Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches
Identifieur interne : 001705 ( Istex/Corpus ); précédent : 001704; suivant : 001706Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches
Auteurs : Ramaiah ArunachalamSource :
- Genetica [ 0016-6707 ] ; 2013-06-01.
English descriptors
Abstract
Abstract: In the twenty-first century, the first pandemic novel human influenza A/H1N1virus (NIV) outbreak was reported at Mexico and USA on March and early April, 2009 respectively. The outbreak occurred among human populations due to the presence of meager or no immune response against newly emerged viruses. The success of vaccines and drugs depends on their low susceptibility to the formation of escape mutants in virus. Identification of excess, non-synonymous substitutions over synonymous ones is a main indicator of positive Darwinian selection in protein-coding genes of NIVs. The positive Darwinian selection operating on each site of proteins were inferred by computing ω, the ratio of the non-synonymous/synonymous substitutions [dN/dS (or) Ka/Ks], which was calculated by three different methods in terms of codon-based maximum likelihood, branch-site and empirical Bayesian methods under various models. Totally, nine sites from PB2, PB1, HA, M2 and NS1 are inferred as positively selected. The function for amino acid sites of NIVs proteins under positive selection are inferred by comparing the sites with experimentally determined functionally known amino acid sites. Completely 4 positively selected sites of PB1, HA and M2 are found to be involved in B-cell epitopes (BCEs). Interestingly, most of these sites are also involving in T-cell epitopes (TCEs). However, more sites under positive selection forces are involved in TCEs than those of BCEs. Amino acid sites engaged in both BCEs and TCEs should be measured as highly suitable targets, because these sites could induce the strong humoral and cellular immune responses against targets.
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DOI: 10.1007/s10709-013-9713-x
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The outbreak occurred among human populations due to the presence of meager or no immune response against newly emerged viruses. The success of vaccines and drugs depends on their low susceptibility to the formation of escape mutants in virus. Identification of excess, non-synonymous substitutions over synonymous ones is a main indicator of positive Darwinian selection in protein-coding genes of NIVs. The positive Darwinian selection operating on each site of proteins were inferred by computing ω, the ratio of the non-synonymous/synonymous substitutions [dN/dS (or) Ka/Ks], which was calculated by three different methods in terms of codon-based maximum likelihood, branch-site and empirical Bayesian methods under various models. Totally, nine sites from PB2, PB1, HA, M2 and NS1 are inferred as positively selected. The function for amino acid sites of NIVs proteins under positive selection are inferred by comparing the sites with experimentally determined functionally known amino acid sites. Completely 4 positively selected sites of PB1, HA and M2 are found to be involved in B-cell epitopes (BCEs). Interestingly, most of these sites are also involving in T-cell epitopes (TCEs). However, more sites under positive selection forces are involved in TCEs than those of BCEs. 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The function for amino acid sites of NIVs proteins under positive selection are inferred by comparing the sites with experimentally determined functionally known amino acid sites. Completely 4 positively selected sites of PB1, HA and M2 are found to be involved in B-cell epitopes (BCEs). Interestingly, most of these sites are also involving in T-cell epitopes (TCEs). However, more sites under positive selection forces are involved in TCEs than those of BCEs. 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The function for amino acid sites of NIVs proteins under positive selection are inferred by comparing the sites with experimentally determined functionally known amino acid sites. Completely 4 positively selected sites of PB1, HA and M2 are found to be involved in B-cell epitopes (BCEs). Interestingly, most of these sites are also involving in T-cell epitopes (TCEs). However, more sites under positive selection forces are involved in TCEs than those of BCEs. 