Typing tool
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Typing tool
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Complete norovirus genomes
| MF140664 | GII.4 US95 | |
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| GII.P4 US95 |
ORF1: 1..5085
ORF2: 5066..6685
ORF3: 6685..7494
LOCUS MF140664 7508 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E7800014_p16_d0
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140664
VERSION MF140664.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7508)
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 7508)
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..7508
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2010/GII.P4-
GII.4/Rotterdam/E7800014_p16_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="18-Jun-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5085
/codon_start=1
/product="ORF1"
/protein_id="ATN23688.1"
/translation="NDASAAAVANSNNDTAKSSSDGVFSNMAVTFKRALGARPKQPPP
REIPQRPPRPPTPELVKKIPPPPPNGEDEAVVSYSVKDGISGLPELSTVRQPDETNTA
FCVPPLSLRENKDAKEPLTGTILEMWDGEFYHYGIYVERGLVLGVHKPPAAVSLARIE
LTPLSLFWRPVYTPQYLISPDSLKKLHGESFPYTAFDNNCYAFCCWVLDLNDSWLNRR
CIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKIKPLN
ILNILASCDWTFAGIVESLILLMELFGIFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKDEA
SELEMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSMVHRAKEELSSRPRPVVMMISGRPGIGKTHLAREVAKKIA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARATGLLH
ERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDLKQ
ALKNITIKKCQIVYSGCTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLRCARIR
YYVKCAQEALYSIIQIAGAAFVTTRIAKRMNIQDFWSKPQVEDTGETINKEGCPKPRD
EEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI
RKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGATEFFGVPIKQIQIHKTGEFCRLRFPKPIRNDVTGMILEEGAPEGTVVSL
LVKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGGAP
KLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPP
KPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGTTF
TGKLADQASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHARYKYHYDADYSRWDSTQQR
AVLATALEIMVKFSSEPHLAQVVAEDLLSPSVMDVGDFKITINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLK
PTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDP
SETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5066..6685
/codon_start=1
/product="ORF2"
/protein_id="ATN23689.1"
/translation="MKMASNDANPSDGSTASLVPAVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPNVIIDVRQLEPVLIPLPD
VRNIFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTIEEMTNSRFPIPLEKLYTGPSSAFQVQPQNGRCTTDGVLLGTT
QLSAVSVCSFRGSVTQVGGTHDYTMNLASQNWNNYDPTEEVPAPLGTPDFKGKIQGVL
TQTTRGNGSTRAHKATVSTGAANFTPKLGKVQFHTDTNTDLNANENTKFTPVGVIQES
DNHRDEPQQWVLPDYAGRGTHNVHLAPAVAPTFPGEQLLFFRSTLPGCGGYPNMDLDC
VLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGPHDLVI
PPNGYFRFDSWVNQFYTLAPMGNGAGRKRAL"
CDS 6685..7494
/codon_start=1
/product="ORF3"
/protein_id="ATN23690.1"
/translation="MAGAVIAGLASDVLSSGLGSLINAGAGVINQKVDFENNRKLQQD
SFQFSSNLQQASFQHDKEMLRAQIEATQKLQQGMMEIKQAMLLKGGFSETDAARGAIN
