Typing tool
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Typing tool
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Complete norovirus genomes
| MF140666 | GII.4 US95 | |
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| GII.P4 US95 |
ORF1: 1..5068
ORF2: 5049..6668
ORF3: 6668..7477
LOCUS MF140666 7518 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2011/GII.P4-GII.4/Rotterdam/E1300289_p16_d202
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140666
VERSION MF140666.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7518)
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 7518)
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..7518
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2011/GII.P4-
GII.4/Rotterdam/E1300289_p16_d202"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="06-Jan-2011"
/note="genotype: GII.P4-GII.4"
CDS <1..5068
/codon_start=2
/product="ORF1"
/protein_id="ATN23694.1"
/translation="AVANSNNDTAKSSSDGVFSNMAVTFKRALGARPKQPPPREIPQR
PPRPPTPELVKKIPPPPPNGEDEAVVSYSVKDGISGLPELSTVRQPDENNTAFCVPPL
SLRENKDAKEPLTGTILEMWDGEFYHYGLYVERGLVLGVHKPPAAVSLARIELTPLSL
FWRPVYTPQYLISPDSLKKLHGESFPYTAFDNNCYAFCCWVLDLNDSWLNRRCIQRTT
GFFRPYQEWNRKPLPTMDDSKLKKVANVFLCALSSLFTRPIKDIIGKIKPLNILNILA
SCDWTFAGIVESLILLVELFGIFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMG
GIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKDEASELEMV
RSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTI
NALLARIAAARSMVHRAKEELSSRPRPVVMMISGRPGIGKTHLAREVAKKIAASLTGD
QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIEN
KGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKRDFPGQPDM
WKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARATGLLHERLDEF
ELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDLKQALKNIT
IKKCQIVYSGCTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLRCARIRYYVKCA
QEALYSIIQIAGAAFVTTRIAKRMNIQDFWSKPQVEDTGEAINKEGCPKPRDEEEFVI
SSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR
DKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPD
DFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIP
QGATEFFGVPIKQIQIHKTGEFCRLRFPKPIRNDVTGMILEEGAPEGTVVSLLVKRPT
GELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGDCGCPYIYKRGN
DYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKT
KFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLE
AAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGTTFTGKLAD
QASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFG
GLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHARYKYHYDADYSRWDSTQQRAVLATA
LEIMVKFSSEPHLAQVVAEDLLSPSVMDVGDFKITINEGLPSGVPCTSQWNSIAHWLL
TLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDK
TEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIP
HSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDL
STWEGDRNLAPSFVNEDGVE"
CDS 5049..6668
/codon_start=1
/product="ORF2"
/protein_id="ATN23695.1"
/translation="MKMASNDANPSDGSTASLVPAVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPNVIIDVRQLEPVLIPLPD
VRNIFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTIEEMTNSRFPIPLEKLYTGPSSAFQVQPQNGRCTTDGVLLGTT
QLSAVSVCSFRGSVTQVGGTHDYTMNLASQNWNNYDPTEEIPAPLGTPDFKGKIQGVL
TQTTRGSGSTRAHKATVSTGAADFTPKLGKVQFHTDTNNDLDANENTKFTPVGIIQEG
