A Comparative Study of Human TLR 7/8 Stimulatory Trimer Compositions in Influenza A Viral Genomes
Identifieur interne : 000746 ( Ncbi/Merge ); précédent : 000745; suivant : 000747A Comparative Study of Human TLR 7/8 Stimulatory Trimer Compositions in Influenza A Viral Genomes
Auteurs : Chu-Wen Yang [République populaire de Chine] ; Sy-Mien Chen [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Variation in the genomes of single-stranded RNA viruses affects their infectivity and pathogenicity in two ways. First, viral genome sequence variations lead to changes in viral protein sequences and activities. Second, viral genome sequence variation produces diversity at the level of nucleotide composition and diversity in the interactions between viral RNAs and host toll-like receptors (TLRs). A viral genome-typing method based on this type of diversity has not yet been established.
In this study, we propose a novel genomic trait called the “TLR stimulatory trimer composition” (TSTC) and two quantitative indicators, Score S and Score N, named “TLR stimulatory scores” (TSS). Using the complete genome sequences of 10,994 influenza A viruses (IAV) and 251 influenza B viruses, we show that TSTC analysis reveals the diversity of Score S and Score N among the IAVs isolated from various hosts. In addition, we show that low values of Score S are correlated with high pathogenicity and pandemic potential in IAVs. Finally, we use Score S and Score N to construct a logistic regression model to recognize IAV strains that are highly pathogenic or have high pandemic potential.
Url:
DOI: 10.1371/journal.pone.0030751
PubMed: 22363482
PubMed Central: 3281872
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000B36
- to stream Pmc, to step Curation: 000B36
- to stream Pmc, to step Checkpoint: 000763
Links to Exploration step
PMC:3281872Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Comparative Study of Human TLR 7/8 Stimulatory Trimer Compositions in Influenza A Viral Genomes</title>
<author><name sortKey="Yang, Chu Wen" sort="Yang, Chu Wen" uniqKey="Yang C" first="Chu-Wen" last="Yang">Chu-Wen Yang</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan, Republic of China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan</wicri:regionArea>
<wicri:noRegion>Taiwan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chen, Sy Mien" sort="Chen, Sy Mien" uniqKey="Chen S" first="Sy-Mien" last="Chen">Sy-Mien Chen</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Mathematics, Fu Jen Catholic University, Xinzhuang, New Taipei City, Taiwan, Republic of China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Department of Mathematics, Fu Jen Catholic University, Xinzhuang, New Taipei City, Taiwan</wicri:regionArea>
<wicri:noRegion>Taiwan</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22363482</idno>
<idno type="pmc">3281872</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281872</idno>
<idno type="RBID">PMC:3281872</idno>
<idno type="doi">10.1371/journal.pone.0030751</idno>
<date when="2012">2012</date>
<idno type="wicri:Area/Pmc/Corpus">000B36</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B36</idno>
<idno type="wicri:Area/Pmc/Curation">000B36</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B36</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000763</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000763</idno>
<idno type="wicri:Area/Ncbi/Merge">000746</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Comparative Study of Human TLR 7/8 Stimulatory Trimer Compositions in Influenza A Viral Genomes</title>
<author><name sortKey="Yang, Chu Wen" sort="Yang, Chu Wen" uniqKey="Yang C" first="Chu-Wen" last="Yang">Chu-Wen Yang</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan, Republic of China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan</wicri:regionArea>
<wicri:noRegion>Taiwan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chen, Sy Mien" sort="Chen, Sy Mien" uniqKey="Chen S" first="Sy-Mien" last="Chen">Sy-Mien Chen</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Mathematics, Fu Jen Catholic University, Xinzhuang, New Taipei City, Taiwan, Republic of China</addr-line>
