Typing tool
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Typing tool
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Complete norovirus genomes
| MF140682 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS MF140682 7538 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2011/GII.P4-GII.4/Rotterdam/E1300320_p6_d18
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140682
VERSION MF140682.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7538)
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 7538)
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..7538
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2011/GII.P4-
GII.4/Rotterdam/E1300320_p6_d18"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="09-Dec-2011"
/note="genotype: GII.P4-GII.4"
CDS <1..5082
/codon_start=1
/product="ORF1"
/protein_id="ATN23742.1"
/translation="DASAAAVANSNNDTAKSSSDKMFSNMAVTLKRALGARPKQPPPR
EISQGPPRPTTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTAF
SVPPLNQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
TPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGRLRPLNI
INILASCDWTFAGIVESLILLAELFGVFWTPPDVSALIAPLLGDFELQGPEDLVVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELKQA
LKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEESTNKDGCPKPKDN
EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSVWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPVKQIQVHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVTLL
IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPK
LSTKTKFWRSSTAPLPPCTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRA
VLATALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKP
TRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPS
ESMIPHSQRPIQLMSLLGEAALHGPTFYNKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5063..6685
/codon_start=1
/product="ORF2"
/protein_id="ATN23743.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGNGSTRGHKATVYTGSAPFTPKLGSVQFSTDTEDDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6685..7491
/codon_start=1
/product="ORF3"
/protein_id="ATN23744.1"
/translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRANPRTPTPVRGSPNTSS
NASTATSIYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gacgcttccg ctgccgctgt tgctaacagc aacaacgaca ccgcaaaatc ttcaagtgac
61 aaaatgtttt ctaacatggc tgtcactctc aaacgagccc tcggggcgcg gcctaagcag
121 ccccccccga gggaaatatc acaaggaccc ccacgaccaa ctactccaga actggtcaaa
181 aagatccctc cccccccgcc caacggagag gacgaagtag tggtttctta tagtgccaaa
241 gatggtgtct ccggtttgcc tgagctttcc accgtcaggc aaccggaaga aaccaatacg
301 gctttcagtg tccctcccct caatcagagg gagaataagg atgctaagga accactgact
361 ggaacaattc tggaaatgtg ggatggagaa atctaccatt atggcctgta tgttgagcga
421 ggtcttgtgc tgggtgtgca caaaccacca gccgccatca gcctcgccaa ggtcgaacta
481 acaccactct ccttgttctg gaggcctgtg tacactcctc agtacctcat ctctccagac
541 actctcaaga aattacacgg agaaacattt ccctacacag ccttcgacaa caattgctat
601 gccttctgtt gctgggtcct ggatctaaac gactcgtggc tgagtaggag aatgatccag
661 agaacaactg gcttcttcag accctaccaa gattggaata ggaaacccct ccccactatg
721 gatgattcca aattaaagaa ggtagctaac atattcctgt gcaccctgtc ttcgctattc
781 accaggccca taaaagacat aatagggagg ctaaggcctc tcaacatcat caacatcctg
841 gcttcatgtg attggacttt cgcaggcata gtggagtcct tgatactctt ggcagagctc
901 tttggagtct tctggacacc cccagatgtg tctgcgttga ttgccccctt actcggtgat
961 ttcgagttac aagggcctga ggaccttgta gtggagctcg ttcctgtagt aatgggggga
1021 attggtttgg tgctaggatt caccaaagag aagattggaa aaatgttatc atctgctgca
1081 tctaccttaa gagcttgtaa agatcttggt gcgtatgggc tagagatcct aaagttagtc
1141 atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac tggctatggt gagatccatc
1201 gaggatgcag tgctagacct tgaggcaatt gaaaacaacc atatgaccac cttgctcaaa
