Typing tool
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Typing tool
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Complete norovirus genomes
| MF140638 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5087
ORF2: 5068..6690
ORF3: 6690..7496
LOCUS MF140638 7496 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.Pe-GII.4/Rotterdam/E1300286_p10_d362
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140638
VERSION MF140638.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7496)
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 7496)
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..7496
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.Pe-
GII.4/Rotterdam/E1300286_p10_d362"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="21-Jan-2014"
/note="genotype: GII.Pe-GII.4"
CDS <1..5087
/codon_start=3
/product="ORF1"
/protein_id="ATN23610.1"
/translation="NDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPP
KEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYNAKDGVSGLPELTTVRQPEETNTA
FSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVE
LAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLN
ILNILATCDWTFAGIVESLILLAELFGAFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHFAREVANKVA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSSDFSHMKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQ
ALKNITIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIR
YYVKCAQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEIVNKDGCLKPKD
DEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI
RKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVTL
LIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAP
KLSAKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
RPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQR
DVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLK
PTRPDKTEGPLVITEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDP
FETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5068..6690
/codon_start=1
/product="ORF2"
/protein_id="ATN23611.1"
/translation="MKMASSDANPSDGSTASLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEVLWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTECLSPSQVTMLPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCSTDGVLLGTT
QLSPVNICTFRGDVTQITGSSTYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTVGSTRGHKATVRTGSADFAPKLGRVRFETDTNNDFEVNQNTKFTPVGVIQDG
DTAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAP"
CDS 6690..7496
/codon_start=1
/product="ORF3"
/protein_id="ATN23612.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSRKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPTTARTRSWVEDQSRNLSPFMSGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 ctaacgacgc ttccgctgcc gctgttgcca acagcaacaa cgacatcgca aaatcttcaa
61 gtgacggtgt gttttctaac atggctgtca cttttaagcg ggccctcggg gcgcggccta
121 aacagccgcc cccgaaggaa ataccaccca gacccccgcg accacccaca ccagaattgg
181 tcaaaaagat ccctcctccc ccacccaacg gggaggatga actagtggtc tcctacaatg
241 ccaaagatgg cgtttccgga ctgcctgagc tcaccactgt cagacaaccg gaagaaacca
301 acacggcgtt cagtgtcccc ccacttaacc aaagggagag cagggacgcc aaggagccac
361 taactggaac aatcattgaa atgtgggatg gagaaatcta ccattacggc ctgtacgtgg
421 aacgaggtct tatacttggt gtgcacaagc caccggcagc cattagcctt gccaaggtcg
481 agctagcacc gctctctttg ttctggagac ctgtatacac cccccagtat ctcatctctc
541 cagacactct taggagatta catggagagt cattccccta cactgcattt gacaacaatt
601 gctacgcctt ttgctgttgg gtattagacc taaacgactc atggctaagc aggagaatga
661 ttcagagaac aacaggcttc ttcaggccgt accaggattg gaacaggaaa cccctcccca
721 ctatggatga ttccaaatta aagaaggtag ccaacatatt cttgtgcact ttgtcttcac
781 tattcaccag acccattaaa gacataatag ggaagttgaa acctcttaac atccttaaca
841 ttctggctac atgtgattgg accttcgcag gcatagtgga atccttaata ctcttggcag
901 aactctttgg agctttctgg acacccccag atgtgtctgc gatgatcgcc cccttgctag
961 gtgattatga actgcaagga cctgaggacc ttgcagtgga actggtccca atagtgatgg
