Typing tool
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Typing tool
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Complete norovirus genomes
| MF140652 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MF140652 7520 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2008/GII.P4-GII.4/Rotterdam/E7800015_p14_d0
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140652
VERSION MF140652.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7520)
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 7520)
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..7520
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2008/GII.P4-
GII.4/Rotterdam/E7800015_p14_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="31-Jan-2008"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23652.1"
/translation="SNDASAAAAANSNNDTAKSSSDKMFSSMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPL
NIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELK
QALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATKKDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSA
PKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQ
RSVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL
KPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHED
PSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23653.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23654.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGRFSTPQPSGALPGRINPRTPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgctgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacaaaa tgttttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcccc ccccgaggga aataccacaa agacccccac gaccacctac tccagaactg
181 gtcaaaaaga tccctcctcc cccgcccaac ggagaggatg aagtagtggt ttcttatagt
241 gccaaagatg gcgtttccgg tttacccgag ctttccaccg tcaggcaacc ggaagaaacc
301 aatacggcct tcagtgtccc tccactcaac cagagggaaa atagagatgc taaggaacca
361 ctgactggaa caattctgga aatgtgggat ggagaaatct accattatgg cctgtatgtt
421 gagcgaggtc ttgtgctggg tgtgcacaaa ccaccagctg ccataagcct cgccaaggtc
481 gaactaacac cactctcctt gttctggaga cctgtgtaca ctccccagta cctcatctct
541 ccagacactc tcaagaaatt acacggagaa acgtttccct acacagcctt tgacaacaat
601 tgctatgcct tttgttgctg ggtcctggat ctaaatgact cgtggctgag taggagaatg
661 atccagagaa caactggctt cttcagaccc taccaagact ggaataggaa acccctcccc
721 actatggatg attccaaatt aaagaaggta gctaacatat tcctgtgcac cctgtcttcg
781 ctattcacca ggcccataaa agacataata ggaaagttaa ggcctctcaa catcatcaac
841 atcctggctt catgtgattg gactttcgca ggcatagtgg agtccttgat actcttggca
901 gagctctttg gagtcttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc
961 ggtgatttcg agttacaagg acctgaggac cttgtagtgg agctcgtccc tgtagtaatg
1021 gggggaattg gtctggtgct aggattcacc aaagagaaga ttggaaaaat gttgtcatct
1081 gctgcgtcca ccttgagagc ttgtaaagat ctcggtgcat acgggctaga gatcctaaag
1141 ttagtcatga agtggttctt cccgaagaaa gaggaggcaa atgaactggc tatggtgaga
1201 tccattgagg atgcagtact ggaccttgag gcaattgaaa acaaccatat gaccaccttg
1261 ctcaaagaca aagacagtct ggcaacctac atgagaaccc ttgacctcga ggaagagaaa
1321 gccagaaaac tctcaaccaa atctgcttca cctgacatcg tgggcacaat caacgccctt
1381 ctggcgagaa tcgccgctgc acgctccctg gtgcaccgag cgaaggagga gctttccagc
1441 agaccaagac ctgtagtctt gatgatatca ggcaaaccag ggatagggaa aacccacctt
1501 gctagggaag tggctaagag aatcgcagcc tccctcacag gagaccagcg tgtaggcctc
1561 atccctcgca atggcgtcga tcactgggat gcgtacaagg gggagagggt cgtcctatgg
1621 gacgactatg gaatgagcaa tcccatccac gacgccctta ggctgcaaga actcgctgac