1261 gacaaagaca gcctggcaac ctatatgaga acccttgacc tcgaggaaga gaaagccaga
1321 aaactctcaa ccaagtctgc ttcacctgac atcgtgggca caatcaacgc ccttctggcg
1381 agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg aggagctttc tagcagaccg
1441 agacctgtag tcttgatgat atcaggcaga ccaggaatag ggaagaccca ccttgctagg
1501 gaagtggcta agagaatcgc agcctccctc acaggagacc agcgcgtagg cctcatccca
1561 cgcaatggcg tcgaccactg ggatgcgtac aagggggaga gggtcgtcct atgggacgac
1621 tatggaatga gcaatcccat ccacgacgct ctcaggctgc aagaactcgc tgacacttgc
1681 cccctcacac taaactgcga caggattgag aataaaggaa aggtctttga cagcgatgtc
1741 atcattatca ctactaacct ggccaaccca gcaccactgg actatgtcaa ctttgaagcg
1801 tgctcgaggc gcattgattt cctcgtgtat gcagaagccc ccgaggttga aaaggcgaag
1861 cgtgacttcc caggccaacc tgacatgtgg aaaaacgctt ttagtcctga tttctcacac
1921 ataaaattgg cactggctcc acaaggtggc tttgataaga acgggaacac cccacatggg
1981 aagggcgtca tgaagactct caccactggc tccctcattg cccgggcatc agggctgctc
2041 catgagagat tggatgagtt tgaactacag ggcccagctc tcaccacctt caactttgac
2101 cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa ataaatacgg gttgatggac
2161 acaatgaaag ttgggaggca gctcaaggat gtcaaaacca tgccagaact taaacaagca
2221 ctcaagaaca tctcaatcaa gaagtgccag attgtgtata gtggttgcac ctacacactt
2281 gagtctgatg gcaagggcaa tgtgaaagtt gacagagttc agagcacctc cgttcagacc
2341 aacaatgagc tggctggcgc cctgcaccac ctgaggtgcg ccagaatcag gtactacgtc
2401 aagtgtgttc aggaggccct gtattctatc atccagattg ctggggctgc gtttgtcacc
2461 acgcgcatca tcaagcgtgt gaacattcaa gacttatggt ccaagccaca agtggaaaac
2521 acagaggagt ccaccaacaa ggacgggtgc ccgaaaccca aagataatga ggagttcgtc
2581 atttcatctg acgacattaa aactgagggt aagaaaggga agaacaagac aggccgtggc
2641 aagaagcaca cagccttctc aagtaaaggt ctcagtgatg aagagtatga tgagtacaag
2701 agaattagag aggaaaggaa tggtaagtac tccatagaag agtaccttca ggacagagac
2761 aaatactatg aggaggtggc tattgccagg gcgaccgagg aagacttctg tgaagaggag
2821 gaggccaaga tccggcaaag gattttcagg ccaacaagga aacaacgcaa ggaagaaaga
2881 gcttctctcg gtttagtcac aggttctgaa attaggaaaa ggaacccgga cgacttcaag
2941 cctaagggga aactatgggc tgacgatgac agaagtgtgg actacaatga aaaactcagt
3001 tttgaggccc caccaagcgt ctggtcaagg atagtcaact ttggctcagg ttggggcttc
3061 tgggtctccc ccagcctgtt tataacatca acccacgtca taccccaggg cgcaaaggag
3121 ttctttggag tccccgtcaa acaaattcag gtacacaagt caggcgagtt ctgtcgcttg
3181 aggttcccaa ggccaatcag gactgatgtg actggcatga tcctggaaga aggcgcgccc
3241 gaaggcaccg tggtcacact actcatcaaa aggtctactg gagaactcat gcccttagca
3301 gctagaatgg ggacccatgc aaccatgaaa attcaagggc gcactgttgg aggtcagatg
3361 ggcatgcttc tgacaggatc caacgccaaa agcatggatc taggcaccac accaggtgat
3421 tgcggctgtc cctacatcta caagagagga aatgactatg tggtcattgg agtccacacg
3481 gctgccgctc gtgggggaaa cactgtcata tgtgccaccc aggggggtga gggggaagct
3541 acacttgaag gcggtgacag taagggaaca tactgtggcg caccaatcct aggcccaggg
3601 agcgccccaa aacttagcac caaaaccaaa ttctggagat catccacagc accactccca
3661 ccttgcacct atgaaccagc ctaccttggt ggcaaggacc ccagggtcaa gggtggcccc
3721 tcgttgcagc aagttatgag ggaccagctg aaaccattta cagagcctag gggtaagcca
3781 ccaaaaccaa gtgtgttaga ggctgccaag aaaaccatca tcaatgtcct tgaacaaaca
3841 attgacccac ctgagaagtg gtcgttcgca caagcttgcg cgtcccttga caagaccact
3901 tctagcggcc atccacacca catgcggaaa aacgactgct ggaacgggga atctttcaca
3961 ggcaagctgg cggaccaggc ttccaaggcc aacctgatgt ttgaagaagg gaagaacatg
4021 actccagtct acacaggtgc acttaaggat gaattagtca aaactgacaa aatttatggt
4081 aagatcaaga agaggttact ctggggctcg gatttggcaa ccatgatccg gtgtgctcga
4141 gcattcggag gcctaatgga tgaactcaaa gcacactgtg tcacactccc tatcagagtt
4201 ggtatgaata tgaatgagga tggccccatc atcttcgaga agcattccag gtacagatac
4261 cactatgatg ctgattactc tcggtgggat tcaacacaac agagagccgt gctggcaact
4321 gctctagaaa tcatggttaa attctcctca gaaccacatt tggctcaggt agtagcagaa
