Typing tool
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Typing tool
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Complete norovirus genomes
| MF140653 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5085
ORF2: 5066..6688
ORF3: 6688..7494
LOCUS MF140653 7494 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2008/GII.P4-GII.4/Rotterdam/E1300305_p14_d39
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140653
VERSION MF140653.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7494)
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 7494)
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..7494
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2008/GII.P4-
GII.4/Rotterdam/E1300305_p14_d39"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="10-Mar-2008"
/note="genotype: GII.P4-GII.4"
CDS <1..5085
/codon_start=1
/product="ORF1"
/protein_id="ATN23655.1"
/translation="NDASAAAAANSNNDTAKSSSDKMFSSMAVTFKRALGARPKQPPP
REIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTA
FSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVE
LTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLN
IINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREVAKRIA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELKQ
ALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIR
YYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATKKDGCPKPKD
DEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI
RKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTL
LIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAP
KLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
KPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQR
SVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLK
PTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDP
SESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5066..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23656.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTDNDFETHQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRDIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6688..7494
/codon_start=1
/product="ORF3"
/protein_id="ATN23657.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGRFSTPQPSGALPGRINPRTPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 aacgacgctt ccgctgccgc tgctgctaac agcaacaacg acaccgcaaa atcttcaagt
61 gacaaaatgt tttctagcat ggctgtcact tttaaacgag ccctcggggc gcggcctaaa
121 cagccccccc cgagggaaat accacaaaga cccccacgac cacctactcc agaactggtc
181 aaaaagatcc ctcctccccc gcccaacgga gaggatgaag tagtggtttc ttatagtgcc
241 aaagatggcg tttccggttt acccgagctt tccaccgtca ggcaaccgga agaaaccaat
301 acggccttca gtgtccctcc actcaaccag agggaaaata gagatgctaa ggaaccactg
361 actggaacaa ttctggaaat gtgggatgga gaaatctacc attatggcct gtatgttgag
421 cgaggtcttg tgctgggtgt gcacaaacca ccagctgcca taagcctcgc caaggtcgaa
481 ctaacaccac tctccttgtt ctggagacct gtgtacactc cccagtacct catctctcca
541 gacactctca agaaattaca cggagaaacg tttccctaca cagcctttga caacaattgc
601 tatgcctttt gttgctgggt cctggatcta aatgactcgt ggctgagtag gagaatgatc
661 cagagaacaa ctggcttctt cagaccctac caagactgga ataggaaacc cctccccact
721 atggatgatt ccaaattaaa gaaggtagct aacatattcc tgtgcaccct gtcttcgcta
781 ttcaccaggc ccataaaaga cataatagga aagttaaggc ctctcaacat catcaacatc
841 ctggcttcat gtgattggac tttcgcaggc atagtggagt ccttgatact cttggcagag
901 ctctttggag tcttctggac acccccagat gtgtctgcga tgattgcccc cttactcggt
961 gatttcgagt tacaaggacc tgaggacctt gtagtggagc tcgtccctgt agtaatgggg
1021 ggaattggtc tggtgctagg attcaccaaa gagaagattg gaaaaatgtt gtcatctgct
1081 gcgtccacct tgagagcttg taaagatctc ggtgcatacg ggctagagat cctaaagtta
1141 gtcatgaagt ggttcttccc gaagaaagag gaggcaaatg aactggctat ggtgagatcc
1201 attgaggatg cagtactgga ccttgaggca attgaaaaca accatatgac caccttgctc