APMTKVLDWNGTRHWAPNARTTTYNAGGFSTPQPSGASPGRTNLRATVPARGSSSSKL
SSTSTATSVYSNQTASTRLGSSAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGALN
TSFVSPPPSRSSSQGTVSTVPKEILDSWTSAFNTHRQPLFAHIRKRGESRV"
ORIGIN
1 aacgacgctt ccgctgccgc tgttgccaac agcaacaacg acactgcaaa atcttcaagt
61 gacggagtgt tttctaacat ggctgtcact tttaaacgag ccctcggggc gcggcctaaa
121 cagccccccc cgagggaaat accacagaga cccccacgac cacctacccc ggaactggtc
181 aaaaagatcc cacctccccc gcccaacggg gaggatgagg cagtggtctc ttatagtgtt
241 aaagatggca tttccggcct gcccgagctc tccactgtca ggcagccgga cgaaaccaac
301 acggccttct gtgtcccccc actcagccta agggagaaca aggatgctaa ggagccactg
361 accggaacaa ttctggagat gtgggatggt gagttctacc actacggcat atatgtggaa
421 cgaggtcttg tacttggcgt gcacaaacca ccggccgccg tcagcctcgc caggatcgag
481 ctaacaccac tctccttgtt ttggaggcct gtgtataccc cccaatatct catctctcca
541 gactccctca agaaactgca cggagaatca ttcccctaca cagcctttga caacaattgt
601 tacgcctttt gttgctgggt cttggaccta aacgactcgt ggctgaatag gagatgtatc
661 cagagaacaa ctggtttctt cagaccttac caagagtgga ataggaaacc cctccccact
721 atggatgact ccaaattaaa gaaggtggct aatatattcc tgtgtgctct atcttcacta
781 ttcaccaggc ccataaaaga cataataggg aagataaagc ctcttaacat cctcaacatc
841 ttggcctcat gcgactggac tttcgcaggc atagtggaat ccttgatact cttgatggag
901 ctctttggaa ttttctggac acccccagac gtgtctgcga tgattgcccc cttactcggc
961 gattacgagt tacaaggacc cgaggacctt gcagtggaac tcgttcctgt ggtgatgggg
1021 ggaattggct tggtgctagg atttaccaag gagaaaattg gaaaaatgtt gtcatctgct
1081 gcatccacct taagagcttg taaagatctt ggtgcatacg ggctggaaat cctaaaatta
1141 gtcatgaagt ggttcttccc aaagaaagat gaagcaagtg agttggagat ggtcaggtcc
1201 atcgaggatg cagtgctgga cctcgaggca attgaaaaca accacatgac caccttgctc
1261 aaagacaaag acagcctggc aacctacatg agaacccttg accttgagga ggagaaagcc
1321 aggaagctct caaccaagtc tgcttcacct gacatcgtgg gcacaatcaa cgcccttttg
1381 gcgagaatcg ctgctgctcg ttccatggtg catcgagcaa aggaggagct ctccagcagg
1441 ccaagacctg ttgtgatgat gatatcaggc agaccaggaa tagggaagac ccatcttgct
1501 agggaagtgg ccaagaaaat cgcagcctcc ctcacaggag accagcgtgt aggcctcatc
1561 ccacgcaacg gcgtcgacca ctgggacgcc tacaaggggg agagggtcgt cctatgggac
1621 gactatggaa tgagcaatcc catccatgat gctctcaggt tacaagaact cgctgacacc
1681 tgccctctca ctctaaactg tgacaggatt gaaaacaaag gaaaggtctt cgacagtgat
1741 gtcataatta tcaccaccaa tttggccaac ccagcaccac tagactatgt caattttgaa
1801 gcatgctcga ggcgcatcga cttcctcgtg tatgcagaag cccctgaagt cgaaaaggcg
1861 aagcgtgact tcccaggtca acctgacatg tggaagaacg ctttcagctc tgatttctca
1921 cacataaaac taacactggc cccacagggt ggtttcgata agaacgggaa caccccacac
1981 gggaagggcg tcatgaagac tctcaccact ggctccctta ttgcccgggc aacagggcta
2041 ctccatgaga ggctagatga gtttgaatta cagggcccag ctctcaccac cttcaatttt
2101 gatcgtaaca aagtgcttgc cttcaggcag cttgctgctg agaacaaata cgggttgatg
2161 gacacaatga gagttggaaa gcagctcaag gatgtcaaaa ccatgccaga tctaaagcaa
2221 gcactcaaga acatcacaat taagaagtgc cagatagtgt acagtggttg cacctacaca
2281 cttgaatctg atggcaaggg caatgtgaaa gttgacagag ttcagagcgc ctccgtacag
2341 accaataacg agctggccgg tgccctacac catctaaggt gcgccaggat caggtattat
