Typing tool
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Typing tool
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Complete norovirus genomes
| MF140665 | GII.4 US95 | |
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| GII.P4 US95 |
ORF1: 1..5088
ORF2: 5069..6688
ORF3: 6688..7497
LOCUS MF140665 7508 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E1300288_p16_d101
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140665
VERSION MF140665.1
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/E1300288_p16_d101"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="27-Sep-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23691.1"
/translation="SHDASAAAVANSNNDTAKSSSDGVFSNMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKKIPPPPPNGEDEAVVSYSVKDGISGLPELSTVRQPDETNT
AFCVPPLSLRENKDAKEPLTGTILEMWDGEFYHYGLYVERGLVLGVHKPPAAVSLARI
ELTPLSLFWRPVYTPQYLISPDSLKKLHGESFPYTAFDNNCYAFCCWVLDLNDSWLNR
RCIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANVFLCALSSLFTRPIKDIIGKIKPL
NILNILASCDWTFAGIVESLILLVELFGIFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKDE
ASELEMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSMVHRAKEELSSRPRPVVMMISGRPGIGKTHLAREVAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKRD
FPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARATGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDLK
QALKNITIKKCQIVYSGCTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLRCARI
RYYVKCAQEALYSIIQIAGAAFVTTRIAKRMNIQDFWSKPQVEDTGEAINKEGCPKPR
DEEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSVWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGATEFFGVPIKQIQIHKTGEFCRLRFPKPIRNDVTGMILEEGAPEGTVVS
LLVKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSA
PKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGTT
FTGKLADQASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHARYKYHYDADYSRWDSTQQ
RAVLATALEIMVKFSSEPHLAQVVAEDLLSPSVMDVGDFKITINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHED
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23692.1"
/translation="MKMASNDANPSDGSTASLVPAVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPNVIIDVRQLEPVLIPLPD
VRNIFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTIEEMTNSRFPIPLEKLYTGPSSAFQVQPQNGRCTTDGVLLGTT
QLSAVSVCSFRGSVTQVGGTHDFTMNLASQNWNNYDPTEEIPAPLGTPDFKGKIQGVL
TQTTRGDGSTRAHKATVSTGAANFTPKLGKVQFHTDTTTDLNANENTKFTPVGVIQEG
DNHRNEPQQWVLPDYAGRGTHNVHLAPAVAPTFPGEQLLFFRSTLPGCGGYPNMDLDC
VLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGPHDLVI
PPNGYFRFDSWVNQFYTLAPMGNGAGRKRAL"
CDS 6688..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23693.1"
/translation="MAGAVIAGLASDVLSSGLGSLINAGAGVINQKVDFENNRKLQQD
SFQFSSNLQQASFQHDKEMLRAQIEATQKLQQGMMEIKQAMLLKGGFSETDAARGAIN
APMTKVLDWNGTRHWAPNARTTTYNAGGFSTPQPSGASPGRTNLRATVPTRGSSSSKL
SSTSTATSVYSNQTVSTRLGSSAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGALN
TSFVSPPPSRSSSQGTVSTVPKEILDSWTSAFNTHRQPLFAHIRKRGESRV"
ORIGIN
