Typing tool
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Typing tool
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Complete norovirus genomes
| MF140634 | GII.4 Den Haag | |
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| GII.P4 Hunter |
ORF1: 1..5088
ORF2: 5069..6688
ORF3: 6688..7488
LOCUS MF140634 7531 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E1300272_p1_d566
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140634
VERSION MF140634.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7531)
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 7531)
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..7531
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2010/GII.P4-
GII.4/Rotterdam/E1300272_p1_d566"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="27-Jul-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23598.1"
/translation="SNDASAAAVANSNTDTVKSSSDGVLSSMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKNIPPPPPNGEDDIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGFVLGVHKPPAAISLARV
ELTPLSLYWRPVYTPQYLISPDALKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDTKLKKVANIFLCALSSLFTRPIKDIIGKLRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
ATSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTMPELK
QALKNISIKKCQIVYSGSTYTLESDGKGNVKVDKVQSASVQTNNELGGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQNLWSKPQVEDTEETASKDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGSNHED
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23599.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHSYTMNLATQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVSTGSADFAPKLGRVQFNTDTNNDFDTNQNTKFTPVGVIQDG
GTHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGSSGYPNMDLDC
LLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVI
PPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6688..7488
/codon_start=1
/product="ORF3"
/protein_id="ATN23600.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQA
SFQFSSNLQQSSFQHDKEMLQAQVEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGHFSTPQPPGALPGRSRAAVPARGSSSTPSNS
STATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNISF
VTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca ccgacaccgt aaaatcttca
61 agcgacggag tgctttctag catggccgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcctc ccccgaggga aataccacaa agacccccac ggccacccac tccagaactg
181 gtcaaaaata tcccccctcc cccacccaac ggggaggatg acatagtggt ttcttatagt
241 gtcaaagatg gtgtctctgg tttgcctgat ctttccaccg tcaggcaacc ggaagaatct
301 aacacggcct tcagtgtccc tccactcaac cagagggaga atagagatgc taaggagcca
361 ctgactggaa caattttgga aatgtgggat ggagaaatct atcactatgg cctgtatgta
421 gagcgaggtt ttgtgttagg tgtgcacaaa ccaccagctg ccatcagcct cgctagggtc
481 gaactaacac cactttcctt gtactggaga cctgtgtata ccccccaata cctcatctct
541 ccagacgctc tcaagaaact acacggagag acgttcccct acacagcctt tgacaacaac
601 tgttatgcct tttgttgttg ggtcctggac ctaaacgact cgtggctgag taggagaatg
661 atccagagaa caactggttt cttcagaccc taccaagatt ggaataggaa acccctcccc
721 actatggatg acaccaagtt aaagaaggta gctaacatat tcctgtgtgc actgtcttca
781 ctattcacca ggcctataaa agatataata gggaagctaa ggcctcttaa catcctcaac
841 atcttggcct catgtgattg gacttttgca ggcatagtgg agtccttgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc
961 ggtgactacg aactgcaagg acctgaggac cttgcagtgg agctcgtccc tgtagtgatg
1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct
1081 gctgcatcca ccttgagagc ttgtaaagac cttggtgcat atgggttaga gatcctaaag
1141 ttggtcatga agtggttctt ccccaagaaa gaggaagcaa atgaattggc tattgtgaga
1201 tccatcgagg atgcagtcct ggatctcgag gcaattgaga acaaccatat gactaccttg
