Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count
Identifieur interne : 000438 ( Pmc/Curation ); précédent : 000437; suivant : 000439Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count
Auteurs : Yoshiko Wada ; Kennosuke Wada ; Yuki Iwasaki ; Shigehiko Kanaya ; Toshimichi IkemuraSource :
- Scientific Reports [ 2045-2322 ] ; 2016.
Abstract
Ebolavirus, MERS coronavirus and influenza virus are zoonotic RNA viruses, which mutate very rapidly. Viral growth depends on many host factors, but human cells may not provide the ideal growth conditions for viruses invading from nonhuman hosts. The present time-series analyses of short and long oligonucleotide compositions in these genomes showed directional changes in their composition after invasion from a nonhuman host, which are thought to recur after future invasions. In the recent West Africa Ebola outbreak, directional time-series changes in a wide range of oligonucleotides were observed in common for three geographic areas, and the directional changes were observed also for the recent MERS coronavirus epidemics starting in the Middle East. In addition, common directional changes in human influenza A viruses were observed for three subtypes, whose epidemics started independently. Long oligonucleotides that showed an evident directional change observed in common for the three subtypes corresponded to some of influenza A siRNAs, whose activities have been experimentally proven. Predicting directional and reoccurring changes in oligonucleotide composition should become important for designing diagnostic RT-PCR primers and therapeutic oligonucleotides with long effectiveness.
The online version of this article (doi:10.1038/srep36197) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1038/srep36197
PubMed: 27808119
PubMed Central: 5093548
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Yoshiko Wada<affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.260493.a</institution-id><institution-id institution-id-type="ISNI">0000 0000 9227 2257</institution-id><institution>Nara Institute of Science and Technology,</institution></institution-wrap>8916-5 Takayama, Ikoma, 630-0192 Nara Japan</nlm:aff><wicri:noCountry code="subfield">630-0192 Nara Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.260493.a</institution-id><institution-id institution-id-type="ISNI">0000 0000 9227 2257</institution-id><institution>Nara Institute of Science and Technology,</institution></institution-wrap>8916-5 Takayama, Ikoma, 630-0192 Nara Japan</nlm:aff><wicri:noCountry code="subfield">630-0192 Nara Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.260493.a</institution-id><institution-id institution-id-type="ISNI">0000 0000 9227 2257</institution-id><institution>Nara Institute of Science and Technology,</institution></institution-wrap>8916-5 Takayama, Ikoma, 630-0192 Nara Japan</nlm:aff><wicri:noCountry code="subfield">630-0192 Nara Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation>Le document en format XML
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institution-id-type="GRID">grid.260493.a</institution-id><institution-id institution-id-type="ISNI">0000 0000 9227 2257</institution-id><institution>Nara Institute of Science and Technology,</institution></institution-wrap>8916-5 Takayama, Ikoma, 630-0192 Nara Japan</nlm:aff><wicri:noCountry code="subfield">630-0192 Nara Japan</wicri:noCountry></affiliation></author><author><name sortKey="Wada, Kennosuke" sort="Wada, Kennosuke" uniqKey="Wada K" first="Kennosuke" last="Wada">Kennosuke Wada</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation></author><author><name sortKey="Iwasaki, Yuki" sort="Iwasaki, Yuki" uniqKey="Iwasaki Y" first="Yuki" last="Iwasaki">Yuki Iwasaki</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation></author><author><name sortKey="Kanaya, Shigehiko" sort="Kanaya, Shigehiko" uniqKey="Kanaya S" first="Shigehiko" last="Kanaya">Shigehiko Kanaya</name><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.260493.a</institution-id><institution-id institution-id-type="ISNI">0000 0000 9227 2257</institution-id><institution>Nara Institute of Science and Technology,</institution></institution-wrap>8916-5 Takayama, Ikoma, 630-0192 Nara Japan</nlm:aff><wicri:noCountry code="subfield">630-0192 Nara Japan</wicri:noCountry></affiliation></author><author><name sortKey="Ikemura, Toshimichi" sort="Ikemura, Toshimichi" uniqKey="Ikemura T" first="Toshimichi" last="Ikemura">Toshimichi Ikemura</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</nlm:aff><wicri:noCountry code="subfield">526-0829 Shiga-ken Japan</wicri:noCountry></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Ebolavirus, MERS coronavirus and influenza virus are zoonotic RNA