
JOURNAL J. Infect. Dis. (2017) In press
PUBMED 29029115
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7539)
AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E.,
Verjans,G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T.,
Cotten,M.L. and Koopmans,M.P.G.
TITLE Direct Submission
JOURNAL Submitted (19-MAY-2017) Centre for infectious Disease Control
(Cib), National Institute for Public Health and the Environment
(RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA,
Netherlands
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 3.9.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7539
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2009/GII.P4-
GII.4/Rotterdam/E7800007_p1_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="07-Jan-2009"
/note="genotype: GII.P4-GII.4"
CDS <1..5085
/codon_start=1
/product="ORF1"
/protein_id="ATN23595.1"
/translation="NDASAAAVANSNIDTVKSSSDGVLSSMAVTFKRALGARPKQPPP
REIPQRPPRPPTPELIKNVPPPPPNGEDDIVVSYSVKDGVSGLPDLSTVRQPEESNTA
FSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLARVE
LTPLSLYWRPVYTPQYLISPDALKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLN
ILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIA
ASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTMPELKQ
ALKNISIKKCQIVYSGSTYTLESDGKGNVRVDRVQSASVQTNNELAGALHHLRCARIR
YYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQNLWSKPQVEDIEETASKDGCPKPKD
DEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI
RKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTL
LIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGCEGEATLEGGDNKGTYCGAPILGPGSAP
KLSNKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
KPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQR
AVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLK
PTRPDKTEGPLAISEDLNGLTFLRRTVTRDPAGWFGKLEQNSILRQMYWTRGSNHEDP
SETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5066..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23596.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLATQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFATDTDNDFDANQNTKFTPVGVIQDG
NTAHRNEPQQWVLPSYSGRNSHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6688..7494
/codon_start=1
/product="ORF3"
/protein_id="ATN23597.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQPPGALPGRANLRAAVPARGSSSTSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARARSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 aacgacgctt ccgctgccgc tgttgctaat agcaacatcg acaccgtaaa atcttcaagt
61 gacggagtgc tttctagcat ggccgtcact ttcaaacgag ccctcggggc gcggcctaaa
121 cagcctcccc cgagggaaat accacaaaga cccccacgac cacccactcc agaactgatc
181 aaaaatgtcc cccctccccc acccaacgga gaggatgaca tagtggtttc ttatagtgtc
241 aaagatggtg tctctggttt gcctgatctt tccaccgtca ggcaaccgga agaatctaac
301 acggccttca gtgtccctcc actcaaccag agggagaata gagatgctaa ggagccactg