1021 gggggatagg tttggtgcta ggatttacca aagagaaaat cggaaagatg ctatcatccg
1081 ctgcatccac tttaagagct tgtaaagacc ttggtgcata cggactggaa atcttaaaat
1141 tggtcatgaa gtggttcttc ccaaagaaag aggaagcaaa tgaactggct atggtgagat
1201 ccatcgagga tgcagtacta gacctcgagg caattgaaaa caaccacatg accaccctac
1261 tcaaagataa agacagcttg gcaacctaca tgagaaccct tgaccttgag gaggagaaag
1321 ccagaaaact ctcaaccaaa tctgcttcac ccgatattgt gggcacaatc aacgctcttc
1381 tggcaagaat cgctgctgca cgctccctag tgcatcgggc gaaagaagag ctctccagca
1441 ggctgagacc tgtcgttgtg atgatatcgg gaaagccagg gatagggaaa actcactttg
1501 ccagggaggt ggccaacaag gtcgcggcct ccctcacagg ggaccagcgt gtgggtctta
1561 tcccacgcaa tggtgtcgac cactgggacg catacaaggg cgaaagagtt gtcctatggg
1621 acgactatgg aatgagcaac cccatccatg atgccctcag gttgcaggag cttgctgaca
1681 cttgccccct cacgctaaat tgtgacagaa ttgagaacaa agggaaagtc tttgacagtg
1741 atgccataat tatcaccacc aatctggcca acccagcacc actggattat gtcaactttg
1801 aagcgtgctc gagacgcatt gatttcctcg tgtacgcaga agcccctgag gtggagaagg
1861 caaagcgcga cttcccaggt caacctgaca tgtggaagaa cgctttcagt tctgacttct
1921 cacacatgaa actgtcattg gctccacaag gtggttttga caagaacggc aacaccccgc
1981 atggaaaagg agtcatgaag accctcacca ctggctccct catcgcccga gcatcagggt
2041 tacttcatga gaggctagat gaatatgaac tacaaggccc agccctcacc actttcaact
2101 ttgaccgcaa caagatactt gcttttagac agcttgctgc tgaaaacaag tatgggctga
2161 tggacacaat gagagttgga aaacagctca aggatgtcaa gaccatgtca gacctcaaac
2221 aagcactcaa gaacatcacg atcaagaagt gccagatagt gtacaatggt ggcacctaca
2281 cacttgaggc tgatggcaag ggtagtgtga aagttgacaa agtgcaaagt gccactgtgc
2341 agaccaacaa tgaactagcc ggtgccctac accacctaag gtgcgctaga atcagatact
2401 atgttaagtg cgcccaggag gcactgtatt ccatcatcca aatcgctggg gctgcattcg
2461 tcaccacgcg catcgctaag cgcatgaata tacagaatct ctggtccaag ccacaggtgg
2521 aagacacaga agagatagtc aacaaagatg gttgcctaaa acccaaagat gatgaagagt
2581 ttgtcgtctc atccgacgac atcaaaactg agggcaagaa agggaagaac aagtccggcc
2641 gtggcaagaa gcacacagcc ttttcaagta aagggctcag tgatgaggag tacgatgagt
2701 acaagaggat cagagaagaa aggaatggta agtactccat agaagagtac cttcaggaca
2761 gagacaggta ctacgaggag gtggccattg ccagggcaac cgaagaggac ttctgtgaag
2821 aagaagaggc caaaatccgg cagagaattt tcagaccaac aaggaaacaa cgtaaagaag
2881 agagggcctc tctcggcttg gtcacaggct ctgaaatcag gaagagaaac ccagaagact
2941 tcaaacccaa gggaaagttg tgggctgatg atgacagaag tgttgactac aatgagaaac
3001 tcaactttga ggccccacca agcatctggt cgcggatagt caactttggt tcaggctggg
3061 gcttctgggt ctctcccagt ctgtttataa catcaaccca tgtcataccc caaggtgcaa
3121 aagagttctt cggagtccct attaagcaaa tccagataca caagtcaggt gaattctgcc
3181 ggttgagatt cccaaggcca atcagaactg atgtgacggg catgattcta gaagaaggtg
3241 cgcccgaggg aaccgtggtc acactgctca tcaagagacc aactggagag ctcatgcctc
3301 tggcagccag aatggggacc catgcaacca tgaaaatcca ggggcgcaca gttggagggc
3361 aaatgggtat gctcctgaca ggatccaacg ccaagagtat ggacctaggc acaacaccag
3421 gcgactgcgg atgcccctac atctacaaga gggggaatga ctacgtggtc ataggagtcc
3481 atacggccgc tgcccgtgga ggaaacactg tcatatgtgc cacccagggg agtgagggag
3541 aagccacact tgaaggaggt gacagtaaag ggacatactg tggcgcacca atcttgggcc
3601 cagggagcgc tccgaagctc agtgccaaga ctaagttttg gagatcatcc acaacaccac
3661 tcccacctgg cacctacgaa ccagcctacc tcggtggcaa agaccctaga gtcaaaggtg
3721 gcccttcatt gcaacaagtt atgagggacc agctgaagcc attcacagaa cccagaggca
3781 aaccaccaag accaaatgtg ttggaagctg ccaagaaaac catcatcaat gtccttgagc
3841 aaacaattga tccaccccaa aaatggtcat ttgcgcaagc ttgcgcatcc cttgacaaaa
3901 ccacctccag cggccacccg caccacatgc ggaaaaacga ctgttggaat ggggagtcct
3961 tcacaggaaa attggctgat caggcctcca aggccaacct aatgtttgaa gagggaaaga
4021 acatgactcc agtctacaca ggtgcactta aagatgagtt ggtaaagacc gataaagttt
4081 atggtaaaat caagaagagg cttctgtggg gttcagatct ggcgaccatg atacggtgcg
4141 cccgagcttt tggaggcctt atggatgaac tcaaggcgca ctgtgtcaca cttcctgtca
4201 gagttggtat gaacatgaat gaggatggcc ccatcatctt tgagaagcac tccagatata
