Typing tool
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Typing tool
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Complete norovirus genomes
| MF140654 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5083
ORF2: 5064..6686
ORF3: 6686..7492
LOCUS MF140654 7554 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2008/GII.P4-GII.4/Rotterdam/E7800023_p14_d109
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140654
VERSION MF140654.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7554)
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 7554)
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..7554
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2008/GII.P4-
GII.4/Rotterdam/E7800023_p14_d109"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="19-May-2008"
/note="genotype: GII.P4-GII.4"
CDS <1..5083
/codon_start=2
/product="ORF1"
/protein_id="ATN23658.1"
/translation="DASAAAAANSNNDTAKSSSDKMFSSMAVTFKRALGARPKQPPPR
EIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELTTVRQPEETNTAF
SVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
TPLSLFWRPVYTPQYLISPDTLKKLQGETFPYTAFDNNCYTFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDESKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNI
INILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKN
ELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREVAKRIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTMPELKQA
LKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGTLHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATKKDGCPKPKDD
EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
KRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL
IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPK
LSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRS
VLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKP
TRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPS
ESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5064..6686
/codon_start=1
/product="ORF2"
/protein_id="ATN23659.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTDNDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6686..7492
/codon_start=1
/product="ORF3"
/protein_id="ATN23660.1"
/translation="MAGAVFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNQQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGRFSTPQPSGALPGRINPRTPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 cgacgcttcc gctgccgctg ctgctaacag caacaacgac accgcaaaat cttcaagtga
61 caaaatgttt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaaaca
121 gccccccccg agggaaatac cacaaagacc cccacgacca cctactccag aactggtcaa
181 aaagatccct cctcccccgc ccaacgggga ggatgaagta gtggtttctt atagtgccaa
241 agatggcgtt tccggtttac ccgagcttac caccgtcagg caaccggaag aaaccaatac
301 ggccttcagt gtccctccac tcaaccagag ggaaaataga gatgctaagg aaccactgac
361 tggaacaatt ctggagatgt gggatggaga gatctaccat tatggcctgt atgttgagcg
421 aggtcttgtg ctgggtgtgc acaaaccacc agctgccata agcctcgcca aggtcgaact
481 aacaccactc tccttgttct ggagacctgt gtacactccc cagtacctca tctctccaga
541 cactctcaag aaattacaag gagaaacgtt tccctacaca gcctttgaca acaattgcta
601 taccttttgt tgctgggtcc tggatctaaa tgactcgtgg ctgagtagga gaatgatcca
661 gagaacaact ggcttcttca gaccctacca agactggaat aggaaacccc tccccactat
721 ggatgaatcc aaattaaaga aggtagctaa catattcctg tgcaccctgt cttcgctatt
781 caccaggccc ataaaagaca taataggaaa gttaaggcct ctcaacatca tcaacatcct
841 ggcttcatgt gattggactt tcgcaggcat agtggagtcc ttgatactct tggcagagct
901 ctttggagtc ttctggacac ccccagatgt gtctgcgatg attgccccct tactcggtga
961 tttcgagtta caaggacctg aggacctcgt agtggagctc gtccctgtag taatgggggg
1021 aattggtctg gtgctaggat tcaccaaaga gaagattgga aaaatgttgt catctgctgc
1081 gtccaccttg agagcttgta aagatctcgg tgcatacggg ctagagatcc taaagttagt
1141 catgaagtgg ttcttcccga agaaagagga gaaaaatgaa ctggctatgg tgagatccat