361 actggaacaa ttttggaaat gtgggatgga gaaatctatc actatggcct gtatgtagag
421 cgaggtcttg tgctaggtgt gcacaaacca ccagctgcca tcagcctcgc tagggtcgaa
481 ctaacaccac tttccttgta ctggagacct gtgtatactc cccaatacct catctctcca
541 gacgctctca agaaactaca cggagagacg ttcccctaca cagcctttga caacaactgt
601 tatgcctttt gttgttgggt cctggaccta aacgactcgt ggctgagtag gagaatgatc
661 cagagaacaa ctggcttctt cagaccctac caagattgga ataggaaacc cctccccact
721 atggatgact ccaagttaaa gaaggtagct aacatattcc tgtgtgcact gtcttcacta
781 ttcaccaggc ctataaaaga tataataggg aagctaaggc ctcttaacat cctcaacatc
841 ttggcctcat gtgattggac ttttgcaggc atagtggagt ccttgatact cttggcagaa
901 ctctttggag ttttctggac acccccagat gtgtctgcga tgattgcccc cttactcggt
961 gactacgagc tacaaggacc tgaggacctt gcagtggagc tcgtccctgt agtgatgggg
1021 ggaattggtt tggtgctagg attcaccaaa gagaagattg gaaaaatgtt gtcatctgct
1081 gcatccacct tgagagcttg taaagatctt ggtgcatatg ggttagagat cctaaagttg
1141 gtcatgaagt ggttcttccc caagaaagag gaagcaaatg aactggctat ggtgagatcc
1201 atcgaggatg cagtcctgga tctcgaagca attgagaaca accatatgac taccttgctc
1261 aaagacaaag acagtctggc aacctacatg agaacccttg accttgagga ggagaaagct
1321 aggaaactct caaccaagtc tgcttcacct gacatcgtgg gcacgatcaa cgcccttctg
1381 gcgagaatcg ctgctgcacg ttctctggtg catcgagcga aggaggaact ttctagcaga
1441 ccaagacctg tagtgttgat gatatcaggc agaccaggaa tagggaagac ccaccttgcc
1501 agggaagtgg ctaagagaat cgcagcctcc cttacaggag accagcgtgt aggcctcgtc
1561 ccacgcaatg gcgtcgacca ttgggatgcg tacaagggag agagggtcgt tctatgggac
1621 gactatggaa tgagcaatcc tatccacgat gccctcagat tgcaagaact cgctgacact
1681 tgtcccctta ccctaaactg tgacaggatt gagaacaaag gaaaggtctt tgacagcgat
1741 gtcatcatta tcaccactaa tctggctaac ccagcaccac tggactatgt caactttgaa
1801 gcatgctcga ggcgtatcga cttcctcgtg tatgcagaag cccctgaggt cgaaaaggcg
1861 aagcgtgact tcccaggcca acccgacatg tggaagaacg ccttcagttc tgatttctca
1921 cacataaaac taacattggc tccacagggt ggtttcgaca agaacgggaa caccccacac
1981 gggaagggcg tcatgaagac tctcaccacc ggctccctta ttgcccgggc atcagggcta
2041 ctccatgaga ggctagatga atttgaacta cagggcccaa ctctcaccac cttcaacttt
2101 gatcgcaata aagtgcttgc ctttagacaa cttgctgctg aaaacaaata tgggttaatg
2161 gacacaatga aagttgggag gcagctcaag gatgtcagaa caatgccaga gctcaagcaa
2221 gcactcaaga atatttcaat caagaagtgc cagatagtat atagtggtag cacctacaca
2281 cttgagtctg atggcaaggg caatgtgagg gttgacagag ttcaaagtgc ctccgtacag
2341 accaacaatg agctggctgg cgccctacac catctaaggt gcgccagaat aagatactat
2401 gtcaggtgtg tccaggaggc cttgtattcc atcatccaga ttgctggggc tgcatttgtc
2461 accacgcgca tcgtcaagcg catgaacata caaaacctat ggtctaagcc acaagtggaa
2521 gatatagagg agactgccag caaggacggg tgtccaaaac ccaaagatga tgaggagttc
2581 gtcatttcat ccgacgacat caaaactgag ggcaagaaag ggaaaaacaa gactggccgc
2641 ggcaagaagc acacagcctt ctcaagcaaa ggactcagtg atgaagagta cgatgagtac
2701 aagaggatta gagaagaaag gaatggtaag tactccatag aagagtacct tcaggacagg