1 tctcacgacg cttccgctgc cgctgttgcc aacagcaaca acgacactgc aaaatcttca
61 agtgacggag tgttttctaa catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcccc ccccgaggga aataccacag agacccccac gaccacctac cccggaactg
181 gtcaaaaaga tcccacctcc cccgcccaac ggggaggatg aggcagtggt ctcttatagt
241 gttaaagatg gcatttccgg cctgcccgag ctttccactg tcaggcagcc ggacgaaacc
301 aacacggcct tctgtgtccc cccgctcagc ctaagggaga acaaggatgc taaggagcca
361 ctgactggga caattctgga gatgtgggat ggtgagttct accactacgg cttatatgtg
421 gaacgaggtc ttgtacttgg cgtgcacaaa ccaccggccg ccgtcagcct cgccaggatc
481 gagctaacac cactctcctt gttttggagg cctgtgtata ctccccaata tctcatctct
541 ccagactccc tcaagaaact gcacggagaa tcattcccct acacagcctt tgacaacaat
601 tgttacgcct tttgttgctg ggtcttggac ctaaacgact cgtggctgaa taggagatgt
661 atccagagaa caactggttt cttcagacct taccaagagt ggaataggaa acccctcccc
721 actatggatg actccaaatt aaagaaggtg gctaatgtat tcctgtgtgc tctatcttca
781 ctattcacca ggcccataaa agacataata gggaagataa agcctcttaa catcctcaac
841 atcttggcct catgcgactg gactttcgca ggcatagtgg aatccttgat actcttggtg
901 gagctctttg gaattttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc
961 ggcgattacg agttacaagg acccgaggac cttgcagtgg aactcgttcc tgtggtgatg
1021 gggggaattg gcttggtgct aggatttacc aaggagaaaa ttggaaaaat gttgtcatct
1081 gctgcatcca ccttaagagc ttgtaaagat cttggtgcat acgggctgga aatcctaaaa
1141 ttagtcatga agtggttctt cccaaagaaa gatgaagcaa gtgagttgga gatggtcagg
1201 tccatcgagg atgcagtgct ggacctcgag gcaattgaaa acaaccacat gaccaccttg
1261 ctcaaagaca aagacagcct ggcaacctac atgagaaccc ttgaccttga ggaggagaaa
1321 gccaggaagc tctcaaccaa gtctgcttca cctgacatcg tgggcacaat caacgccctt
1381 ttggcgagaa tcgctgctgc tcgttccatg gtgcatcgag caaaggaaga gctctccagc
1441 agaccaagac ctgttgtgat gatgatatca ggcagaccag gaatagggaa gacccacctt
1501 gctagggaag tggccaagaa aatcgcagcc tccctcacag gagaccagcg tgtaggcctc
1561 atcccacgca acggcgtcga ccactgggac gcctacaagg gggagagggt cgtcctatgg
1621 gacgactatg gaatgagcaa tcccatccat gacgctctca ggttacaaga acttgctgac
1681 acctgccctc tcactctaaa ctgtgacagg attgaaaaca aaggaaaggt ctttgacagt
1741 gatgtcataa ttatcaccac caatttggcc aacccagcac cactagacta tgtcaatttt
1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctgg agtcgaaaag
1861 gcgaaacgtg acttcccagg tcaacctgac atgtggaaga acgctttcag ctctgatttc
1921 tcacacataa aactaacact ggccccacag ggtggtttcg ataagaacgg gaacacccca
1981 cacgggaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcaacaggg
2041 ctactccatg agaggctaga tgagtttgaa ttacagggcc cagctctcac caccttcaat
2101 tttgatcgta acaaagtgct tgccttcagg cagcttgctg ctgagaacaa atacgggttg
2161 atggacacaa tgagagttgg aaagcagctc aaggatgtca aaaccatgcc agatctaaag
2221 caagcactca agaacatcac aatcaagaag tgccagatag tgtacagtgg ttgcacctac
2281 acacttgaat ctgatggcaa gggcaatgtg aaagttgaca gagttcagag cgcctccgta
2341 cagaccaata acgagctggc cggtgcccta caccatctaa ggtgcgccag gatcaggtat
2401 tatgtcaagt gtgctcagga ggctttatat tccatcattc agattgctgg agctgcattt
2461 gtcaccacgc gcattgctaa gcgcatgaac atacaagact tctggtcaaa accacaagtg