DNHRNEPQQWVLPDYAGRGTHNVHLAPAVAPTFPGEQLLFFRSTLPGCGGYPNMDLDC
VLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGPHDLVI
PPNGYFRFDSWVNQFYTLAPMGNGTGRKRAL"
CDS 6668..7477
/codon_start=1
/product="ORF3"
/protein_id="ATN23696.1"
/translation="MAGAVIAGLASDVLSSGLGSLINAGAGVINQKVDFENNRKLQQD
SFQFSSNLQQASFQHDKEMLQAQIEATQKLQQGMMEIKQAMLLKGGFSETDAARGAIN
APMTKVLDWNGTRYWAPNARTTTYNAGGFSTPQPSGASPGRTNLRATVPTRGSSSSKL
SSTSTATSVYSNQTVSTRLGSSAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGALN
TSFVSPPPSRSSSQGTVSTVPKEILDSWTSAFNTHRQPLFAHIRKQGESRV"
ORIGIN
1 cgctgttgcc aacagcaaca acgacactgc aaaatcttca agtgacggag tgttttctaa
61 catggctgtc acttttaaac gagccctcgg ggcgcggcct aaacagcccc ccccgaggga
121 aataccacag agacccccac gaccacctac cccggaactg gtcaaaaaga tcccacctcc
181 cccgcccaac ggggaggatg aggcagtggt ctcttatagt gttaaagatg gcatttccgg
241 cctgcccgag ctttccactg tcaggcagcc ggacgaaaac aacacggcct tctgtgtccc
301 cccgctcagc ctaagggaga acaaggatgc taaggagcca ctgaccggga caattctgga
361 gatgtgggat ggtgagttct accactacgg cttatatgtg gaacgaggtc ttgtacttgg
421 cgtgcataaa ccaccggccg ccgtcagcct cgccaggatc gagctaacac cactctcctt
481 gttttggagg cctgtgtata ctccccaata tctcatctct ccagactccc tcaagaaact
541 gcacggagaa tcattcccct acacagcctt tgacaacaat tgttacgcct tttgttgctg
601 ggtcttggac ctaaacgact cgtggctgaa taggagatgt atccagagaa caactggttt
661 cttcagacct taccaagagt ggaataggaa acccctcccc actatggatg actccaaatt
721 aaagaaggtg gctaatgtat tcctgtgtgc tctatcttca ctattcacca ggcccataaa
781 agacataata gggaagataa agcctcttaa catcctcaac atcttggcct catgcgactg
841 gactttcgca ggcatagtgg aatccttgat actcttggtg gagctctttg gaattttctg
901 gacaccccca gatgtgtctg cgatgattgc ccccttactc ggcgattacg agttacaagg
961 acccgaggac cttgcagtgg aactcgttcc tgtggtgatg gggggaattg gcttggtgct
1021 aggatttacc aaggagaaaa ttggaaaaat gttgtcatct gctgcatcca ccttaagagc
1081 ttgtaaagat cttggtgcat acgggttgga aatcctaaaa ttagtcatga agtggttctt
1141 cccaaagaaa gatgaagcaa gtgagttgga gatggtcagg tccatcgagg atgcagtgct
1201 ggacctcgag gcgattgaaa acaaccacat gaccaccttg ctcaaagaca aagacagcct
1261 ggcaacctac atgagaaccc ttgaccttga ggaggagaaa gccaggaagc tctcaaccaa
1321 gtctgcttca cctgacatcg tgggcacaat caacgccctt ttggcgagaa tcgctgctgc
1381 tcgttccatg gtgcatcgag caaaggaaga gctctccagc agaccaagac ctgttgtgat
1441 gatgatatca ggcagaccag gaatagggaa gacccacctt gctagggaag tggccaagaa
1501 gatcgcagcc tccctcacag gagaccagcg tgtaggcctc atcccacgca acggcgtcga
1561 ccactgggac gcctacaagg gggagagggt cgtcctatgg gacgactatg gaatgagcaa
1621 tcccatccat gacgctctca ggttacaaga acttgctgac acctgccctc tcactctaaa
1681 ctgtgacagg attgaaaaca aaggaaaagt ctttgacagt gatgtcataa ttatcaccac
1741 caatttggcc aacccagcac cactagacta tgtcaatttt gaagcatgct cgaggcgcat
1801 cgacttcctc gtgtatgcag aagcccctgg agtcgaaaag gcgaagcgtg acttcccagg
1861 tcaacctgac atgtggaaga acgctttcag ctctgatttc tcacacataa aactaacact
1921 ggccccacag ggtggtttcg ataagaacgg gaacacccca cacgggaagg gcgtcatgaa
1981 gactctcacc actggctccc ttatcgcccg ggcaacaggg ctactccatg agaggctaga
2041 tgagtttgaa ttacagggcc cagctctcac caccttcaat tttgatcgca acaaagtgct
2101 tgccttcagg cagcttgctg ctgagaacaa atacgggttg atggacacaa tgagagttgg
2161 aaaacagctc aaggatgtca aaaccatgcc agatctaaag caagcactca agaacatcac