4381 gaccttcttt ctcccagcgt ggtggacgtg ggggacttca caatatcaat caacgagggt
4441 cttccctctg gggtgccctg cacctcccaa tggaactcca tcgcccactg gcttctcact
4501 ctctgtgcac tctctgaagt tacaaatttg tccccagaca tcatacaggc taattctctc
4561 ttctccttct atggtgatga tgaaattgtt agtacagaca taaaattaga cccagagaag
4621 ttgacagcaa agcttaagga atacgggttg aaaccaaccc gccctgataa aactgaagga
4681 cctcttgtta tttctgaaga cttagatggc ttgaccttcc tgcggagaac tgtgacccgc
4741 gacccagcag gttggtttgg aaaactggag cagagctcaa tactcaggca aatgtactgg
4801 actaggggcc ctaaccatga agatccatct gaatcaatga ttccacactc tcaaagaccc
4861 atacaattga tgtccttact gggagaggcc gcactccacg gcccaacatt ctacaataaa
4921 atcagcaaat tagtcattgc agagttaaaa gaaggtggta tggattttta cgtgcccagg
4981 caagagccaa tgttcagatg gatgagattc tcagatctga gcacgtggga gggcgatcgc
5041 aatctggctc ccagttttgt gaatgaagat ggcgtcgaat gacgccaacc catctgatgg
5101 gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt atggctttgg agcccgttgt
5161 cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5221 aaataatttt gtacaagccc ctggtggaga gttcacagta tcccctagaa acgctccagg
5281 tgaaatacta tggagcgctc ccttaggccc tgatctgaat ccctacctat ctcatttggc
5341 cagaatgtat aatggttatg caggtggttt tgaagtgcag gtaatcctcg cggggaacgc
5401 gttcaccgcc ggaaaaatca tatttgcagc agtcccacca aatttcccga ctgaaggctt
5461 gagtcccagc caggtcacta tgttccccca cataatagtg gatgttaggc aattggaacc
5521 tgtgttgatc cccttacctg atgttaggaa taacttctat cattataatc aatcaaatga
5581 ttctaccatt aaattgatag caatgctgta tacaccactt agggctaata atgctgggga
5641 agatgtcttc acagtctctt gtcgagtcct cacgaggcca tcccctgatt ttgattttat
5701 atttttggtg ccacctacag ttgagtcaag aactaaacca tttactgtcc caatcttgac
5761 tgttgaggaa atgaccaatt caagattccc cattcctttg gaaaagttgt tcacgggtcc
5821 cagcagtgcc tttgttgttc aaccacaaaa tggcagatgc acgactgatg gcgtgctctt
5881 aggcaccacc caactgtctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat
5941 tgcaggttct cgtaattaca caatgaattt ggcttctcta aattggaaca attatgaccc
6001 aacagaagaa attccagccc ctctaggaac tccagatttc gtgggaaaga ttcaaggtgt
6061 gctcactcaa accacaaagg gaaatggttc gacccgtggc cataaagcta cagtttacac
6121 tgggagtgcc ccctttactc caaagctggg cagtgttcaa ttcagtactg atacagaaga
6181 tgattttgaa actcaccaaa acacaaaatt taccccagtc ggtgtcatcc aggatggtgg
6241 caccacccac cgaaatgaac cccaacaatg ggtgctccca agttattcag gtagagatgt
6301 ccctaatgta cacctagccc ctgctgtagc ccccactttc ccgggtgaac aacttctttt
6361 ctttaggtct actatgcccg gatgcagcgg gtatcccaac atggatttgg attgcctact
6421 cccccaggag tgggtgcagc acttctacca agaggcagct ccagcacaat ctgatgtggc
6481 tctactgaga tttgtgaatc cagacacggg tagggttttg tttgagtgca agcttcataa
6541 atcaggctat gtcacagtgg ctcacaccgg ccagcatgat ttggtcatcc cccccaatgg
6601 ttattttagg tttgattcct gggttaatca attctacaca cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgctt tataatggct ggagctttct ttgctgggtt ggcatctgat
6721 gtccttagct ctggacttgg ttccctaatc aatgctgggg ctggggccat caaccaaaag
6781 attgattttg aaaacaacag aaaattgcag caagcttcct tccagttcag cagtaatcta
6841 caacaggctt cctttcaaca tgataaagaa atgctccaag cacaaattga ggccaccaaa
6901 aagttgcaac aggaaatgat gaaagtcaaa caggcagtgc tcttagaagg tgggttctct
6961 gaaacagatg cagcccgtgg ggcaatcaac gcccctatga caaaggctct ggactggagc
7021 ggaacaaggt actgggcccc tgatgctagg actacaacat acaacgcagg ccgtttttcc
7081 acccctcaac cttcgggggt actgccagga agagccaatc ccaggactcc tacccccgtt
7141 cggggctccc ccaatacatc ttctaatgct tctactgcta cttctatata ctcaaatcaa
7201 actgtttcaa cgagacttgg ttctacagct ggttctggta ccagtgtctc gagtctcccg
7261 tcaactgcaa ggactaggag ttgggttgag gatcaaaaca gaaacttgtc acctttcatg
7321 aggggggctc acaacatatc gtttgtcacc ccaccatcta gcagatcctc cagccaaggc
7381 acagtctcaa ccgtgcctaa agaagttttg gactcctgga ctggcgcttt caacacgcgc
7441 aggcagcctc tcttcgctca cattcgtagg cgaggggagt cacgggtgta atgtgaaaag
7501 acaaaattga ttatctttcc ctttctttag tgtctttt
//