4261 gatatcacta tgatgctgat tattcccggt gggactcaac acaacaaagg gatgtgctag
4321 cagcagcact agaaatcatg gttaagttct ctccagaacc acacctggcc cagatagttg
4381 cagaagacct cctttcccct agcgtgatgg atgtaggtga ctttcaaata tcaataagtg
4441 agggtctccc ctctggggta ccttgtacct cccagtggaa ttccatcgcc cactggctcc
4501 tcactctgtg tgcactctct gaagtcacag acctgtcccc tgatatcatt caggccaact
4561 cccttttctc cttctatggt gatgatgaga ttgtaagcac agacataaag ttggacccag
4621 agaagctgac agcaaaactc aaggagtacg ggctgaaacc aacccgcccc gacaaaactg
4681 aaggacccct cgttatcact gaagacctgg atggcctgac attcctccgg agaactgtga
4741 cccgtgatcc agctggctgg tttggaaagt tggaacaaag ttcaattctc aggcaaatgt
4801 actggaccag gggtcccaat catgaagatc catttgaaac aatgatacca cactcccaaa
4861 gacccataca attgatgtcc ttgctgggcg aggctgcact ccacggcccg gcattctata
4921 gcaaaattag caaattagtc attgcagagt tgaaggaagg tggcatggat ttttacgtgc
4981 ccagacaaga gccaatgttc agatggatga gattctcaga tctgagcacg tgggagggcg
5041 atcgcaatct ggctcccagt tttgtgaatg aagatggcgt cgagtgacgc caacccatct
5101 gatgggtcca cagccagcct cgtcccagag gtcaacaatg aggttatggc tctggagccc
5161 gttgttggtg ccgccattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg
5221 attagaaata attttgtaca agcccctggt ggagagttta cagtatcccc cagaaacgct
5281 ccaggtgaag tactatggag cgcgcccttg ggccctgatc taaatcccta cctatcccat
5341 ttggccagaa tgtacaatgg ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg
5401 aacgcgttca ccgccgggaa gatcatattt gcagcggtcc caccaaattt tccaactgaa
5461 tgtttgagcc ccagccaggt cactatgctc ccccatataa tagtagatgt taggcaatta
5521 gaacctgtgt tgattccctt acccgatgtt aggaataatt tctatcatta caatcaatca
5581 aatgactcca ccattaagtt gatagcaatg ttgtatacac cacttagggc taataatgct
5641 ggggatgatg tcttcacagt ttcttgccga gttctcacga gaccatcccc cgattttgat
5701 ttcatatttt tagtgccacc cacagttgag tcaagaacta aaccattctc tgtcccagtt
5761 ttaactgttg aggagatgac caattcaaga ttccccattc ctttggaaaa gttgttcacg
5821 ggtcccagca gtgcctttgt tgtccaacca caaaacggta ggtgctcgac tgatggcgtg
5881 ctcctaggca ccacccagct gtctcctgtc aacatctgca ccttcagagg agatgtcacc
5941 cagatcacag gtagtagtac ctacacaatg aatttggctt ctcaaaattg gagcaactat
6001 gacccaacag aagaaatccc agcccctcta ggaactccag attttgtggg gaagattcaa
6061 ggcgtgctca cccaaaccac aaggacagtt ggctcaacac gcggccacaa agccacagtg
6121 cgcactggga gcgccgactt tgctccaaaa ctgggtagag ttcgatttga aactgacaca
6181 aacaatgatt ttgaagttaa ccaaaataca aagttcaccc cagttggtgt catccaagat
6241 ggtgacaccg cccaccgaaa tgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga
6301 aacactccta atgtacatct ggcccccgct gtagccccca cttttccggg tgagcaactt
6361 ctcttcttca gatccaccat gcccggatgc agcgggtacc ccaacatgga tttggactgt
6421 ctgctccccc aggaatgggt gcagtacttc taccaagagg cagccccagc acaatctgat
6481 gtggctctgc taagatttgt gaatccagac acaggtaggg ttttgtttga gtgtaagctt
6541 cataaatcag gctatattac agtggctcac actggccaac atgatttggt tatccccccc
6601 aatggttatt ttaggtttga ttcctgggtc aatcagtttt acacgcttgc ccccatggga
6661 aatggaacgg ggcgtagacg tgcaccataa tggctggagc tttctttgct ggattggcat
6721 ctgatgtcct tggctctgga cttggttccc ttatcaatgc tggggctggg gccatcaacc
6781 aaaaagttga gtttgaaaat aacagaaaat tgcaacaagc atccttccaa tttagcagca
6841 atctacaaca ggcttccttt caacatgaca aagagatgct ccaagcacaa attgaggcca
6901 ccaaaaggct acaacaggaa atgatgaaag tcaaacaggc aatgctccta gagggtgggt
6961 tttctgagac agatgcagcc cgcggggcaa tcaacgcccc catgacaaaa gttttggact
7021 ggagcgggac aaggtactgg gctcccgatg ctaggactac aacatacaat gcaggccgct
7081 tttccacccc tcaaccatcg ggggcactgc caggaagagc taatcttagg gatgctgtcc
7141 ctgctcgggg ttcctccaga aagtcttcta attcttccac tgctacttct gtgtactcaa
7201 atcaaactac ttcaacgaga cttggttcta cagctggttc tggtaccagt gtctcgagct
7261 tcccgacaac tgcaaggact aggagctggg ttgaggatca aagtaggaat ttgtcacctt
7321 tcatgagtgg ggcccacaac atatcgtttg tcaccccacc atctagcaga tcctctagcc
7381 aaggcacagt ctcaaccgtg cctaaagaga ttttggactc ctggactggc gctttcaaca
7441 cgcgcaggca gccactcttc gctcacattc gtaagcgagg ggagtcacgg gcgtaa
//