1261 aaagacaaag acagtctggc aacctacatg agaacccttg acctcgagga agagaaagcc
1321 agaaaactct caaccaaatc tgcttcacct gacatcgtgg gcacaatcaa cgcccttctg
1381 gcgagaatcg ccgctgcacg ctccctggtg caccgagcga aggaggagct ttccagcaga
1441 ccaagacctg tagtcttgat gatatcaggc aaaccaggga tagggaaaac ccaccttgct
1501 agggaagtgg ctaagagaat cgcagcctcc ctcacaggag accagcgtgt aggcctcatc
1561 cctcgcaatg gcgtcgatca ctgggatgcg tacaaggggg agagggtcgt cctatgggac
1621 gactatggaa tgagcaatcc catccacgac gcccttaggc tgcaagaact cgctgacact
1681 tgccccctta ctctaaattg tgacaggatt gagaataaag gaaaggtctt tgacagcgat
1741 gtcatcatta tcactactaa tctggccaac ccagcaccac tggattatgt caactttgaa
1801 gcgtgctcga ggcgcatcga tttccttgtg tatgcagaag cccccgaggt cgaaaaggcg
1861 aagcgtgact tcccgggcca acctgacatg tggaaaaacg ctttcagttc tgatttctca
1921 cacataaaat tggcactggc tccacaaggt ggctttgata agaacgggaa caccccacac
1981 gggaagggcg tcatgaagac tctcaccact ggctccctca ttgcccgggc atcagggctg
2041 ctccatgaga gattggatga gtttgaacta cagggcccag ctcttaccac cttcaacttt
2101 gaccgcaaca aagtgcttgc cttcaggcag cttgctgctg aaaacaaata tgggttgatg
2161 gacacaatga aagttgggag gcagctcaag gatgtcaaaa ccatgccaga acttaaacaa
2221 gcactcaaaa acatctcaat caagaagtgc cagattgtgt atagtggttg cacctacaca
2281 cttgagtctg atggcaaggg caatgtgaaa gttgacagag ttcagagcac ctccgtgcag
2341 accaacaatg agttggctgg cgccctgcat catctgaggt gcgccagaat caggtactat
2401 gtcaagtgtg tccaggaggc cctgtattct atcatccaga ttgctggggc tgcatttgtc
2461 actacgcgca ttatcaagcg tgtgaacatt caagacttat ggtcaaagcc acaagtggaa
2521 aacacagagg aggctaccaa aaaggacggg tgcccaaaac ccaaagatga tgaggagttc
2581 gtcatttcat ctgacgacat caaaactgag ggtaagaaag ggaagaacaa gactggccgt
2641 ggcaagaagc acacagcctt ctcaagtaaa ggtctcagtg atgaagagta tgatgagtac
2701 aagagaatta gagaggaaag gaatggcaag tactccatag aagagtacct tcaggacagg
2761 gacaaatact atgaggaggt ggccattgcc agggcgaccg aggaagactt ctgtgaagag
2821 gaggaggcca agatccggca aaggatcttc agaccaacaa ggaaacaacg caaggaagaa
2881 agagcttctc tcggtttagt cacaggttct gaaattagga aaagaaaccc agaagacttc
2941 aagcccaagg ggaaactatg ggctgacgat gacagaagtg tggactacaa tgagaaactc
3001 agttttgagg ccccaccaag catttggtca aggatagtca actttggttc aggttggggc
3061 ttctgggtct cccctagcct gttcataaca tcaacccacg tcatacccca gggcgcgaag
3121 gagttctttg gggtccccat caaacaaatt caggtacaca agtcaggcga attctgtcgc
3181 ttgaggttcc caaaaccaat caggactgat gtgactggca tgatcctgga agaaggtgcg
3241 cccgaaggca ccgtggtcac actactcatc aaaaggtcta ctggagaact catgccccta
3301 gcagccagaa tggggaccca tgcaaccatg aaaattcaag ggcgcactgt tggaggtcag
3361 atgggcatgc ttctgacagg atccaacgcc aaaagcatgg atctaggcac cacaccaggt
3421 gattgcggct gtccctacat ctacaagaga ggaaatgact atgtggtcat tggagtccac
3481 acggctgccg ctcgtggggg aaacactgtc atatgtgcca cccagggggg cgagggggaa
3541 gctacacttg aaggtggtga cagtaaggga acatactgtg gtgcaccaat cctaggccca
3601 gggagtgccc cgaaacttag caccaaaacc aaattctgga gatcatccac agcaccactc
3661 ccacctggca cctatgaacc agcctacctt ggtggcaagg accccagagt caagggtggc
3721 ccttcgttgc agcaagtcat gagggaccag ctgaaaccat ttacagagcc caggggtaag
3781 ccaccaaagc caagtgtgtt agaagctgcc aagaaaacca tcatcaatgt ccttgaacaa
3841 acaattgacc cacctgagaa gtggtcgttc gcacaagctt gcgcgtccct tgacaagacc
3901 acttctagcg gccatccgca ccatatgcgg aaaaacgact gctggaacgg ggagtccttc
3961 acaggcaagc tggcggacca ggcttccaag gccaacctga tgtttgaaga agggaagaac
4021 atgaccccag tctacacagg tgcacttaag gatgaattag tcaaaactga caaaatttat
4081 ggcaagatca agaagaggct tctctggggc tcggatttag caaccatgat ccggtgcgct
4141 cgagcattcg gaggcctaat ggatgaactc aaagcgcact gtgtcacact tcctatcaga
4201 gttggtatga atatgaatga ggatggcccc atcatcttcg agaaacattc caggtacaga
4261 taccactatg atgctgatta ctctcggtgg gattcaacac aacagagaag cgtgctggca
4321 gctgctctag aaatcatggt taaattctcc tcagaaccac atttggccca ggtagtcgca