2521 gaagacacag gggaggccat caacaaagaa gggtgcccaa aacccagaga tgaagaggag
2581 ttcgtcattt catctgacga catcaaagct gaaggcaaga aggggaagaa caagactggc
2641 cgcggcaaga agcacacagc cttctcaagt aaaggtctca gtgatgaaga gtatgatgag
2701 tacaagagaa ttagagaaga aagaaatggc aagtactcca tagaagagta ccttcaggac
2761 agagacaaat actatgagga ggtggccatt gccagggcaa ccgaggagga cttctgtgag
2821 gaggaggagg ccaagattcg gcaaaggatt ttcaggccaa caagaaaaca acgcaaggaa
2881 gaaagggcct ctctcggttt ggtcacaggc tctgaaatca ggaaaagaaa ccccgatgac
2941 ttcaagccca aggggaagct gtgggccgat gatgacagaa gtgtggacta caatgagaga
3001 ctcagctttg aggccccacc aagcgtttgg tcgaggatag tcaactttgg ttcaggttgg
3061 ggcttttggg tctctcccag cctgtttata acatcaactc acgttatacc ccagggtgca
3121 acggagttct ttggagtccc cattaagcag attcaaatac acaaaacagg cgaattctgt
3181 cgcttgagat tcccaaaacc aatcaggaat gatgtgactg gcatgatctt agaagaaggt
3241 gcgcccgaag gcaccgtggt ctcactactc gtcaaaaggc ctactggaga acttatgccc
3301 ctagcagcta ggatggggac ccatgcaacc atgaaaattc aagggcgcac tgttggaggt
3361 cagatgggca tgcttttgac agggtccaac gccaaaaaca tggacctagg caccacacca
3421 ggtgactgcg gctgtcccta catctacaaa aggggaaatg actatgtagt cattggagtc
3481 cacacggctg ccgctcgtgg gggaaacact gtcatatgtg ccacccaggg gagtgaggga
3541 gaggctacac ttgaaggtgg tgatagtaag ggaacatact gtggtgcacc aattctaggc
3601 ccagggagtg ctccaaaact cagcactaag accaaattct ggagatcgtc cacaacacca
3661 ctcccacctg gcacctatga accagcctac ctcggtggta aggaccccag agtcaagggt
3721 ggcccttcat tgcaacaagt tatgagggaa cagttgaagc catttacaga gcccagaggc
3781 aaaccaccaa agccaagtgt gttggaagct gccaagaaaa ccatcattaa tgtccttgaa
3841 caaacaattg atccacctga gaaatggtca tttgcgcaag cttgtgcgtc ccttgacaag
3901 accacttcca gtggccaccc gcaccacatg cggaaaaatg actgctggaa cgggactact
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgttcga agaggggaaa
4021 agcatgaccc cggtctacac aggtgcgctt aaggatgagc tggtcaaaac tgacaaaatt
4081 tatggcaaga tcaagaagag gctcctctgg ggctcggact tggcaaccat gatccggtgc
4141 gctcgagcat tcggaggctt aatggatgaa ctcaaagcac actgtgtcac actccctatc
4201 agagttggta tgaatatgaa tgaggatggc cccatcatct ttgagaagca tgccaggtac
4261 aaatatcatt atgatgctga ttactctcgg tgggattcaa cacaacaaag ggccgtattg
4321 gcaacagccc tagaaatcat ggttaaattt tcctcagaac cacatttggc tcaggtggtt
4381 gcagaagacc ttctttctcc tagcgtgatg gatgtgggtg acttcaaaat aacaatcaat
4441 gagggtctcc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcactctc tgaagttaca aatctgtccc ctgatattat acaggctaat
4561 tctctcttct ccttttatgg tgatgatgaa attgttagta cagatataaa attggaccca
4621 gagaaattga cagcaaaact caaggaatat gggttgaaac caacccgccc tgacaaaact
4681 gaaggacccc ttgttatttc tgaagacttg aatggcctaa ccttcctgcg gagaactgtg
4741 actcgcgacc cagctggttg gtttggaaaa ttggagcaga gttcaatact cagacaaatg
4801 tactggacta gaggccctaa ccatgaagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aattgatgtc cctactggga gaggccgcac tacacggccc ggcattctac
4921 agcaaaatta gcaaattagt tattgcagag ctaaaagaag gtggcatgga tttttacgtg