2221 aatcaagaag tgccagatag tgtacagtgg ttgcacctac acacttgaat ctgatggcaa
2281 gggcaatgtg aaagttgaca gagttcagag cgcctccgta cagaccaata atgagctggc
2341 cggcgcccta caccatctaa ggtgcgccag gatcaggtat tatgtcaagt gtgctcagga
2401 ggctctatat tccatcattc agattgctgg agctgcattt gtcaccacgc gcattgctaa
2461 gcgcatgaat atacaagact tctggtcaaa accacaagtg gaagacacag gggaggccat
2521 caacaaagaa gggtgcccaa aacccagaga tgaagaggag ttcgtcattt catctgacga
2581 catcaaagct gaaggcaaga aggggaaaaa caagactggc cgcggcaaga agcacacagc
2641 cttctcaagt aaaggtctca gtgatgaaga gtacgacgag tacaagagaa tcagagaaga
2701 aagaaatggc aagtactcca tagaagagta ccttcaggac agagacaaat actatgagga
2761 ggtggccatt gccagggcaa ccgaggagga cttctgtgag gaggaggagg ccaagattcg
2821 gcaaaggatt ttcaggccaa caagaaaaca acgcaaggaa gaaagggcct ctctcggttt
2881 ggtcacaggc tctgaaatca ggaagagaaa ccccgatgac ttcaagccca aggggaagct
2941 gtgggccgat gatgacagaa gtgtggacta caatgagaga ctcagctttg aggccccacc
3001 aagcatttgg tcgaggatag tcaactttgg ttcaggttgg ggcttttggg tctctcccag
3061 cctgtttata acatcaactc acgttatacc ccagggtgca acggagttct ttggagtccc
3121 cattaagcag attcaaatac acaaaacagg cgaattctgt cgcttgagat tcccaaaacc
3181 aatcaggaat gatgtgactg gcatgatctt agaagaaggt gcgcccgaag gcaccgtggt
3241 ctcactactc gtcaaaaggc ctactggaga acttatgccc ctagcagcta ggatggggac
3301 ccatgcaacc atgaaaattc aagggcgcac tgttggaggt cagatgggca tgcttttgac
3361 agggtccaat gccaaaaaca tggacctagg caccacacca ggtgactgcg gctgtcccta
3421 catctacaaa aggggaaatg actatgtagt cattggagtc cacacggctg ccgctcgtgg
3481 gggaaacact gtcatatgtg ccacccaggg gagtgaggga gaggctacac ttgaaggtgg
3541 tgatagtaag ggaacatact gtggtgcacc aattctaggc ccagggagtg ctccaaaact
3601 cagcactaag accaaattct ggagatcgtc cacaacacca ctcccacctg gcacctatga
3661 accagcctac ctcggtggta aggaccccag agttaagggt ggcccttcat tgcaacaagt
3721 tatgagggaa cagttgaagc catttacaga gcccagaggc aaaccaccaa agccaagtgt
3781 gttggaagct gccaagaaaa ccatcattaa tgtccttgaa caaacaattg atccacctga
3841 gaaatggtca tttgcgcaag cttgtgcgtc ccttgacaag accacttcca gtggtcaccc
3901 gcaccacatg cggaaaaatg actgctggaa cgggactact ttcacaggca agctggcaga
3961 ccaggcttcc aaggccaacc tgatgttcga agaggggaaa agcatgaccc cggtctacac
4021 aggtgcgctt aaggatgagc tggtcaaaac tgacaaaatt tatggcaaga tcaagaagag
4081 gctcctctgg ggctcggact tggcaaccat gatccggtgc gctcgagcat tcggaggctt
4141 aatggatgaa ctcaaagcac actgtgtcac actccctatc agagttggta tgaatatgaa
4201 tgaggatggc cccatcatct ttgagaagca tgccaggtac aaataccatt atgatgctga
4261 ttactctcgg tgggattcaa cacaacaaag ggccgtattg gcaacagccc tagaaatcat
4321 ggttaaattt tcctcagaac cacatttggc tcaggtggtt gcagaagacc ttctttctcc
4381 tagcgtgatg gatgtgggtg acttcaaaat aacaatcaat gagggtctcc cctctggggt
4441 gccctgcacc tcccaatgga attccatcgc ccactggctt ctcactctct gtgcactctc
4501 tgaagttaca aatctgtccc ctgacattat acaggctaat tctctcttct ccttttatgg
4561 tgatgatgaa attgttagta cagatataaa attggaccca gagaaattga cagcaaaact
4621 caaggaatat gggttgaaac caacccgccc tgacaaaact gaaggacccc ttgttatttc
4681 tgaagacttg aatggcctaa ccttcctgcg gagaactgtg actcgcgacc cagctggttg
4741 gtttggaaaa ttggagcaga gttcaatact cagacaaatg tactggacta gaggccctaa
4801 ccatgaagac ccatctgaaa caatgattcc acactcccaa agacccatac aattgatgtc