1201 tgaggatgca gtactggacc ttgaggcaat tgaaaacaac catatgaccg ccttgctcaa
1261 agacaaagac agtctggcaa cctacatgag aacccttgac ctcgaggaag agaaagccag
1321 aaaactctca accaaatctg cttcacctga catcgtgggc acaatcaacg cccttctggc
1381 gagaatcgcc gctgcacgct ccctggtgca ccgagcgaag gaggagcttt ccagcagacc
1441 aagacctgta gtcttgatga tatcaggcaa accagggata gggaaaaccc accttgctag
1501 ggaagtggct aagagaatcg cagcctccct cacaggagac cagcgtgtag gcctcatccc
1561 tcgcaatggc gtcgatcact gggatgcgta caagggggag agggtcgtcc tatgggacga
1621 ctatggaatg agcaatccca tccacgacgc ccttaggctg caagaactcg ctgacacttg
1681 cccccttact ctaaattgtg acaggattga gaataaagga aaggtctttg acagcgatgt
1741 catcattatc actactaatc tggccaaccc agcaccactg gattatgtca actttgaagc
1801 gtgctcgagg cgcatcgatt tccttgtgta tgcagaagcc cccgaggtcg aaaaggcgaa
1861 gcgtgacttc ccgggccaac ctgacatgtg gaaaaacgct ttcagttctg atttctcaca
1921 cataaaattg gcactggctc cacaaggtgg ctttgataag aacgggaaca ccccacacgg
1981 gaagggcgtc atgaagactc tcaccactgg ctccctcatt gcccgggcat cagggctgct
2041 ccatgagaga ttggatgagt ttgaactaca gggcccagct cttaccacct tcaactttga
2101 ccgcaacaaa gtgcttgcct tcaggcagct tgctgctgaa aacaaatatg ggttgatgga
2161 cacaatgaaa gttgggaggc agctcaagga tgtcagaacc atgccagaac ttaaacaagc
2221 actcaaaaac atctcaatca agaagtgcca gattgtgtat agtggttgca cctacacact
2281 tgagtctgat ggcaagggca atgtgaaagt tgacagagtt cagagcacct ccgtgcagac
2341 caacaatgag ttggctggca ccctgcatca tctgaggtgc gccagaatca ggtactacgt
2401 caagtgtgtc caggaggccc tgtattctat catccagatt gctggggctg catttgtcac
2461 tacgcgcatt atcaagcgtg tgaacattca agacttatgg tcaaagccac aggtggaaaa
2521 cacagaggag gctaccaaaa aggacgggtg cccaaaaccc aaagatgatg aggagttcgt
2581 catttcatct gacgacatca aaactgaggg taagaaaggg aagaacaaga ctggccgtgg
2641 caagaagcac acagccttct caagtaaagg tctcagtgat gaagagtatg atgagtacaa
2701 gagaattaga gaggaaagga atggcaagta ctccatagaa gagtaccttc aggacaggga
2761 caaatactat gaggaggtgg ccattgccag ggcgaccgag gaagacttct gtgaagagga
2821 ggaggccaag atccggcaaa ggatcttcag accaacaagg aaacaacgca aggaagaaag
2881 agcttctctc ggtttagtca caggttctga aattaggaaa agaaacccag aagacttcaa
2941 gcccaagggg aaactatggg ctgacgatga cagaagtgtg gactacaatg agaaactcag
3001 ttttgaggcc ccaccaagca tttggtcaag gatagtcaac tttggttcag gttggggctt
3061 ctgggtctcc cctagcctgt tcataacatc aacccacgtc ataccccagg gcgcgaagga
3121 gttctttggg gtccccatca aacaaattca ggtgcacaag tcaggcgaat tctgtcgctt
3181 gaggttccca aaaccaatca ggactgatgt gactggcatg atcctggaag aaggtgcgcc
3241 cgaaggcacc gtggtcacac tactcatcaa aaggtctact ggagaactca tgcccctagc
3301 agccagaatg gggacccatg caaccatgaa aattcaaggg cgcactgttg gaggtcagat
3361 gggcatgctt ctgacaggat ccaacgccaa aagcatggat ctaggcacca caccaggtga
3421 ttgcggctgt ccctacatct acaagagagg aaatgactac gtggtcattg gagtccacac
3481 ggctgccgct cgtgggggaa acactgtcat atgtgccacc caggggggcg agggggaagc
3541 tacacttgaa ggtggtgaca gtaagggaac atactgtggt gcaccaatcc taggcccagg
3601 gagtgccccg aaacttagca ccaaaaccaa attctggaga tcatccacag caccactccc
3661 acctggcacc tatgaaccag cctaccttgg tggcaaggac cccagagtca agggtggccc
3721 ttcgttgcag caagtcatga gggaccagct gaaaccattt actgagccca ggggtaagcc
3781 accaaagcca agtgtgttag aagctgccaa gaaaaccatc atcaatgtcc ttgaacaaac
3841 aattgaccca cctgaaaagt ggtcgttcgc acaagcttgc gcgtcccttg acaagaccac
3901 ttctagcggc catccgcacc atatgcggaa aaacgactgc tggaacgggg agtccttcac
3961 aggcaagctg gcggaccagg cttccaaggc caacctgatg tttgaagaag ggaagaacat
4021 gaccccagtc tacacaggtg cacttaagga tgaattagtc aagactgaca aaatttatgg
4081 caagatcaag aagaggcttc tctggggctc ggatttagca accatgatcc gatgcgctcg
4141 agcattcgga ggcctaatgg atgaactcaa agcgcactgt gtcacacttc ctatcagagt
4201 tggtatgaat atgaatgagg atggccccat catcttcgag aagcattcca ggtacagata
4261 ccactatgat gctgattact ctcggtggga ttcaacacaa cagagaagcg tgctggcagc
4321 tgctctagaa atcatggtta aattctcctc agaaccacat ttggcccagg tagtcgcaga