1681 acttgccccc ttactctaaa ttgtgacagg attgagaata aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcactac taatctggcc aacccagcac cactggatta tgtcaacttt
1801 gaagcgtgct cgaggcgcat cgatttcctt gtgtatgcag aagcccccga ggtcgaaaag
1861 gcgaagcgtg acttcccggg ccaacctgac atgtggaaaa acgctttcag ttctgatttc
1921 tcacacataa aattggcact ggctccacaa ggtggctttg ataagaacgg gaacacccca
1981 cacgggaagg gcgtcatgaa gactctcacc actggctccc tcattgcccg ggcatcaggg
2041 ctgctccatg agagattgga tgagtttgaa ctacagggcc cagctcttac caccttcaac
2101 tttgaccgca acaaagtgct tgccttcagg cagcttgctg ctgaaaacaa atatgggttg
2161 atggacacaa tgaaagttgg gaggcagctc aaggatgtca aaaccatgcc agaacttaaa
2221 caagcactca aaaacatctc aatcaagaag tgccagattg tgtatagtgg ttgcacctac
2281 acacttgagt ctgatggcaa gggcaatgtg aaagttgaca gagttcagag cacctccgtg
2341 cagaccaaca atgagttggc tggcgccctg catcatctga ggtgcgccag aatcaggtac
2401 tatgtcaagt gtgtccagga ggccctgtat tctatcatcc agattgctgg ggctgcattt
2461 gtcactacgc gcattatcaa gcgtgtgaac attcaagact tatggtcaaa gccacaagtg
2521 gaaaacacag aggaggctac caaaaaggac gggtgcccaa aacccaaaga tgatgaggag
2581 ttcgtcattt catctgacga catcaaaact gagggtaaga aagggaagaa caagactggc
2641 cgtggcaaga agcacacagc cttctcaagt aaaggtctca gtgatgaaga gtatgatgag
2701 tacaagagaa ttagagagga aaggaatggc aagtactcca tagaagagta ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ccgaggaaga cttctgtgaa
2821 gaggaggagg ccaagatccg gcaaaggatc ttcagaccaa caaggaaaca acgcaaggaa
2881 gaaagagctt ctctcggttt agtcacaggt tctgaaatta ggaaaagaaa cccagaagac
2941 ttcaagccca aggggaaact atgggctgac gatgacagaa gtgtggacta caatgagaaa
3001 ctcagttttg aggccccacc aagcatttgg tcaaggatag tcaactttgg ttcaggttgg
3061 ggcttctggg tctcccctag cctgttcata acatcaaccc acgtcatacc ccagggcgcg
3121 aaggagttct ttggggtccc catcaaacaa attcaggtac acaagtcagg cgaattctgt
3181 cgcttgaggt tcccaaaacc aatcaggact gatgtgactg gcatgatcct ggaagaaggt
3241 gcgcccgaag gcaccgtggt cacactactc atcaaaaggt ctactggaga actcatgccc
3301 ctagcagcta gaatggggac ccatgcaacc atgaaaattc aagggcgcac tgttggaggt
3361 cagatgggca tgcttctgac aggatccaac gccaaaagca tggatctagg caccacacca
3421 ggtgattgcg gctgtcccta catctacaag agaggaaatg actatgtggt cattggagtc
3481 cacacggctg ccgctcgtgg gggaaacact gtcatatgtg ccacccaggg gggcgagggg
3541 gaagctacac ttgaaggtgg tgacagtaag ggaacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccgaaact tagcaccaaa accaaattct ggagatcatc cacagcacca
3661 ctcccacctg gcacctatga accagcctac cttggtggca aggaccccag agtcaagggt
3721 ggcccttcgt tgcagcaagt catgagggac cagctgaaac catttacaga gcccaggggt
3781 aagccaccaa agccaagtgt gttagaagct gccaagaaaa ccatcatcaa tgtccttgaa
3841 caaacaattg acccacctga gaagtggtcg ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacttcta gcggccatcc gcaccacatg cggaaaaacg actgctggaa cggggagtcc
3961 ttcacaggca agctggcgga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 aacatgaccc cagtctacac aggtgcactt aaggatgaat tagtcaaaac tgacaaaatt
4081 tatggcaaga tcaagaagag gcttctctgg ggctcggatt tagcaaccat gatccggtgc
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcgc actgtgtcac acttcctatc
4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaaaca ttccaggtac
4261 agataccact atgatgctga ttactctcgg tgggattcaa cacaacagag aagcgtgctg
4321 gcagctgctc tagaaatcat ggttaaattc tcctcagaac cacatttggc ccaggtagtc
4381 gcagaagacc ttctttcccc tagcgtggtg gatgtgggtg acttcacaat atcaatcaac
4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcactctc cgaagttaca aatttgtccc cagacatcat acaggctaat