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approaches</ArticleTitle><ArticleFirstPage>143</ArticleFirstPage><ArticleLastPage>155</ArticleLastPage><ArticleHistory><RegistrationDate><Year>2013</Year><Month>3</Month><Day>18</Day></RegistrationDate><Received><Year>2012</Year><Month>11</Month><Day>15</Day></Received><Accepted><Year>2013</Year><Month>3</Month><Day>18</Day></Accepted><OnlineDate><Year>2013</Year><Month>3</Month><Day>26</Day></OnlineDate></ArticleHistory><ArticleCopyright><CopyrightHolderName>Springer Science+Business Media Dordrecht</CopyrightHolderName><CopyrightYear>2013</CopyrightYear></ArticleCopyright><ArticleGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ArticleGrants></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1 Aff2" CorrespondingAffiliationID="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Ramaiah</GivenName><FamilyName>Arunachalam</FamilyName></AuthorName><Contact><Email>arunachalamphd@gmail.com</Email></Contact></Author><Affiliation ID="Aff1"><OrgDivision>Sri Paramakalyani Centre for Environmental Sciences</OrgDivision><OrgName>Manonmaniam Sundaranar University</OrgName><OrgAddress><City>Alwarkurichi</City><Postcode>627412</Postcode><State>Tamil Nadu</State><Country Code="IN">India</Country></OrgAddress></Affiliation><Affiliation ID="Aff2"><OrgDivision>Structural Bioinformatics Laboratory, Department of Biosciences</OrgDivision><OrgName>Åbo Akademi University</OrgName><OrgAddress><Postcode>20520</Postcode><City>Turku</City><Country Code="FI">Finland</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En" OutputMedium="All"><Heading>Abstract</Heading><Para>In the twenty-first century, the first pandemic novel human influenza A/H1N1virus (NIV) outbreak was reported at Mexico and USA on March and early April, 2009 respectively. The outbreak occurred among human populations due to the presence of meager or no immune response against newly emerged viruses. The success of vaccines and drugs depends on their low susceptibility to the formation of escape mutants in virus. Identification of excess, non-synonymous substitutions over synonymous ones is a main indicator of positive Darwinian selection in protein-coding genes of NIVs. The positive Darwinian selection operating on each site of proteins were inferred by computing ω, the ratio of the non-synonymous/synonymous substitutions [dN/dS (or) K<Subscript>a</Subscript>/K<Subscript>s</Subscript>], which was calculated by three different methods in terms of codon-based maximum likelihood, branch-site and empirical Bayesian methods under various models. Totally, nine sites from PB2, PB1, HA, M2 and NS1 are inferred as positively selected. The function for amino acid sites of NIVs proteins under positive selection are inferred by comparing the sites with experimentally determined functionally known amino acid sites. Completely 4 positively selected sites of PB1, HA and M2 are found to be involved in B-cell epitopes (BCEs). Interestingly, most of these sites are also involving in T-cell epitopes (TCEs). However, more sites under positive selection forces are involved in TCEs than those of BCEs. Amino acid sites engaged in both BCEs and TCEs should be measured as highly suitable targets, because these sites could induce the strong humoral and cellular immune responses against targets.</Para></Abstract><KeywordGroup Language="En" OutputMedium="All"><Heading>Keywords</Heading><Keyword>Novel influenza A/H1N1 virus</Keyword><Keyword>Genome</Keyword><Keyword>Natural selection</Keyword><Keyword>Amino acid function</Keyword></KeywordGroup><ArticleNote Type="ESMHint"><Heading>Electronic supplementary material</Heading><SimplePara>The online version of this article (doi:<ExternalRef><RefSource>10.1007/s10709-013-9713-x</RefSource><RefTarget Address="10.1007/s10709-013-9713-x" TargetType="DOI"></RefTarget></ExternalRef>) contains supplementary material, which is available to authorized users.