4381 agaccttctt tcccctagcg tggtggatgt gggtgacttc acaatatcaa tcaacgaggg
4441 tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact ggcttctcac
4501 tctctgtgca ctctctgaag ttacaaattt gtccccagac atcatacagg ctaattctct
4561 cttctccttc tatggtgatg atgaaattgt tagtacagac ataaaattag acccagagaa
4621 gttgacagca aagcttaagg aatatggatt gaagccaacc cgccctgaca aaactgaagg
4681 acctcttgtt atttctgaag acttagatgg tttgactttc ctgcggagga ctgtgacccg
4741 cgacccagct ggttggtttg gaaaactgga gcagagctca atactcaggc aaatgtactg
4801 gactaggggc cccaaccatg aagatccatc tgaatcaatg attccacact ctcagagacc
4861 catacaattg atgtccttac tgggagaggc cgcactccac ggcccaacat tctacagtaa
4921 aatcagcaaa ttagtcattg cagagctaaa agaaggtggt atggattttt acgtgcccag
4981 gcaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg agggcgatcg
5041 caatctggct cccagttttg tgaatgaaga tggcgtcgaa tgacgccaac ccatctgatg
5101 ggtccgcagc caacctcgtc ccagaggtca gcaatgaggt tatggctttg gagcccgttg
5161 ccggtgccgc tattgcggcg cctgtagcgg gccaacaaaa tgtaattgac ccctggatta
5221 gaaataattt tgtacaagcc cctggtggag agttcacagt atcccctaga aacgctccag
5281 gtgaaatact atggagcgcg cccttaggcc ctgatctgaa tccctaccta tctcatttgg
5341 ccagaatgta taatggttac gcgggtggct ttgaagtgca ggtgatcctc gcggggaacg
5401 cgttcaccgc cggaaaaatt atatttgcag cagtcccacc aaattttcca actgaaggcc
5461 tgagtcccag ccaggtcact atgttccccc acataatagt ggatgttagg caattggaac
5521 ctgtgctgat ccctttacct gatgttagga ataacttcta tcactataat cagtcaaatg
5581 attctaccat taaattgata gcaatgctgt atacaccact tagggccaat aatgctgggg
5641 aagatgtctt cacagtctct tgtcgagtcc tcacgaggcc gtcccctgat tttgatttta
5701 tatttttggt gccacccaca gttgagtcaa gaactaaacc atttactgtc ccaatcttaa
5761 ctgttgaaga aatgaccaat tcaagattcc ccattccttt ggaaaagttg ttcacgggtc
5821 ccagcggtgc ctttgttgtc caaccacaaa atggcaggtg cacgactgat ggcgtgctct
5881 taggcaccac ccaactgtct cctgtcaaca tctgcacctt cagaggggat gtcacccaca
5941 ttgctggttc tcgtaattac acaatgaact tggcatctct aaattggaac aattatgacc
6001 caacagagga aattccagcc cctctgggaa ctccagattt cgtggggaag atccaaggtg
6061 tgctcactca aaccacaaag ggagatggct cgacccgtgg ccataaagct acagtttaca
6121 ctgggagtgc cccctttact ccaaagctgg gcagtgtcca attcagtact gatacagaca
6181 atgattttga aactcaccaa aacacaaaat tcaccccagt cggtgtcatc caggatggtg
6241 gcaccaccca ccgaaatgaa ccccaacaat gggtgctccc aagttattca ggtagagata
6301 tccataatgt acacctagcc cctgctgtag cccccacttt tccgggtgaa caacttcttt
6361 tcttcaggtc caccatgccc ggatgcagcg ggtatcccaa catggatttg gattgcctac
6421 tcccccagga gtgggtgcag cacttctacc aagaggcagc tccagcacaa tctgatgtgg
6481 ccctattgag atttgtgaat ccagacacag gtagggtcct gtttgagtgc aaacttcata
6541 aatcaggcta tgtcacagtg gctcacaccg gccagcatga tttggtcatc ccccccaacg
6601 gctattttag gtttgattcc tgggttaatc aattctacac acttgccccc atgggaaatg
6661 gaacggggcg tagacgtgct ttataatggc tggagctgtc tttgctggat tggcatctga
6721 tgtccttggc tctggacttg gttccctaat caatgctggg gctggggcta tcaaccaaaa
6781 gattgatttt gaaaataaca gaaaattgca gcaagcttcc ttccagttta gcagtaatca
6841 acaacaggct tcctttcaac atgataaaga gatgctccaa gcacaaattg aggccactaa
6901 aaagttgcaa caggaaatga tgaaagtcaa acaggcaatg ctcttagaag gtggattctc
6961 tgaaacagat gcagcccgtg gggcaatcaa cgcccccatg acaaaggctt tggactggag
7021 cggaacaagg tactgggccc ctgatgctag gattacaaca tacaatgcag gccgcttttc
7081 cacccctcaa ccttcggggg cactgccagg aagaattaat cccaggactc ctacccccgc
7141 tcggggctcc tccagcacat cttctaatgc ttctactgct acttctatat attcaaatca
7201 aactgtttca acgagacttg gttctacagc tggttctggc actaatgtct cgagtctccc
7261 gtcaactgca aggactagga gttgggttga ggatcaaaac agaaatctgt cacctttcat
7321 gaggggggct cacaacatat cgtttgtcac cccaccatct agcagatcct ctagccaagg
7381 cacagtctca accgtgccta aagaagtttt ggactcctgg actggcgctt tcaacacgcg
7441 caggcagcct ctcttcgctc acattcgtag gcgaggggag tcacgggtgt aatgtgaaaa
7501 gacaaaattg attatctttc cttttcttta gtgtctttta aaaaaaaaat taaa
//