4861 cctactggga gaggccgcac tacacggccc ggcattctac agcaaaatta gcaaattagt
4921 tattgcagag ctaaaagaag gtggcatgga tttttacgtg cccagacaag agccgatgtt
4981 cagatggatg agattctcag atctgagcac gtgggaaggc gatcgcaatc tggctcccag
5041 ttttgtgaat gaagatggcg tcgaatgacg ccaacccatc tgatgggtct acagccagcc
5101 tcgtcccagc ggtcaacaat gaggtcatgg ctttggaacc cgttgttggt gccgctattg
5161 cggctcctgt agcgggccaa caaaatgtaa ttgacccctg gattagaaat aattttgtac
5221 aagcccctgg tggagagttt acagtgtccc ctagaaacgc tccgggtgag atactctgga
5281 gcgcgcccct tggccctgat ctaaacccat acctttccca tttggccaga atgtacaatg
5341 gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg gaacgcgttc accgccggaa
5401 aaatcatatt tgcagcagtc ccaccaaatt ttccaactga aggtttgagc cccagtcagg
5461 tcactatgtt ccccaatgta ataatagatg ttaggcaatt ggaacctgtg ctaatcccct
5521 tacctgatgt taggaatatt ttctatcatt ataatcaatc aaatgattct actattaaat
5581 tgatagcaat gttgtataca ccacttaggg ctaataatgc tggggatgat gtcttcacag
5641 tctcttgccg agtcctcacg aggccatccc ctgattttga ttttatattc ttggtgccac
5701 ccacagttga atcaagaact aaaccattca ctgtcccaat cttaactatt gaggaaatga
5761 ccaattctag attccctatc cctctggaaa agttgtacac gggccccagc agtgctttcc
5821 aagtccaacc acaaaatggc aggtgcacga ctgatggcgt gctcttaggc accacccagc
5881 tgtctgccgt cagcgtctgc tccttcagag gaagtgtcac ccaagttgga ggaacccatg
5941 attacacaat gaatttggcc tctcaaaatt ggaacaacta tgacccaaca gaggaaatcc
6001 cagcccctct gggaactcca gactttaaag gaaaaatcca aggtgtgctc acccaaacaa
6061 cgagggggag tggctcgacc cgcgcacaca aagctacagt gagcactggg gctgccgact
6121 tcactccaaa attgggtaaa gttcaattcc acactgacac aaacaatgat ttggacgcta
6181 acgaaaacac caaattcacc ccagtcggca tcatccaaga aggtgacaac caccgaaatg
6241 aaccccaaca atgggtgctc ccagactacg caggcagagg tacccacaat gtgcacttag
6301 cccctgccgt tgctcccact tttccaggtg aacaacttct attctttagg tccactctgc
6361 ccgggtgtgg cgggtacccc aacatggatc tggattgcgt gctcccccag gaatgggtgc
6421 agcacttcta ccaagaagca gccccggcac aatctgatgt ggctttactg aggtttgtga
6481 atccagacac aggtagggtt ctgtttgagt gtaaactcca taaatcaggc tatgtcacag
6541 tggcttacac tggtccacat gatttggtta tcccccccaa tggttatttt agatttgatt
6601 cttgggttaa tcagttttac acacttgccc ccatgggaaa tggaacgggg cgcaaacgtg
6661 cattataatg gctggagctg tcattgctgg attggcatct gacgtcctta gttctggact
6721 tggttctctg atcaatgctg gggctggggt catcaaccaa aaagttgatt ttgaaaacaa
6781 cagaaaatta caacaagact ccttccaatt tagtagtaac ctgcaacagg cttcctttca
6841 acatgacaaa gagatgctcc aagctcaaat tgaggccact caaaaattgc aacagggtat
6901 gatggaaatt aaacaggcaa tgctcctaaa gggtggattc tctgaaacag atgcagcccg
6961 tggggcaatc aacgccccca tgacaaaagt tctggactgg aatggaacaa ggtactgggc
7021 tcctaatgct aggaccacaa catacaatgc aggcggtttt tccacccccc agccatcggg
7081 ggcatcacca ggaagaacca accttagggc cactgtcccc actcggggct cttcttcttc
7141 taaactttct agtacttcta ctgctacttc tgtatactca aatcaaacag tttcaacgag
7201 acttggttct tcagctggtt ctggtaccag tgtctcgagt ctcccgtcaa ctgcaaggac
7261 taggagctgg gttgaggatc aaaacagaaa tctgtcacct ttcatgaggg gggctctcaa
7321 cacatcattc gtctccccac cacctagcag atcctctagc caaggcacag tctcaaccgt
7381 gcctaaagaa attttggact cctggactag tgctttcaac acgcacaggc agcctctctt
7441 cgctcacatt cgtaagcaag gggagtcacg ggtgtaatgt gaaaagacaa attaattatc
7501 tttcctttct ttactgtc
//