</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Department of Mathematics, Fu Jen Catholic University, Xinzhuang, New Taipei City, Taiwan</wicri:regionArea>
<wicri:noRegion>Taiwan</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Variation in the genomes of single-stranded RNA viruses affects their infectivity and pathogenicity in two ways. First, viral genome sequence variations lead to changes in viral protein sequences and activities. Second, viral genome sequence variation produces diversity at the level of nucleotide composition and diversity in the interactions between viral RNAs and host toll-like receptors (TLRs). A viral genome-typing method based on this type of diversity has not yet been established.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>In this study, we propose a novel genomic trait called the “TLR stimulatory trimer composition” (TSTC) and two quantitative indicators, Score S and Score N, named “TLR stimulatory scores” (TSS). Using the complete genome sequences of 10,994 influenza A viruses (IAV) and 251 influenza B viruses, we show that TSTC analysis reveals the diversity of Score S and Score N among the IAVs isolated from various hosts. In addition, we show that low values of Score S are correlated with high pathogenicity and pandemic potential in IAVs. Finally, we use Score S and Score N to construct a logistic regression model to recognize IAV strains that are highly pathogenic or have high pandemic potential.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p><xref ref-type="sec" rid="s2">Results</xref>
from the TSTC analysis indicate that there are large differences between human and avian IAV genomes (except for segment 3), as illustrated by Score S. Moreover, segments 1, 2, 3 and 4 may be major determinants of the stimulatory activity exerted on human TLRs 7 and 8. We also find that a low Score S value is associated with high pathogenicity and pandemic potential in IAV. The <italic>π</italic>
value from the TSS-derived logistic regression model is useful for recognizing emerging IAVs that have high pathogenicity and pandemic potential.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Nelson, Mi" uniqKey="Nelson M">MI Nelson</name>
</author>
<author><name sortKey="Holmes, Ec" uniqKey="Holmes E">EC Holmes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A Rambaut</name>
</author>
<author><name sortKey="Pybus, Og" uniqKey="Pybus O">OG Pybus</name>
</author>
<author><name sortKey="Nelson, Mi" uniqKey="Nelson M">MI Nelson</name>
</author>
<author><name sortKey="Viboud, C" uniqKey="Viboud C">C Viboud</name>
</author>
<author><name sortKey="Taubenberger, Jk" uniqKey="Taubenberger J">JK Taubenberger</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tscherne, Dm" uniqKey="Tscherne D">DM Tscherne</name>
</author>
<author><name sortKey="Garcia Sastre, A" uniqKey="Garcia Sastre A">A García-Sastre</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, Gw" uniqKey="Chen G">GW Chen</name>
</author>
<author><name sortKey="Shih, Sr" uniqKey="Shih S">SR Shih</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Diebold, Ss" uniqKey="Diebold S">SS Diebold</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Miller, Rl" uniqKey="Miller R">RL Miller</name>
</author>
<author><name sortKey="Meng, Tc" uniqKey="Meng T">TC Meng</name>
</author>
<author><name sortKey="Tomai, Ma" uniqKey="Tomai M">MA Tomai</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kawai, T" uniqKey="Kawai T">T Kawai</name>
</author>
<author><name sortKey="Akira, S" uniqKey="Akira S">S Akira</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hornung, V" uniqKey="Hornung V">V Hornung</name>
</author>
<author><name sortKey="Barchet, W" uniqKey="Barchet W">W Barchet</name>
</author>
<author><name sortKey="Schlee, M" uniqKey="Schlee M">M Schlee</name>
</author>
<author><name sortKey="Hartmann, G" uniqKey="Hartmann G">G Hartmann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bauer, S" uniqKey="Bauer S">S Bauer</name>