</SimplePara></ArticleNote></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches</title></titleInfo><name type="personal" displayLabel="corresp"><namePart type="given">Ramaiah</namePart><namePart type="family">Arunachalam</namePart><affiliation>Sri Paramakalyani Centre for Environmental Sciences, Manonmaniam Sundaranar University, 627412, Alwarkurichi, Tamil Nadu, India</affiliation><affiliation>Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, 20520, Turku, Finland</affiliation><affiliation>E-mail: arunachalamphd@gmail.com</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>Springer Netherlands</publisher><place><placeTerm type="text">Dordrecht</placeTerm></place><dateCreated encoding="w3cdtf">2012-11-15</dateCreated><dateIssued encoding="w3cdtf">2013-06-01</dateIssued><copyrightDate encoding="w3cdtf">2013</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: In the twenty-first century, the first pandemic novel human influenza A/H1N1virus (NIV) outbreak was reported at Mexico and USA on March and early April, 2009 respectively. The outbreak occurred among human populations due to the presence of meager or no immune response against newly emerged viruses. The success of vaccines and drugs depends on their low susceptibility to the formation of escape mutants in virus. Identification of excess, non-synonymous substitutions over synonymous ones is a main indicator of positive Darwinian selection in protein-coding genes of NIVs. The positive Darwinian selection operating on each site of proteins were inferred by computing ω, the ratio of the non-synonymous/synonymous substitutions [dN/dS (or) Ka/Ks], which was calculated by three different methods in terms of codon-based maximum likelihood, branch-site and empirical Bayesian methods under various models. Totally, nine sites from PB2, PB1, HA, M2 and NS1 are inferred as positively selected. The function for amino acid sites of NIVs proteins under positive selection are inferred by comparing the sites with experimentally determined functionally known amino acid sites. Completely 4 positively selected sites of PB1, HA and M2 are found to be involved in B-cell epitopes (BCEs). Interestingly, most of these sites are also involving in T-cell epitopes (TCEs). However, more sites under positive selection forces are involved in TCEs than those of BCEs. Amino acid sites engaged in both BCEs and TCEs should be measured as highly suitable targets, because these sites could induce the strong humoral and cellular immune responses against targets.</abstract><subject lang="en"><genre>Keywords</genre><topic>Novel influenza A/H1N1 virus</topic><topic>Genome</topic><topic>Natural selection</topic><topic>Amino acid function</topic></subject><relatedItem type="host"><titleInfo><title>Genetica</title><subTitle>An International Journal of Genetics and Evolution</subTitle></titleInfo><titleInfo type="abbreviated"><title>Genetica</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">2013-06-27</dateIssued><copyrightDate encoding="w3cdtf">2013</copyrightDate></originInfo><subject><genre>Journal-Subject-Collection</genre><topic authority="SpringerSubjectCodes" authorityURI="SC3">Biomedical and Life Sciences</topic></subject><subject><genre>Journal-Subject-Group</genre><topic authority="SpringerSubjectCodes" authorityURI="SCL">Life Sciences</topic><topic authority="SpringerSubjectCodes" authorityURI="SCL00004">Life Sciences, general</topic><topic authority="SpringerSubjectCodes" authorityURI="SCL25023">Animal Genetics and Genomics</topic><topic authority="SpringerSubjectCodes" authorityURI="SCL24027">Plant Genetics & Genomics</topic><topic authority="SpringerSubjectCodes" authorityURI="SCB12008">Human Genetics</topic><topic authority="SpringerSubjectCodes" authorityURI="SCL23039">Microbial Genetics and Genomics</topic></subject><identifier type="ISSN">0016-6707</identifier><identifier type="eISSN">1573-6857</identifier><identifier type="JournalID">10709</identifier><identifier type="IssueArticleCount">14</identifier><identifier type="VolumeIssueCount">12</identifier><part><date>2013</date><detail type="volume"><number>141</number><caption>vol.</caption></detail><detail type="issue"><number>4-6</number><caption>no.</caption></detail><extent unit="pages"><start>143</start><end>155</end></extent></part><recordInfo><recordOrigin>Springer Science+Business Media Dordrecht, 2013</recordOrigin></recordInfo></relatedItem><identifier type="istex">90E94B1E6C56E7D6EB85AE7F147A15EFF402162E</identifier><identifier type="ark">ark:/67375/VQC-ML3GKP9M-6</identifier><identifier type="DOI">10.1007/s10709-013-9713-x</identifier><identifier type="ArticleID">9713</identifier><identifier type="ArticleID">s10709-013-9713-x</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer Science+Business Media Dordrecht, 2013</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Springer Science+Business Media Dordrecht, 2013</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-ML3GKP9M-6/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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