2401 gtcaagtgtg ctcaggaggc tttatattcc atcattcaga ttgctggagc tgcatttgtc
2461 accacgcgca ttgctaagcg catgaacata caagacttct ggtcaaaacc acaagtggaa
2521 gacacagggg agaccatcaa caaagaaggg tgcccaaaac ccagagatga agaggagttc
2581 gtcatttcat ctgacgacat caaagctgaa ggcaagaagg ggaagaacaa gactggccgc
2641 ggcaagaagc acacagcctt ctcaagtaaa ggtctcagtg atgaagagta cgacgagtac
2701 aagagaatca gagaagaaag aaatggcaag tactccatag aagagtacct tcaggacaga
2761 gacaaatact atgaggaggt ggccattgcc agggcgaccg aggaggactt ctgtgaggag
2821 gaggaggcca agattcggca aaggattttc aggccaacaa gaaaacaacg caaggaagaa
2881 agggcctctc tcggtttggt cacaggctct gaaatcagga agagaaaccc cgatgacttc
2941 aagcccaagg ggaagctgtg ggccgatgat gacagaagtg tggactacaa tgagagactc
3001 agctttgagg ccccaccaag catttggtcg aggatagtca actttggttc aggttggggc
3061 ttttgggtct ctcccagcct gtttataaca tcaactcacg ttatacccca gggtgcaacg
3121 gagttctttg gagtccccat taagcagatt caaatacaca aaacaggcga attctgtcgc
3181 ttgagattcc caaaaccaat caggaatgat gtgactggca tgatcttaga agaaggtgcg
3241 cccgaaggca ccgtggtctc actactcgtc aaaaggccta ctggagaact tatgccccta
3301 gcagctagga tggggaccca tgcaaccatg aaaattcaag ggcgcactgt tggaggtcag
3361 atgggcatgc ttttgacagg gtccaacgcc aaaaacatgg acctaggcac cacaccaggt
3421 gactgcggct gtccctacat ctacaaaagg ggaaatgact atgtagtcat tggagtccac
3481 acggctgccg ctcgtggggg aaacactgtc atatgtgcca cccaggggag tgagggagag
3541 gctacacttg aaggtggtga tagtaaggga acatactgtg gtgctccaat tctaggccca
3601 gggggtgctc caaaacttag cactaagacc aaattctgga gatcgtccac aacaccactc
3661 ccacctggca cctatgaacc agcctacctc ggtggtaagg accccagagt taagggtggc
3721 ccttcattgc aacaagttat gagggaacag ttgaagccat ttacagagcc cagaggcaaa
3781 ccaccaaagc caagtgtgtt ggaagctgcc aagaaaacca tcattaatgt ccttgaacaa
3841 acaattgatc cacctgagaa atggtcattt gcgcaagctt gtgcgtccct tgacaagacc
3901 acttccagtg gccacccgca ccacatgcgg aaaaatgact gctggaacgg gactactttc
3961 acaggcaagc tggcagacca agcttccaag gccaacctga tgttcgaaga ggggaaaagc
4021 atgaccccgg tctacacagg tgcgcttaag gatgagctgg tcaaaactga caaaatttat
4081 ggcaagatca agaagaggct cctctggggc tcggacttgg caaccatgat ccggtgcgct
4141 cgagcattcg gaggcttgat ggatgaactt aaagcacact gtgtcacact ccctatcaga
4201 gttggtatga atatgaatga ggatggcccc atcatctttg agaagcatgc caggtacaaa
4261 tatcattatg atgctgacta ctctcggtgg gattcaacac aacaaagggc cgtattggca
4321 acagccctag aaatcatggt taaattttcc tcagaaccac atttggctca ggtggttgca
4381 gaagaccttc tttctcctag cgtgatggat gtgggtgact tcaaaataac aatcaatgag
4441 ggtctcccct ctggggtgcc ctgcacctcc caatggaact ccatcgccca ctggcttctc
4501 actctctgtg cactctctga agttacaaat ctgtcccctg atattataca ggctaattct
4561 ctcttctcct tttatggtga tgatgaaatt gttagtacag atataaaatt ggacccagag
4621 aaattgacag caaaactcaa ggaatatggg ttgaaaccaa cccgccctga caaaactgaa
4681 ggaccccttg ttatttctga agacttgaat ggcctaacct tcctgcggag aactgtgact
4741 cgcgacccag ctggttggtt tggaaaattg gagcagagtt caatactcag acaaatgtac
4801 tggactagag gccctaacca tgaagaccca tctgaaacaa tgattccaca ctcccaaaga
4861 cccatacaat tgatgtccct actgggagag gccgcactac acggcccggc attctacagc
4921 aaaattagca aattagttat tgcagagcta aaagaaggtg gcatggattt ttacgtgccc