</author>
<author><name sortKey="Pigisch, S" uniqKey="Pigisch S">S Pigisch</name>
</author>
<author><name sortKey="Hangel, D" uniqKey="Hangel D">D Hangel</name>
</author>
<author><name sortKey="Kaufmann, A" uniqKey="Kaufmann A">A Kaufmann</name>
</author>
<author><name sortKey="Hamm, S" uniqKey="Hamm S">S Hamm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Von Landenberg, P" uniqKey="Von Landenberg P">P von Landenberg</name>
</author>
<author><name sortKey="Bauer, S" uniqKey="Bauer S">S Bauer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hale, Bg" uniqKey="Hale B">BG Hale</name>
</author>
<author><name sortKey="Randall, Re" uniqKey="Randall R">RE Randall</name>
</author>
<author><name sortKey="Ortin, J" uniqKey="Ortin J">J Ortín</name>
</author>
<author><name sortKey="Jackson, D" uniqKey="Jackson D">D Jackson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fernandez Sesma, A" uniqKey="Fernandez Sesma A">A Fernandez-Sesma</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lund, J" uniqKey="Lund J">J Lund</name>
</author>
<author><name sortKey="Alexopoulou, L" uniqKey="Alexopoulou L">L Alexopoulou</name>
</author>
<author><name sortKey="Sato, A" uniqKey="Sato A">A Sato</name>
</author>
<author><name sortKey="Karow, M" uniqKey="Karow M">M Karow</name>
</author>
<author><name sortKey="Adams, N" uniqKey="Adams N">N Adams</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Diebold, Ss" uniqKey="Diebold S">SS Diebold</name>
</author>
<author><name sortKey="Kaisho, T" uniqKey="Kaisho T">T Kaisho</name>
</author>
<author><name sortKey="Hemmi, H" uniqKey="Hemmi H">H Hemmi</name>
</author>
<author><name sortKey="Akira, S" uniqKey="Akira S">S Akira</name>
</author>
<author><name sortKey="Reise Sousa, C" uniqKey="Reise Sousa C">C Reise Sousa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heil, F" uniqKey="Heil F">F Heil</name>
</author>
<author><name sortKey="Hemmi, H" uniqKey="Hemmi H">H Hemmi</name>
</author>
<author><name sortKey="Hochrein, H" uniqKey="Hochrein H">H Hochrein</name>
</author>
<author><name sortKey="Ampenberger, F" uniqKey="Ampenberger F">F Ampenberger</name>
</author>
<author><name sortKey="Kirschning, C" uniqKey="Kirschning C">C Kirschning</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, Jp" uniqKey="Wang J">JP Wang</name>
</author>
<author><name sortKey="Liu, P" uniqKey="Liu P">P Liu</name>
</author>
<author><name sortKey="Latz, E" uniqKey="Latz E">E Latz</name>
</author>
<author><name sortKey="Golenbock, Dt" uniqKey="Golenbock D">DT Golenbock</name>
</author>
<author><name sortKey="Finberg, Rw" uniqKey="Finberg R">RW Finberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lee, Hk" uniqKey="Lee H">HK Lee</name>
</author>
<author><name sortKey="Lund, Jm" uniqKey="Lund J">JM Lund</name>
</author>
<author><name sortKey="Ramanathan, B" uniqKey="Ramanathan B">B Ramanathan</name>
</author>
<author><name sortKey="Mizushima, N" uniqKey="Mizushima N">N Mizushima</name>
</author>
<author><name sortKey="Iwasaki, A" uniqKey="Iwasaki A">A Iwasaki</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gannage, M" uniqKey="Gannage M">M Gannagé</name>
</author>
<author><name sortKey="Dormann, D" uniqKey="Dormann D">D Dormann</name>
</author>
<author><name sortKey="Albrecht, R" uniqKey="Albrecht R">R Albrecht</name>
</author>
<author><name sortKey="Dengjel, J" uniqKey="Dengjel J">J Dengjel</name>
</author>
<author><name sortKey="Torossi, T" uniqKey="Torossi T">T Torossi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rossman, Js" uniqKey="Rossman J">JS Rossman</name>
</author>
<author><name sortKey="Lamb, Ra" uniqKey="Lamb R">RA Lamb</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhou, Z" uniqKey="Zhou Z">Z Zhou</name>
</author>
<author><name sortKey="Jiang, X" uniqKey="Jiang X">X Jiang</name>
</author>
<author><name sortKey="Liu, D" uniqKey="Liu D">D Liu</name>
</author>
<author><name sortKey="Fan, Z" uniqKey="Fan Z">Z Fan</name>
</author>
<author><name sortKey="Hu, X" uniqKey="Hu X">X Hu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hatta, M" uniqKey="Hatta M">M Hatta</name>