4381 gaagaccttc tttcccctag cgtggtggat gtgggtgact tcacaatatc aatcaacgag
4441 ggtcttccct ctggggtgcc ctgcacctcc caatggaact ccatcgccca ctggcttctc
4501 actctctgtg cactctccga agttacaaat ttgtccccag acatcataca ggctaattct
4561 ctcttctcct tctatggtga tgatgaaatt gttagtacag acataaaatt agacccagag
4621 aagttgacag caaagcttaa ggaatatgga ttgaagccaa cccgccctga caaaactgaa
4681 ggacctcttg ttatttctga agacttagat ggtttgactt tcctgcggag aactgtgacc
4741 cgcgacccag ctggttggtt tggaaaactg gagcagagct caatactcag gcaaatgtac
4801 tggactaggg gccccaacca tgaagatcca tctgaatcaa tgattccaca ctctcagaga
4861 cccatacaat tgatgtcctt actgggagag gccgcactcc acggcccaac attctacagt
4921 aaaatcagca aattagtcat tgcagagcta aaagaaggtg gtatggattt ttacgtgccc
4981 aggcaagagc caatgttcag atggatgaga ttctcagatc tgagcacgtg ggagggcgat
5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg aatgacgcca acccatctga
5101 tgggtccgca gccaacctcg tcccagaggt cagcaatgag gttatggctt tggagcccgt
5161 tgtcggtgcc gctattgcgg cgcctgtagc gggccaacaa aatgtaattg acccctggat
5221 tagaaataat tttgtacaag cccctggtgg agagttcaca gtatccccta gaaacgctcc
5281 aggtgaaata ctatggagcg cgcccttagg ccctgatctg aatccctacc tatctcattt
5341 ggccagaatg tataatggtt acgcgggtgg ctttgaagtg caggtgatcc tcgcggggaa
5401 cgcgttcacc gccggaaaaa ttatatttgc agcagtccca ccaaattttc caactgaagg
5461 cctgagtccc agccaggtca ctatgttccc ccacataata gtggatgtta ggcaattgga
5521 acctgtgctg atccctttac ctgatgttag gaataacttc tatcactata atcagtcaaa
5581 tgattctacc attaaattga tagcaatgct gtatacacca cttagggcca ataatgctgg
5641 ggaagatgtc ttcacagtct cttgtcgagt cctcacgagg ccgtcccctg attttgattt
5701 tatatttttg gtgccaccca cagttgagtc aagaactaaa ccatttactg tcccaatctt
5761 aactgttgaa gaaatgacca attcaagatt ccccattcct ttggaaaagt tgttcacggg
5821 tcccagcggt gcctttgttg tccaaccaca aaatggcagg tgcacgactg atggcgtgct
5881 cttaggcacc acccaactgt ctcctgtcaa catctgcacc ttcagagggg atgtcaccca
5941 cattgctggt tctcgtaatt acacaatgaa cttggcatct ctaaattgga acaattatga
6001 cccaacagag gaaattccag cccctctggg aactccagat ttcgtgggaa agatccaagg
6061 tgtgctcact caaaccacaa agggagatgg ctcgacccgt ggccataaag ctacagttta
6121 cactgggagt gcccccttta ctccaaagct gggcagtgtc caattcagta ctgatacaga
6181 caatgatttt gaaactcacc aaaacacaaa attcacccca gtcggtgtca tccaggatgg
6241 tagcaccacc caccgaaatg aaccccaaca atgggtgctc ccaagttatt caggtagaga
6301 tatccataat gtacacctag cccctgctgt agcccccact tttccgggtg aacaacttct
6361 tttcttcagg tccaccatgc ccggatgcag cgggtatccc aacatggatt tggattgcct
6421 actcccccag gagtgggtgc agcacttcta ccaagaggca gctccagcac aatctgatgt
6481 ggccctattg agatttgtga atccagacac aggtagggtc ctgtttgagt gcaaacttca
6541 taaatcaggc tatgtcacag tggctcacac cggccagcat gatttggtca tcccccccaa
6601 tggctatttt aggtttgatt cctgggttaa tcaattctac acacttgccc ccatgggaaa
6661 tggaacgggg cgtagacgtg ctttataatg gctggagctt tctttgctgg attggcatct
6721 gatgtccttg gctctggact tggttcccta atcaatgctg gggctggggc tatcaaccaa
6781 aagattgatt ttgaaaataa cagaaaattg cagcaagctt ccttccagtt tagcagtaat
6841 ctacaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat tgaggccact
6901 aaaaagttgc aacaggaaat gatgaaagtc aaacaggcaa tgctcttaga aggtggattc
6961 tctgaaacag atgcagcccg tggggcaatc aacgccccca tgacaaaggc tttggactgg
7021 agcggaacaa ggtactgggc ccctgatgct aggattacaa catacaatgc aggtcgcttt
7081 tccacccctc aaccttcggg ggcactgcca ggaagaatca atcccaggac tcctaccccc
7141 gctcggggct cctccagcac atcttctaat gcttctactg ctacttctat atattcaaat
7201 caaactgttt caacgagact tggttctaca gctggttctg gcaccaatgt ctcgagtctc
7261 ccgtcaactg caaggactag gagttgggtt gaggatcaaa acagaaattt gtcacctttc
7321 atgagggggg ctcacaacat atcgtttgtc accccaccat ctagcagatc ctctagccaa
7381 ggcacagtct caaccgtgcc taaagaagtt ttggactcct ggactggcgc tttcaacacg
7441 cgcaggcagc ctctcttcgc tcacattcgt aggcgagggg agtcacgggt gtaa
//