4981 agacaagagc caatgttcag atggatgaga ttttcagatc tgagcacgtg ggagggcgat
5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg aatgacgcca acccatctga
5101 tgggtctaca gccagcctcg tcccagcggt caacaatgag gtcatggctt tggaacccgt
5161 tgttggtgcc gctattgcgg ctcctgtagc gggccaacaa aatgtaattg acccctggat
5221 tagaaataat tttgtacaag cccctggtgg agagtttaca gtgtccccta gaaacgctcc
5281 gggtgagata ctctggagcg cgccccttgg ccctgatcta aacccatacc tttcccattt
5341 ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg caggtaatcc tcgcggggaa
5401 cgcgttcacc gccggaaaaa tcatatttgc agcagtccca ccgaattttc caactgaagg
5461 tttgagcccc agtcaggtca ctatgttccc caatgtaata atagatgtta ggcaattgga
5521 acctgtgcta atccccttac ctgatgttag gaatattttc tatcattata atcaatcaaa
5581 tgattctact attaaattga tagcaatgtt gtatacacca cttagggcta ataatgctgg
5641 ggatgatgtc ttcacagtct cttgccgagt cctcacgagg ccatcccctg attttgattt
5701 tatattcttg gtgccaccca cagttgaatc aagaactaaa ccattcactg tcccaatctt
5761 aactattgag gaaatgacta attctagatt ccctatccct ctggaaaagt tgtacacggg
5821 ccccagcagt gctttccaag tccaaccaca aaatggcagg tgcacgactg atggcgtgct
5881 cttaggcacc acccagctgt ctgccgtcag cgtctgctcc ttcagaggaa gtgtcaccca
5941 agttggagga acccatgatt acacaatgaa tttggcctct caaaattgga acaactatga
6001 cccaacagag gaagtcccag cccctctggg aactccagat tttaaaggaa aaatccaagg
6061 tgtgctcacc caaacaacaa gggggaatgg ctcgacccgc gcacacaaag ctacagtgag
6121 cactggggct gccaacttca ctccaaaatt gggtaaagtt caattccaca ctgacacaaa
6181 cactgatttg aacgctaacg agaacaccaa attcacccca gtcggcgtca tccaagaaag
6241 tgacaaccac cgagatgaac cccaacaatg ggtgctccca gactacgcag gcagaggtac
6301 ccacaatgtg cacttagccc ctgccgttgc tcccactttt ccaggtgaac aacttctatt
6361 ctttaggtcc actctgcccg ggtgtggcgg gtaccccaac atggatctgg attgcgtgct
6421 cccccaggaa tgggtgcagc acttctacca agaagcagcc ccggcacaat ctgatgtggc
6481 tttactgaga tttgtgaatc cagacacagg tagggttctg tttgagtgta aactccataa
6541 atcaggctat gtcacagtgg cttacactgg tccacatgat ttggttatcc cccccaatgg
6601 ttattttaga tttgattctt gggttaatca gttttacaca cttgccccca tgggaaatgg
6661 agcggggcgt aaacgtgcat tataatggct ggagctgtca ttgctggatt ggcatctgac
6721 gtccttagtt ctggacttgg ttctctgatc aatgctgggg ctggggtcat caaccaaaaa
6781 gttgattttg aaaataacag aaaattacaa caagactcct tccaatttag tagtaacctg
6841 caacaggctt cctttcaaca tgacaaagag atgctccgag ctcaaattga ggccactcaa
6901 aaattgcaac agggtatgat ggaaattaaa caggcaatgc tcctaaaggg tggattctct
6961 gaaacagatg cagcccgtgg ggcaatcaac gcccccatga caaaagttct ggactggaat
7021 ggaacaaggc actgggctcc taatgctaga accacaacat acaatgcagg cggtttttcc
7081 accccccaac catcgggggc atcaccagga agaaccaacc ttagggccac tgtccccgct
7141 cggggctctt cttcttctaa actttctagt acttctactg ctacttctgt atactcaaat
7201 caaacagctt caacgagact tggttcttca gctggttctg gtaccagtgt ctcgagtctc
7261 ccgtcaactg caaggactag gagctgggtt gaggatcaaa acagaaatct gtcacctttc
7321 atgagggggg ctctcaacac atcattcgtc tccccaccac ctagcagatc ctctagccaa
7381 ggcacagtct caaccgtgcc taaagaaatt ttggactcct ggactagtgc tttcaacacg
7441 cacaggcagc ctctcttcgc tcacattcgt aagcgagggg agtcacgggt gtaatgtgaa
7501 aagacaaa
//