2761 gacaaatact atgaggaggt ggccattgcc agggcgactg aggaagactt ctgtgaagag
2821 gaggaggcca agatccggca aaggatcttc aggccaacaa ggaaacagcg caaggaggaa
2881 agagcttctc tcggtttagt tacaggttct gaaattagga aaagaaatcc agatgatttc
2941 aaacccaagg ggaaactgtg ggctgacgat gacagaagtg tggactacaa tgagaaactc
3001 agttttgaag ccccaccaag catctggtcg aggatagtca actttggttc aggttgggga
3061 ttctgggtct cccccagttt gttcataaca tcaacccatg tcatacccca gggagcaaag
3121 gagttctttg gagtccccat caaacaaatt caagtacata agtcaggcga attctgtcgc
3181 ttgagattcc caaaaccaat cagaactgat gtgacgggca tgatcttaga agaaggtgca
3241 cccgagggca ccgtggttac actactcatc aaaagatcca ctggagaact catgccccta
3301 gcagctagga tggggaccca tgcaaccatg aaaatccaag gacgcactgt tggaggtcaa
3361 atgggcatgc ttctgacagg atccaacgcc aaaagcatgg atctgggtac cacaccaggt
3421 gattgtggct gtccctacat ctacaagaga ggaaatgact atgtggtcat tggagtccac
3481 acggctgccg ctcgtggggg caacactgtc atatgtgcca cccaggggtg tgagggagag
3541 gctacacttg aaggtggtga caataaaggg acatactgtg gtgcaccaat cctaggccca
3601 gggagtgccc caaaacttag caacaagacc aaattctgga gatcgtccac agcaccactc
3661 ccacctggca cctatgaacc agcctatctt ggtggtaagg accccagagt caagggtgga
3721 ccttcactgc agcaggtcat gagggatcag ctgaagccat tcacagagcc caggggcaag
3781 ccaccaaagc caagtgtgtt ggaagctgct aagaaaacca tcatcaatgt ccttgagcaa
3841 acaattgatc cacctgagaa atggtcgttc gcacaagctt gcgcgtccct tgacaagacc
3901 acctccagtg gccatccgca tcacatgcgg aaaaacgact gctggaatgg ggagtccttc
3961 acaggcaagc tggcagacca ggcttccaag gccaacctga tgtttgaaga agggaagaac
4021 atgacgccag tctatacagc tgcgcttaag gatgaattag tcaaaactga caaaatttat
4081 ggcaagatca agaagaggct tctctggggc tcggatttgg cgaccatgat ccggtgtgct
4141 cgagcattcg gaggcctaat ggatgaactc aaagcgcact gtgtcacact tcccattaga
4201 gttggtatga atatgaatga ggatggcccc atcatcttcg agaggcactc caggtacacg
4261 taccactatg atgctgacta ctctcgatgg gattcaacac aacagagagc cgtgttggca
4321 gcagctctag aaatcatggt taagttctcc ccagaaccac atttggccca ggtagtcgca
4381 gaagaccttc tttctcctag cgtggtggac gtgggtgact tcacaatatc aattaatgag
4441 ggtcttccct ctggggtgcc ctgcacctcc caatggaact ccatcgccca ctggcttctc
4501 accctctgtg cgctctctga agttaccaac ttgtctcctg acaccataca agctaattcc
4561 ctcttctctt tttatggtga tgatgaaatt gttagcacag acataaagtt ggacccagaa
4621 aagttgacag caaagctcag ggagtatggg ttaaagccaa cccgccccga caaaactgaa
4681 ggaccccttg ccatctctga agacttgaat ggcctgactt tcctgcggag gactgtgacc
4741 cgcgacccag ctggttggtt tggaaaactg gagcagaatt caatactcag gcaaatgtac
4801 tggactaggg gttccaacca tgaagaccca tctgaaacaa tgattccaca ctcccaaaga
4861 cccatacaac tgatgtccct actgggggag gccgcactcc acggcccagc attctacagc
4921 aaagtcagca agttagtcat tgcagagcta aaagaaggtg gcatggattt ttacgtgccc
4981 agacaagagc caatgttcag atggatgaga ttctcagatc tgagcacgtg ggagggcgat
5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg agtgacgcca acccatctga
5101 tgggtccgca gccaacctcg tcccagaggt caacaatgag gttatggctt tggaacccgt