4561 tctctcttct ccttctatgg tgatgatgaa attgttagta cagacataaa attagaccca
4621 gagaagttga cagcaaagct taaggaatat ggattgaagc caacccgccc tgacaaaact
4681 gaaggacctc ttgttatttc tgaagactta gatggtttga ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gctcaatact caggcaaatg
4801 tactggacta ggggccccaa ccatgaagat ccatctgaat caatgattcc acactctcag
4861 agacccatac aattgatgtc cttactggga gaggccgcac tccacggccc aacattctac
4921 agtaaaatca gcaaattagt cattgcagag ctaaaagaag gtggtatgga tttttacgtg
4981 cccaggcaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaacccatc
5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcagcaat gaggttatgg ctttggagcc
5161 cgttgtcggt gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaat aattttgtac aagcccctgg tggagagttc acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaatccct acctatctca
5341 tttggccaga atgtataatg gttacgcggg tggctttgaa gtgcaggtga tcctcgcggg
5401 gaacgcgttc accgccggaa aaattatatt tgcagcagtc ccaccaaatt ttccaactga
5461 aggcctgagt cccagccagg tcactatgtt cccccacata atagtggatg ttaggcaatt
5521 ggaacctgtg ctgatccctt tacctgatgt taggaataac ttctatcact ataatcagtc
5581 aaatgattct accattaaat tgatagcaat gctgtataca ccacttaggg ccaataatgc
5641 tggggaagat gtcttcacag tctcttgtcg agtcctcacg aggccgtccc ctgattttga
5701 ttttatattt ttggtgccac ccacagttga gtcaagaact aaaccattta ctgtcccaat
5761 cttaactgtt gaagaaatga ccaattcaag attccccatt cctttggaaa agttgttcac
5821 gggtcccagc ggtgcctttg ttgtccaacc acaaaatggc aggtgcacga ctgatggcgt
5881 gctcttaggc accacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac
5941 ccacattgct ggttctcgta attacacaat gaacttggca tctctaaatt ggaacaatta
6001 tgacccaaca gaggaaattc cagcccctct gggaactcca gatttcgtgg gaaagatcca
6061 aggtgtgctc actcaaacca caaagggaga tggctcgacc cgtggccata aagctacagt
6121 ttacactggg agtgccccct ttactccaaa gctgggcagt gtccaattca gtactgatac
6181 agaaaatgat tttgaaactc accaaaacac aaaattcacc ccagtcggtg tcatccagga
6241 tggtagcacc acccaccgaa atgaacccca acaatgggtg ctcccaagtt attcaggtag
6301 agatgtccat aatgtacacc tagcccctgc tgtagccccc acttttccgg gtgaacaact
6361 tcttttcttc aggtccacca tgcccggatg cagcgggtat cccaacatgg atttggattg
6421 cctactcccc caggagtggg tgcagcactt ctaccaagag gcagctccag cacaatctga
6481 tgtggcccta ttgagatttg tgaatccaga cacaggtagg gtcctgtttg agtgcaaact
6541 tcataaatca ggctatgtca cagtggctca caccggccag catgatttgg tcatcccccc
6601 caatggctat tttaggtttg attcctgggt taatcaattc tacacacttg cccccatggg
6661 aaatggaacg gggcgtagac gtgctttata atggctggag ctttctttgc tggattggca
6721 tctgatgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggctatcaac
6781 caaaagattg attttgaaaa taacagaaaa ttgcagcaag cttccttcca gtttagcagt
6841 aatctacaac aggcttcctt tcaacatgat aaagagatgc tccaagcaca aattgaggcc
6901 actaaaaagt tgcaacagga aatgatgaaa gtcaaacagg caatgctctt agaaggtgga
6961 ttctctgaaa cagatgcagc ccgtggggca atcaacgccc ccatgacaaa ggctttggac
7021 tggagcggaa caaggtactg ggcccctgat gctaggatta caacatacaa tgcaggtcgc
7081 ttttccaccc ctcaaccttc gggggcactg ccaggaagaa tcaatcccag gactcctacc
7141 cccgctcggg gctcctccag cacatcttct aatgcttcta ctgctacttc tatatattca
7201 aatcaaactg tttcaacgag acttggttct acagctggtt ctggcaccaa tgtctcgagt
7261 ctcccgtcaa ctgcaaggac taggagttgg gttgaggatc aaaacagaaa tttgtcacct
7321 ttcatgaggg gggctcacaa catatcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcctaaagaa gttttggact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgctcacatt cgtaggcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattgattat
//