1261 ctcaaagaca aagacagtct tgcaacctac atgagaaccc ttgaccttga ggaggagaaa
1321 gctaggaaac tctcaaccaa gtctgcttca cctgacatcg tgggcacgat caacgccctt
1381 ctggcgagaa tcgctgctgc acgttctctg gtgcatcgag cgaaggagga actttctagc
1441 agaccaagac ctgtggtgtt gatgatatca ggcagaccag gaataggaaa gacccacctt
1501 gccagggaag tggctaagag aatcgcaacc tcccttacag gagaccagcg tgtaggcctc
1561 atcccacgca atggcgtcga ccattgggat gcgtacaagg gagagagggt cgttctatgg
1621 gacgactatg gaatgagcaa tcccatccac gatgccctca gattgcaaga actcgctgac
1681 acttgtcccc ttaccctaaa ctgtgacagg attgagaaca aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcaccac taatctggct aacccagcac cactggacta tgtcaacttt
1801 gaagcatgct cgaggcgtat cgacttcctc gtgtatgcag aagcccctga ggtcgaaaag
1861 gcgaagcgtg acttcccagg ccaacccgac atgtggaaga acgccttcag ttctgatttc
1921 tcacacataa aactaacatt ggctccacag ggtggtttcg acaagaacgg gaacacccca
1981 cacgggaagg gcgtcatgaa gactctcacc accggctccc ttattgcccg ggcatcaggg
2041 ctactccatg agaggctaga tgaatttgaa ctacagggcc caactctcac caccttcaac
2101 tttgatcgca ataaagtgct tgcctttaga caacttgctg ctgaaaacaa atatgggttg
2161 atggatacaa tgaaagttgg gaggcagctc aaggatgtca gaacaatgcc agagctcaag
2221 caagcactca aaaatatttc aatcaagaag tgccagatag tatatagtgg tagcacctac
2281 acacttgagt ctgatggcaa aggcaatgtg aaggttgaca aagttcaaag tgcctccgta
2341 cagaccaaca atgagctggg tggcgcccta caccatctaa ggtgcgccag aataagatat
2401 tatgtcaagt gtgtccagga agccttgtat tccatcatcc agattgctgg ggctgcattt
2461 gtcaccacgc gcatcgtcaa gcgcatgaac atacaaaacc tatggtctaa gccacaagtg
2521 gaagatacag aggagactgc cagcaaggac gggtgtccaa aacccaaaga tgatgaggag
2581 ttcgtcattt catccgacga catcaaaact gagggcaaga aagggaaaaa caagactggc
2641 cgcggcaaaa agcacacagc cttctcaagc aaaggactca gtgatgaaga gtacgatgag
2701 tacaagagga ttagagaaga gaggaatggt aagtactcca tagaagagta ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgag
2821 gaggaggagg ccaagatccg gcaaaggatc ttcaggccaa caaggaaaca gcgcaaggag
2881 gaaagagctt ccctcggttt agtcacaggc tctgaaatta ggaaaagaaa tccagatgat
2941 ttcaaaccca aggggaaact gtgggctgac gatgacagaa atgtggacta caatgagaaa
3001 ctcagttttg aagccccacc aagcatctgg tcgaggatag tcaactttgg ttcaggttgg
3061 ggattctggg tctcccccag tctgttcata acatcaaccc atgtcatacc ccagggagca
3121 aaggagttct ttggagtccc catcaaacaa attcaagtac ataagtcagg cgaattttgt
3181 cgcttgagat tcccaagacc aatcaggact gatgtgacgg gcatgatctt agaagaaggt
3241 gcacccgagg gcaccgtggt tacactactc atcaaaagat ccactggaga actcatgccc
3301 ctagcagcta ggatggggac ccatgcaacc atgaaaatcc aaggacgtac tgttggaggt
3361 caaatgggca tgcttctgac aggatccaac gccaaaagca tggatctggg taccacacca
3421 ggtgattgtg gctgccccta catctacaag agaggaaatg actatgtggt cattggagtc
3481 cacacggctg ccgctcgtgg gggcaacact gtcatatgtg ccacccaggg gtctgaggga
3541 gaggctacac ttgaaggtgg tgacaataag gggacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaaaact tagcaccaag accaaattct ggagatcgtc cacagcacca
3661 ctcccacctg gaacctatga accagcctac cttggtggca aggaccccag agtcaagggt
3721 ggaccttcac tgcagcaggt catgagagat cagctgaagc cattcacaga gcccaggggc
3781 aagccaccaa agccaagtgt gttggaagct gctaagaaaa ccatcatcaa tgtccttgag
3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacctcca gtggccatcc gcatcatatg cggaaaaacg actgctggaa tggagagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 aacatgacgc cagtctacac agctgcactt aaggatgaat tggttaaaac tgacaaaatt
4081 tatggcaaga tcaagaagag acttctctgg ggctcggatt tggcgaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcgc actgtgtcac acttcccatt
4201 agagttggta tgaacatgaa tgaggatggc cccatcatct tcgagaggca ctccaggtac
4261 acgtaccact atgatgctga ctactctcga tgggattcaa cacaacagag agccgtgttg
4321 gcagcagctc tagaaatcat ggttaagttc tccccagaac cacatttggc ccaggtagta
4381 gcagaagacc ttctttctcc tagcgtggtg gacgtgggtg acttcacaat atcaattaat
4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcaccctct gtgcgctctc tgaagttacc aacttgtcac ctgacaccat acaagctaat
4561 tccctcttct ctttttatgg tgatgatgaa attgtcagca cagacataaa attggaccca
4621 gaaaagttga cagcaaagct cagggagtat gggttaaagc caacccgccc cgacaaaact
4681 gaaggacccc ttgccatctc tgaagacttg gatggcctga ctttcctgcg gaggactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggttccaa ccatgaagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aactgatgtc cctactgggg gaggccgcac tccacggccc agcattctac
4921 agcaaaatca gcaagttagt cattgcagag ctaaaagaag gtggaatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc
5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggaacc
5161 cgttgttggt gccgctattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaac aattttgtac aagcccctgg tggagagttc acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgcccct aggccctgat ttgaatccct acctttccca
5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg
5401 gaacgcgttc accgccggaa aaatcatatt tgcagcagtc ccaccaaatt ttccaactga
5461 aggcttgagc cccagccagg tcactatgtt cccccacata atagtagatg ttaggcaatt
5521 ggaacctgtg ttgatcccct tacccgatgt taggaataac ttctatcact ataatcaatc
5581 aaatgactcc accatcaaat tgatagcaat gttgtataca ccacttaggg ccaataatgc
5641 tggggacgac gtcttcacag tttcttgtcg ggttctcacg agaccatccc ccgattttga
5701 tttcatattt ttagtgccac ccacagttga atcaagaact aaaccattct ctgtcccgat
5761 cttaactgtt gaggagatga ccaattcaag attccccatt cctttggaaa aattgttcac
5821 gggtcccagc agtgcctttg ttgttcaacc acaaaacggc aggtgcacga ctgatggcgt
5881 gctcctaggt accacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac
5941 ccacatcaca ggtagccata gctacacaat gaatttggct actcaaaatt ggaatagtta
6001 tgacccaaca gaagaaatcc cagcccccct aggaactcca gatttcgtgg ggaagattca
6061 aggtgtgctc actcaaacca caaggacaga tggctcgacc cgcggccaca aagctacagt
6121 atccactggg agcgccgact ttgctccaaa attgggtaga gttcaattca acactgacac
6181 aaacaatgat tttgacacta accaaaacac aaagttcacc ccagtcggag tcatccagga
6241 tggtggcacc caccgaaatg aaccccaaca atgggtgctc ccaagttact caggcagaaa
6301 tattcacaat gtgcacctgg cccccgctgt ggcccccact tttccgggtg agcaacttct
6361 cttcttcaga tccactatgc ccgggtccag cgggtacccc aacatggatt tggactgcct
6421 gctcccccag gaatgggtgc agtatttcta tcaagaggca gccccagcac aatctgatgt
6481 ggctttgcta agatttgtga atccagatac aggtagggtc ttatttgagt gtaaacttca
6541 taaatcaggc tatgttacag tggctcacac cggtcaacat gatttggtta tcccccccaa
6601 tggttatttc agatttgatt cctgggtcaa tcagttctac acacttgccc ccatgggaaa
6661 tggaacgggg cgtaggcgtg cattataatg gctggagctt tctttgctgg attggcatct
6721 gatgttcttg gctccggact tggttctctg atcaatgccg gggctggggt catcaaccaa
6781 aaagttgact ttgaaaataa cagaaaattg caacaagctt ccttccaatt tagcagcaat
6841 ctacaacagt cttcctttca acatgataaa gagatgctcc aagcacaagt tgaggccacc
6901 aaaaagttgc aacaggaaat gatgagagtt aaacaggcaa tgctcctaga gggtggattc
6961 tctgagacag atgcagcccg tggggcaatt aacgccccca tgacaaaaac tttggactgg
7021 agtgggacaa ggtactgggc tcccgacgct aggactacaa catacaatgc aggccacttt
7081 tccacccctc aacccccggg ggcactgcca gggagatcta gggctgctgt ccccgctcgg
7141 ggctcctcca gcacaccttc taattcttct actgctacct ctgtgtactc aaatcaaacc
7201 acttcaacga gacttggttc tacagctggt tctggtacca gtgtctcgag cctcccgtca
7261 actgcaagga ctaggagctg ggtggaggat caaaatagga atttgtcacc tttcatgagg
7321 ggggcccaca acatatcatt tgtcacccca ccatctagca gatcctctag ccaaggcaca
7381 gtctcaaccg tgcccaaaga agttttggac tcctggactg gcgctttcaa cacgcgcagg
7441 cagcctctct tcgctcacat tcgtaagcga ggggagtcac gggtgtaatg tgaaaagaca
7501 aaattgatta tctttctttt ctttagtgtc t
//