4981 cccaggcaag agccaatgtt cagatggatg agattttcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaacccatc
5101 tgatgggtct acagccagcc tcgtcccagc ggtcaacaat gaggtcatgg ctttggaacc
5161 cgttgttggt gccgctattg cggctcctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaat aattttgtac aagcccctgg tggagagttt acagtgtccc ctagaaacgc
5281 tccgggtgag atactctgga gcgcgcccct tggccctgat ctaaacccat acctttccca
5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg
5401 gaacgcgttc accgccggaa aaatcatatt tgcagcagtc ccaccaaatt ttccaactga
5461 aggtttgagc cccagtcagg tcactatgtt ccccaatgta ataatagatg ttaggcaatt
5521 ggaacctgtg ctaatcccct tacctgatgt taggaatatt ttctatcatt ataatcaatc
5581 aaatgattct actattaaat tgatagcaat gttgtataca ccacttaggg ctaataatgc
5641 tggggatgat gtcttcacag tctcttgccg agtcctcacg aggccatccc ctgattttga
5701 ttttatattc ttggtgccac ccacagttga atcaagaact aaaccattca ctgtcccaat
5761 cttaactatt gaggaaatga ctaattctag attccctatc cctctggaaa agttgtacac
5821 gggccccagc agtgctttcc aagtccaacc acaaaatggc aggtgcacga ctgatggcgt
5881 gctcttaggc accacccagc tgtctgccgt cagcgtctgc tccttcagag gaagtgtcac
5941 ccaagttgga ggaacccatg atttcacaat gaatttggcc tctcaaaatt ggaacaacta
6001 tgacccaaca gaggaaatcc cagcccctct gggaactcca gattttaaag gaaaaatcca
6061 aggtgtgctc acccaaacaa caagggggga tggctcgacc cgcgcacaca aagccacagt
6121 gagcactggg gctgccaact tcactccaaa attgggtaaa gttcaattcc acactgacac
6181 aaccactgat ttgaacgcta acgagaacac caaattcacc ccagtcggcg tcatccaaga
6241 aggtgacaac caccgaaatg aaccccaaca atgggtgctc ccagactacg caggcagagg
6301 tacccacaat gtgcacttag cccctgccgt tgctcccact tttccaggtg aacaacttct
6361 attctttagg tccactctgc ccgggtgtgg cgggtacccc aacatggatc tggattgcgt
6421 gctcccccag gaatgggtgc agcacttcta ccaagaagca gccccggcac aatctgatgt
6481 ggctttactg agatttgtga atccagacac aggtagggtt ctgtttgagt gcaaacttca
6541 taaatcaggc tatgtcacag tggcttacac tggtccacat gatttggtta tcccccccaa
6601 tggttatttt agatttgatt cttgggttaa tcagttttac acacttgccc ccatgggaaa
6661 tggagcgggg cgcaaacgtg cattataatg gctggagctg tcattgctgg attggcatct
6721 gacgtcctta gttctggact tggttctctg atcaatgctg gggctggggt catcaaccaa
6781 aaagttgatt ttgaaaacaa cagaaaatta caacaagact ccttccaatt tagtagtaac
6841 ctgcaacagg cttcctttca acatgacaaa gagatgctcc gagctcaaat tgaggccact
6901 caaaaattgc aacagggtat gatggaaatt aaacaggcaa tgctcctaaa gggtggattc
6961 tctgaaacag atgcagcccg tggggcaatc aacgccccca tgacaaaagt tctggactgg
7021 aatggaacaa ggcactgggc tcctaatgct agaaccacaa catacaatgc aggcggtttt
7081 tccacccccc agccatcggg ggcatcacca ggaagaacca accttagggc cactgtcccc
7141 actcggggct cttcttcttc taaactttct agtacttcta ctgctacttc tgtatactca
7201 aatcaaacag tttcaacgag acttggttct tcagctggtt ctggtaccag tgtctcgagt
7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaacagaaa tctgtcacct
7321 ttcatgaggg gggctctcaa cacatcattc gtctccccac cacctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcctaaagaa attttggact cctggactag tgctttcaac
7441 acgcacaggc agcctctctt cgctcacatt cgtaagcgag gggagtcacg ggtgtaatgt
7501 gaaaagac
//