Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses
Identifieur interne : 000407 ( Main/Exploration ); précédent : 000406; suivant : 000408Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses
Auteurs : Haifen Chen [Singapour] ; Xinrui Zhou [Singapour] ; Jie Zheng [Singapour] ; Chee-Keong Kwoh [Singapour]Source :
- BMC Medical Genomics [ 1755-8794 ] ; 2016.
Abstract
The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune system. Therefore, the vaccine has to be updated every year to stay effective. There is a need to characterize the evolution of influenza viruses for better selection of vaccine candidates and the prediction of pandemic strains. Studies have shown that the influenza hemagglutinin evolution is driven by the simultaneous mutations at antigenic sites. Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution.
We obtain the rules of mutation co-occurrence using association rule mining after extracting HA1 sequences and detect co-mutation sites under strong selective pressure. Then we predict the potential drifts with specific mutations of the viruses based on the rules and compare the results with the “observed” mutations in different years.
The sites under frequent mutations are in antigenic regions (epitopes) or receptor binding sites.
Our study demonstrates the co-occurring site mutations obtained by rule mining can capture the evolution of influenza viruses, and confirms that cooperative interactions among sites of HA1 protein drive the influenza antigenic evolution.
The online version of this article (doi:10.1186/s12920-016-0230-5) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12920-016-0230-5
PubMed: 28117657
PubMed Central: 5260787
Affiliations:
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type="main">Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses</title><author><name sortKey="Chen, Haifen" sort="Chen, Haifen" uniqKey="Chen H" first="Haifen" last="Chen">Haifen Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2224 0361</institution-id><institution-id institution-id-type="GRID">grid.59025.3b</institution-id><institution>School of Computer Science and Engineering,</institution><institution>Nanyang Technological University,</institution></institution-wrap>50 Nanyang Avenue, 639798 Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>50 Nanyang Avenue, 639798 Singapore</wicri:regionArea><wicri:noRegion>639798 Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Xinrui" sort="Zhou, Xinrui" uniqKey="Zhou X" first="Xinrui" last="Zhou">Xinrui Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2224 0361</institution-id><institution-id institution-id-type="GRID">grid.59025.3b</institution-id><institution>School of Computer Science and Engineering,</institution><institution>Nanyang Technological University,</institution></institution-wrap>50 Nanyang Avenue, 639798 Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>50 Nanyang Avenue, 639798 Singapore</wicri:regionArea><wicri:noRegion>639798 Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Zheng, Jie" sort="Zheng, Jie" uniqKey="Zheng J" first="Jie" last="Zheng">Jie Zheng</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2224 0361</institution-id><institution-id institution-id-type="GRID">grid.59025.3b</institution-id><institution>School of Computer Science and Engineering,</institution><institution>Nanyang Technological University,</institution></institution-wrap>50 Nanyang Avenue, 639798 Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>50 Nanyang Avenue, 639798 Singapore</wicri:regionArea><wicri:noRegion>639798 Singapore</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0620 715X</institution-id><institution-id institution-id-type="GRID">grid.418377.e</institution-id><institution></institution><institution>Genome Institute of Singapore, A*STAR,</institution></institution-wrap>Biopolis, 138672 Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Biopolis, 138672 Singapore</wicri:regionArea><wicri:noRegion>138672 Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Kwoh, Chee Keong" sort="Kwoh, Chee Keong" uniqKey="Kwoh C" first="Chee-Keong" last="Kwoh">Chee-Keong Kwoh</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2224 0361</institution-id><institution-id institution-id-type="GRID">grid.59025.3b</institution-id><institution>School of Computer Science and Engineering,</institution><institution>Nanyang Technological University,</institution></institution-wrap>50 Nanyang Avenue, 639798 Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>50 Nanyang Avenue, 639798 Singapore</wicri:regionArea><wicri:noRegion>639798 Singapore</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Medical Genomics</title><idno type="eISSN">1755-8794</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune system. Therefore, the vaccine has to be updated every year to stay effective. There is a need to characterize the evolution of influenza viruses for better selection of vaccine candidates and the prediction of pandemic strains. Studies have shown that the influenza hemagglutinin evolution is driven by the simultaneous mutations at antigenic sites. Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution.</p></sec><sec><title>Methods</title><p>We obtain the rules of mutation co-occurrence using association rule mining after extracting HA1 sequences and detect co-mutation sites under strong selective pressure. Then we predict the potential drifts with specific mutations of the viruses based on the rules and compare the results with the “observed” mutations in different years.</p></sec><sec><title>Results</title><p>The sites under frequent mutations are in antigenic regions (epitopes) or receptor binding sites.</p></sec><sec><title>Conclusions</title><p>Our study demonstrates the co-occurring site mutations obtained by rule mining can capture the evolution of influenza viruses, and confirms that cooperative interactions among sites of HA1 protein drive the influenza antigenic evolution.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12920-016-0230-5) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kilbourne, Ed" uniqKey="Kilbourne E">ED 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Seok</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, Yp" uniqKey="Lin Y">YP Lin</name></author><author><name sortKey="Xiong, X" uniqKey="Xiong X">X Xiong</name></author><author><name sortKey="Wharton, Sa" uniqKey="Wharton S">SA Wharton</name></author><author><name sortKey="Martin, Sr" uniqKey="Martin S">SR Martin</name></author><author><name sortKey="Coombs, Pj" uniqKey="Coombs P">PJ Coombs</name></author><author><name sortKey="Vachieri, Sg" uniqKey="Vachieri S">SG Vachieri</name></author><author><name sortKey="Gamblin, Sj" uniqKey="Gamblin S">SJ Gamblin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ni, F" uniqKey="Ni F">F Ni</name></author><author><name sortKey="Mbawuike, In" uniqKey="Mbawuike I">IN Mbawuike</name></author><author><name sortKey="Kondrashkina, E" uniqKey="Kondrashkina E">E Kondrashkina</name></author><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pettersen, Ef" uniqKey="Pettersen E">EF Pettersen</name></author><author><name sortKey="Goddard, Td" uniqKey="Goddard T">TD Goddard</name></author><author><name sortKey="Huang, Cc" uniqKey="Huang C">CC Huang</name></author><author><name sortKey="Couch, Gs" uniqKey="Couch G">GS Couch</name></author><author><name sortKey="Greenblatt, Dm" uniqKey="Greenblatt D">DM Greenblatt</name></author><author><name sortKey="Meng, Ec" uniqKey="Meng E">EC Meng</name></author><author><name sortKey="Ferrin, Te" uniqKey="Ferrin T">TE Ferrin</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lee, M S" uniqKey="Lee M">M-S Lee</name></author><author><name sortKey="Chen, Js E" uniqKey="Chen J">JS-E Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, J W" uniqKey="Huang J">J-W Huang</name></author><author><name sortKey="Lin, W F" uniqKey="Lin W">W-F Lin</name></author><author><name sortKey="Yang, J M" uniqKey="Yang J">J-M Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, R" uniqKey="Xu R">R Xu</name></author><author><name sortKey="Ekiert, Dc" uniqKey="Ekiert D">DC Ekiert</name></author><author><name sortKey="Krause, Jc" uniqKey="Krause J">JC Krause</name></author><author><name sortKey="Hai, R" uniqKey="Hai R">R Hai</name></author><author><name sortKey="Crowe, Je" uniqKey="Crowe J">JE Crowe</name></author><author><name sortKey="Wilson, Ia" uniqKey="Wilson I">IA Wilson</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q Wang</name></author><author><name sortKey="Cheng, F" uniqKey="Cheng F">F Cheng</name></author><author><name sortKey="Lu, M" uniqKey="Lu M">M Lu</name></author><author><name sortKey="Tian, X" uniqKey="Tian X">X Tian</name></author><author><name sortKey="Ma, J" uniqKey="Ma J">J Ma</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Singapour</li></country></list><tree><country name="Singapour"><noRegion><name sortKey="Chen, Haifen" sort="Chen, Haifen" uniqKey="Chen H" first="Haifen" last="Chen">Haifen Chen</name></noRegion><name sortKey="Kwoh, Chee Keong" sort="Kwoh, Chee Keong" uniqKey="Kwoh C" first="Chee-Keong" last="Kwoh">Chee-Keong Kwoh</name><name sortKey="Zheng, Jie" sort="Zheng, Jie" uniqKey="Zheng J" first="Jie" last="Zheng">Jie Zheng</name><name sortKey="Zheng, Jie" sort="Zheng, Jie" uniqKey="Zheng J" first="Jie" last="Zheng">Jie Zheng</name><name sortKey="Zhou, Xinrui" sort="Zhou, Xinrui" uniqKey="Zhou X" first="Xinrui" last="Zhou">Xinrui Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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