</author>
<author><name sortKey="Gao, P" uniqKey="Gao P">P Gao</name>
</author>
<author><name sortKey="Halfmann, P" uniqKey="Halfmann P">P Halfmann</name>
</author>
<author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gabriel, G" uniqKey="Gabriel G">G Gabriel</name>
</author>
<author><name sortKey="Herwig, A" uniqKey="Herwig A">A Herwig</name>
</author>
<author><name sortKey="Klenk, Hd" uniqKey="Klenk H">HD Klenk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Conenello, Gm" uniqKey="Conenello G">GM Conenello</name>
</author>
<author><name sortKey="Zamarin, D" uniqKey="Zamarin D">D Zamarin</name>
</author>
<author><name sortKey="Perrone, La" uniqKey="Perrone L">LA Perrone</name>
</author>
<author><name sortKey="Tumpey, T" uniqKey="Tumpey T">T Tumpey</name>
</author>
<author><name sortKey="Palese, P" uniqKey="Palese P">P Palese</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name>
</author>
<author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Seo, Sh" uniqKey="Seo S">SH Seo</name>
</author>
<author><name sortKey="Hoffmann, E" uniqKey="Hoffmann E">E Hoffmann</name>
</author>
<author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Obenauer, Jc" uniqKey="Obenauer J">JC Obenauer</name>
</author>
<author><name sortKey="Denson, J" uniqKey="Denson J">J Denson</name>
</author>
<author><name sortKey="Mehta, Pk" uniqKey="Mehta P">PK Mehta</name>
</author>
<author><name sortKey="Su, X" uniqKey="Su X">X Su</name>
</author>
<author><name sortKey="Mukatira, S" uniqKey="Mukatira S">S Mukatira</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jackson, D" uniqKey="Jackson D">D Jackson</name>
</author>
<author><name sortKey="Hossain, Mj" uniqKey="Hossain M">MJ Hossain</name>
</author>
<author><name sortKey="Hickman, D" uniqKey="Hickman D">D Hickman</name>
</author>
<author><name sortKey="Perez, Dr" uniqKey="Perez D">DR Perez</name>
</author>
<author><name sortKey="Lamb, Ra" uniqKey="Lamb R">RA Lamb</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Greninger, Al" uniqKey="Greninger A">AL Greninger</name>
</author>
<author><name sortKey="Chen, Ec" uniqKey="Chen E">EC Chen</name>
</author>
<author><name sortKey="Sittler, T" uniqKey="Sittler T">T Sittler</name>
</author>
<author><name sortKey="Scheinerman, A" uniqKey="Scheinerman A">A Scheinerman</name>
</author>
<author><name sortKey="Roubinian, N" uniqKey="Roubinian N">N Roubinian</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hastie, T" uniqKey="Hastie T">T Hastie</name>
</author>
<author><name sortKey="Tibshirani, R" uniqKey="Tibshirani R">R Tibshirani</name>
</author>
<author><name sortKey="Friedman, J" uniqKey="Friedman J">J Friedman</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">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22363482</article-id>
<article-id pub-id-type="pmc">3281872</article-id>
<article-id pub-id-type="publisher-id">PONE-D-11-17481</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0030751</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genomics</subject>
</subj-group>
</subj-group>
<subj-group><subject>Immunology</subject>
<subj-group><subject>Immunity</subject>
</subj-group>
</subj-group>
<subj-group><subject>Microbiology</subject>
<subj-group><subject>Immunity</subject>
</subj-group>
<subj-group><subject>Virology</subject>
<subj-group><subject>Viral Classification</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Medicine</subject>
<subj-group><subject>Clinical Immunology</subject>
<subj-group><subject>Immunity</subject>
</subj-group>
</subj-group>
<subj-group><subject>Infectious Diseases</subject>
<subj-group><subject>Viral Diseases</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>A Comparative Study of Human TLR 7/8 Stimulatory Trimer Compositions in Influenza A Viral Genomes</article-title>
<alt-title alt-title-type="running-head">hTLR 7/8 Stimulatory Composition of Viral Genome</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Yang</surname>