viruses, which mutate very rapidly. Viral growth depends on many host factors, but human cells may not provide the ideal growth conditions for viruses invading from nonhuman hosts. The present time-series analyses of short and long oligonucleotide compositions in these genomes showed directional changes in their composition after invasion from a nonhuman host, which are thought to recur after future invasions. In the recent West Africa Ebola outbreak, directional time-series changes in a wide range of oligonucleotides were observed in common for three geographic areas, and the directional changes were observed also for the recent MERS coronavirus epidemics starting in the Middle East. In addition, common directional changes in human influenza A viruses were observed for three subtypes, whose epidemics started independently. Long oligonucleotides that showed an evident directional change observed in common for the three subtypes corresponded to some of influenza A siRNAs, whose activities have been experimentally proven. Predicting directional and reoccurring changes in oligonucleotide composition should become important for designing diagnostic RT-PCR primers and therapeutic oligonucleotides with long effectiveness.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1038/srep36197) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Tong, Yg" uniqKey="Tong Y">YG Tong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Park, Dj" uniqKey="Park D">DJ Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carroll, Mw" uniqKey="Carroll M">MW Carroll</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nichol, St" uniqKey="Nichol S">ST Nichol</name></author><author><name sortKey="Arikawa, J" uniqKey="Arikawa J">J Arikawa</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author><author><name sortKey="Campbell, Am" uniqKey="Campbell A">AM Campbell</name></author><author><name sortKey="Mrazek, J" uniqKey="Mrazek J">J Mrazek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Garcia Sastre, A" uniqKey="Garcia Sastre A">A García-Sastre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Voinnet, O" uniqKey="Voinnet O">O Voinnet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Randall, Re" uniqKey="Randall R">RE Randall</name></author><author><name sortKey="Goodbourn, S" uniqKey="Goodbourn S">S Goodbourn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rabadan, R" uniqKey="Rabadan R">R Rabadan</name></author><author><name sortKey="Levine, Aj" uniqKey="Levine A">AJ Levine</name></author><author><name sortKey="Robins, H" uniqKey="Robins H">H Robins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jimenez Baranda, S" uniqKey="Jimenez Baranda S">S Jimenez-Baranda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanaya, S" uniqKey="Kanaya S">S Kanaya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abe, T" uniqKey="Abe T">T Abe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Iwasaki, Y" uniqKey="Iwasaki Y">Y Iwasaki</name></author><author><name sortKey="Abe, T" uniqKey="Abe T">T Abe</name></author><author><name sortKey="Wada, K" uniqKey="Wada K">K Wada</name></author><author><name sortKey="Itoh, M" uniqKey="Itoh M">M Itoh</name></author><author><name sortKey="Ikemura, T" uniqKey="Ikemura T">T Ikemura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Iwasaki, Y" uniqKey="Iwasaki Y">Y Iwasaki</name></author><author><name sortKey="Abe, T" uniqKey="Abe T">T Abe</name></author><author><name sortKey="Wada, Y" uniqKey="Wada Y">Y Wada</name></author><author><name sortKey="Wada, K" uniqKey="Wada K">K Wada</name></author><author><name sortKey="Ikemura, T" uniqKey="Ikemura T">T Ikemura</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Neumann, G" uniqKey="Neumann G">G Neumann</name></author><author><name sortKey="Noda, T" uniqKey="Noda T">T Noda</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Gj" uniqKey="Smith G">GJ Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crooke, St" uniqKey="Crooke S">ST Crooke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kageyama, T" uniqKey="Kageyama T">T Kageyama</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Opalinska, Jb" uniqKey="Opalinska J">JB Opalinska</name></author><author><name sortKey="Gewirtz, Am" uniqKey="Gewirtz A">AM Gewirtz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meister, G" uniqKey="Meister G">G Meister</name></author><author><name sortKey="Tuschl, T" uniqKey="Tuschl T">T Tuschl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bennett, Cf" uniqKey="Bennett C">CF Bennett</name></author><author><name sortKey="Swayze, Ee" uniqKey="Swayze E">EE Swayze</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brister, Jr" uniqKey="Brister J">JR Brister</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Azhar, Ei" uniqKey="Azhar E">EI Azhar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ithete, Nl" uniqKey="Ithete N">NL Ithete</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Squires, Rb" uniqKey="Squires R">RB Squires</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xie, Z" uniqKey="Xie Z">Z Xie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thakur, N" uniqKey="Thakur N">N Thakur</name></author><author><name sortKey="Qureshi, A" uniqKey="Qureshi A">A Qureshi</name></author><author><name sortKey="Kumar, M" uniqKey="Kumar M">M Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bhatt, S" uniqKey="Bhatt S">S Bhatt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paixao, Es" uniqKey="Paixao E">ES Paixão</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Sci Rep</journal-id><journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id><journal-title-group><journal-title>Scientific Reports</journal-title></journal-title-group><issn pub-type="epub">2045-2322</issn><publisher><publisher-name>Nature Publishing Group UK</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27808119</article-id><article-id pub-id-type="pmc">5093548</article-id><article-id pub-id-type="publisher-id">BFsrep36197</article-id><article-id pub-id-type="doi">10.1038/srep36197</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wada</surname><given-names>Yoshiko</given-names></name><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Wada</surname><given-names>Kennosuke</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Iwasaki</surname><given-names>Yuki</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Kanaya</surname><given-names>Shigehiko</given-names></name><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Ikemura</surname><given-names>Toshimichi</given-names></name><address><email>t_ikemura@nagahama-i-bio.ac.jp</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="GRID">grid.419056.f</institution-id><institution>Department of Bioscience,</institution><institution>Nagahama Institute of Bio-Science and Technology,</institution></institution-wrap>Tamura-cho 1266, Nagahama-shi, 526-0829 Shiga-ken Japan</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="GRID">grid.260493.a</institution-id><institution-id institution-id-type="ISNI">0000 0000 9227 2257</institution-id><institution>Nara Institute of Science and Technology,</institution></institution-wrap>8916-5 Takayama, Ikoma, 630-0192 Nara Japan</aff></contrib-group><pub-date pub-type="epub"><day>3</day><month>11</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>3</day><month>11</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>6</volume><elocation-id>36197</elocation-id><history><date date-type="received"><day>4</day><month>7</month><year>2016</year></date><date date-type="accepted"><day>11</day><month>10</month><year>2016</year></date></history><permissions><copyright-statement>© The Author(s) 2016</copyright-statement><license license-type="OpenAccess"><license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract id="Abs1"><p>Ebolavirus, MERS coronavirus and influenza virus are zoonotic RNA viruses, which mutate very rapidly. Viral growth depends on many host factors, but human cells may not provide the ideal growth conditions for viruses invading from nonhuman hosts. The present time-series analyses of short and long oligonucleotide compositions in these genomes showed directional changes in their composition after invasion from a nonhuman host, which are thought to recur after future invasions. In the recent West Africa Ebola outbreak, directional time-series changes in a wide range of oligonucleotides were observed in common for three geographic areas, and the directional changes were observed also for the recent MERS coronavirus epidemics starting in the Middle East. In addition, common directional changes in human influenza A viruses were observed for three subtypes, whose epidemics started independently. Long oligonucleotides that showed an evident directional change observed in common for the three subtypes corresponded to some of influenza A siRNAs, whose activities have been experimentally proven. Predicting directional and reoccurring changes in oligonucleotide composition should become important for designing diagnostic RT-PCR primers and therapeutic oligonucleotides with long effectiveness.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1038/srep36197) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group kwd-group-type="npg-subject"><title>Subject terms</title><kwd>Data mining</kwd><kwd>Molecular evolution</kwd><kwd>Ebola virus</kwd><kwd>Influenza virus</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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