5161 tgttggtgcc gctattgcgg cacctgtagc gggccaacaa aatgtaattg acccctggat
5221 tagaaacaat tttgtacaag cccctggtgg agagttcaca gtatccccta gaaacgctcc
5281 aggtgaaata ctatggagcg cgcccctagg ccctgatttg aatccctacc tttcccattt
5341 ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg caggtaatcc tcgcggggaa
5401 cgcgttcacc gccggaaaaa tcatatttgc agcagtccca ccaaattttc caactgaagg
5461 cttgagcccc agccaggtca ctatgttccc ccacataata gtagatgtta ggcaactgga
5521 acctgtgttg atccccttac ccgatgttag gaataatttc tatcactaca atcaatcaaa
5581 tgaccccacc atcaaactga tagcaatgtt gtatacacca cttagggcta ataatgctgg
5641 ggacgacgtc ttcacagttt cttgtcgggt tctcacgaga ccatcccccg attttgattt
5701 catattttta gtgccaccca cagttgagtc aagaactaaa ccattctctg tcccgatctt
5761 aactgttgag gagatgacca attcaagatt ccccattcct ttggaaaaat tgttcacggg
5821 tcccagcagt gcctttgttg ttcaaccaca aaacggcagg tgcacgactg atggcgtgct
5881 cctaggtacc acccaactgt ctcctgtcaa catctgcacc ttcagagggg atgtcaccca
5941 catcacaggt agtcgtaact acacaatgaa tttggctact caaaattgga acagttatga
6001 cccaacagaa gaaatcccag cccccctagg aactccagat ttcgtgggga agattcaagg
6061 tgtgctcact caaaccacaa gggcagatgg ctcgacccgc ggccacaaag ctacagtgta
6121 cactgggagc gccgattttg ctccaaaact gggtagagtt caatttgcca ctgacacaga
6181 caatgatttt gacgctaacc aaaacacaaa gttcacccca gtcggtgtca tccaggatgg
6241 taatactgcc caccgaaatg aaccccaaca atgggtgctc ccaagttact caggcagaaa
6301 tagtcacaat gtgcacctgg cccccgctgt agcccccact tttccgggtg agcaacttct
6361 cttcttcaga tccactatgc ccgggtgcag cgggtacccc aacatggatt tggactgcct
6421 gctcccccag gaatgggtgc agtatttcta tcaagaggca gccccagcac aatctgatgt
6481 ggctctgcta agatttgtga atccagatac aggtagggtt ttgtttgagt gtaaacttca
6541 taaatcaggc tatgttacag tggctcacac cggccaacat gatttggtta tcccccccaa
6601 tggttatttc agatttgatt cctgggtcaa tcagttctac acacttgccc ccatgggaaa
6661 tggaacgggg cgtaggcgtg cattataatg gctggagctt tctttgctgg gttggcatct
6721 gacgttcttg gctccggact tggttctctg atcaatgccg gggctggggc catcaaccaa
6781 aaagttgaat ttgaaaataa cagaaagttg caacaagctt ccttccaatt tagcagcaat
6841 ctacaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat tgaggccacc
6901 aaaaagttgc aacaggaaat gatgagagtt aaacaggcaa tgctcctaga gggtggattc
6961 tctgagacag atgcagcccg tggggcaatt aacgccccca tgacaaaggc tttggactgg
7021 agtgggacaa ggtactgggc tcccgacgct aggactacaa catacaatgc aggccacttt
7081 tccacccctc aacccccggg ggcactgcca ggaagagcta atcttagggc tgctgtcccc
7141 gctcggggct cctccagcac atcttctaac tcttctactg ctacctctgt gtactcaaat
7201 caaaccactt caacgagact tggttctaca gctggttctg gtaccagtgt ctcgagcctc
7261 ccgtcaactg caagggctag gagctgggtt gaggatcaaa ataggaattt gtcacctttc
7321 atgagggggg cccacaacat atcgtttgtc accccaccat ctagcagatc ctctagccaa
7381 ggcacagtct caaccgtgcc caaagaagtt ttggactcct ggactggcgc tttcaacacg
7441 cgcaggcagc ctctcttcgc tcacattcgt aagcgagggg agtcacgggc gtaatgtgaa
7501 aagacaaaat tgattatctt tcttttcttt agtgtcttt
//