<given-names>Chu-Wen</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Sy-Mien</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Department of Microbiology, Soochow University, Shih-Lin, Taipei, Taiwan, Republic of China</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Department of Mathematics, Fu Jen Catholic University, Xinzhuang, New Taipei City, Taiwan, Republic of China</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Park</surname>
<given-names>Man-Seong</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">Hallym University, Republic of Korea</aff>
<author-notes><corresp id="cor1">* E-mail: <email>smchen@mail.fju.edu.tw</email>
</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: CWY SMC. Performed the experiments: CWY. Analyzed the data: CWY SMC. Wrote the paper: CWY SMC.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>2</month>
<year>2012</year>
</pub-date>
<volume>7</volume>
<issue>2</issue>
<elocation-id>e30751</elocation-id>
<history><date date-type="received"><day>4</day>
<month>9</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>23</day>
<month>12</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>Yang, Chen.</copyright-statement>
<copyright-year>2012</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>Variation in the genomes of single-stranded RNA viruses affects their infectivity and pathogenicity in two ways. First, viral genome sequence variations lead to changes in viral protein sequences and activities. Second, viral genome sequence variation produces diversity at the level of nucleotide composition and diversity in the interactions between viral RNAs and host toll-like receptors (TLRs). A viral genome-typing method based on this type of diversity has not yet been established.</p>
</sec>
<sec><title>Methodology/Principal Findings</title>
<p>In this study, we propose a novel genomic trait called the “TLR stimulatory trimer composition” (TSTC) and two quantitative indicators, Score S and Score N, named “TLR stimulatory scores” (TSS). Using the complete genome sequences of 10,994 influenza A viruses (IAV) and 251 influenza B viruses, we show that TSTC analysis reveals the diversity of Score S and Score N among the IAVs isolated from various hosts. In addition, we show that low values of Score S are correlated with high pathogenicity and pandemic potential in IAVs. Finally, we use Score S and Score N to construct a logistic regression model to recognize IAV strains that are highly pathogenic or have high pandemic potential.</p>
</sec>
<sec><title>Conclusions/Significance</title>
<p><xref ref-type="sec" rid="s2">Results</xref>
from the TSTC analysis indicate that there are large differences between human and avian IAV genomes (except for segment 3), as illustrated by Score S. Moreover, segments 1, 2, 3 and 4 may be major determinants of the stimulatory activity exerted on human TLRs 7 and 8. We also find that a low Score S value is associated with high pathogenicity and pandemic potential in IAV. The <italic>π</italic>
value from the TSS-derived logistic regression model is useful for recognizing emerging IAVs that have high pathogenicity and pandemic potential.</p>
</sec>
</abstract>
<counts><page-count count="18"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
</list>
<tree><country name="République populaire de Chine"><noRegion><name sortKey="Yang, Chu Wen" sort="Yang, Chu Wen" uniqKey="Yang C" first="Chu-Wen" last="Yang">Chu-Wen Yang</name>
</noRegion>
<name sortKey="Chen, Sy Mien" sort="Chen, Sy Mien" uniqKey="Chen S" first="Sy-Mien" last="Chen">Sy-Mien Chen</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/H2N2V1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000746 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000746 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= H2N2V1 |flux= Ncbi |étape= Merge |type= RBID |clé= PMC:3281872 |texte= A Comparative Study of Human TLR 7/8 Stimulatory Trimer Compositions in Influenza A Viral Genomes }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:22363482" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \ | NlmPubMed2Wicri -a H2N2V1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |