Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees
Identifieur interne : 001673 ( Istex/Corpus ); précédent : 001672; suivant : 001674Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees
Auteurs : Rasmus Hovmöller ; Boyan Alexandrov ; Jori Hardman ; Daniel JaniesSource :
- Cladistics [ 0748-3007 ] ; 2010-02.
Abstract
Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high‐quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum‐length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled “Routemap” (http://routemap.osu.edu). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data. © The Willi Hennig Society 2009.
Url:
DOI: 10.1111/j.1096-0031.2009.00297.x
Links to Exploration step
ISTEX:910816E6EA8157FB9FCFA042E363963040321663Le document en format XML
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A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high‐quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum‐length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled “Routemap” (http://routemap.osu.edu). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. 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xml:lang="en">UNITED STATES</country></address></affiliation><affiliation><orgName type="division">Department of Biomedical Informatics</orgName><orgName type="institution">The Ohio State University</orgName><address><addrLine>Columbus</addrLine><addrLine>OH, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">Boyan</forename><surname>Alexandrov</surname></persName><affiliation><orgName type="division">Department of Biomedical Informatics</orgName><orgName type="institution">The Ohio State University</orgName><address><addrLine>Columbus</addrLine><addrLine>OH, USA</addrLine><country key="US" xml:lang="en">UNITED STATES</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Jori</forename><surname>Hardman</surname></persName><affiliation><orgName type="division">Department of Biomedical Informatics</orgName><orgName 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<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract xml:lang="en" style="main"><head>Abstract</head><p>Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high‐quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum‐length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled “Routemap” (<ref type="url">http://routemap.osu.edu</ref>). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data.</p><p>© The Willi Hennig Society 2009.</p></abstract><textClass><keywords rend="tocHeading1"><term>BIOGEOGRAPHY</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-M4QQX498-6/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1096-0031</doi><issn type="print">0748-3007</issn><issn type="electronic">1096-0031</issn><idGroup><id type="product" value="CLA"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="CLADISTICS">Cladistics</title></titleGroup></publicationMeta><publicationMeta level="part" position="02001"><doi origin="wiley">10.1111/cla.2009.26.issue-1</doi><numberingGroup><numbering type="journalVolume" number="26">26</numbering><numbering type="journalIssue" number="1">1</numbering></numberingGroup><coverDate startDate="2010-02">February 2010</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="1" status="forIssue"><doi origin="wiley">10.1111/j.1096-0031.2009.00297.x</doi><idGroup><id type="unit" value="CLA297"></id></idGroup><countGroup><count type="pageTotal" number="13"></count></countGroup><titleGroup><title type="tocHeading1">BIOGEOGRAPHY</title></titleGroup><copyright>© The Willi Hennig Society 2009</copyright><eventGroup><event type="firstOnline" date="2009-11-13"></event><event type="publishedOnlineFinalForm" date="2010-01-05"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.3.2 mode:FullText source:FullText result:FullText" date="2010-03-04"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-15"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-16"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="1">1</numbering><numbering type="pageLast" number="13">13</numbering></numberingGroup><correspondenceTo>
*Corresponding authors:
<i>E‐mail addresses:</i><email>Daniel.Janies@osumc.edu</email> and <email>rhovmoller@mbi.osu.edu</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:CLA.CLA297.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Accepted 6 October 2009</unparsedEditorialHistory><countGroup><count type="figureTotal" number="4"></count><count type="tableTotal" number="0"></count></countGroup><titleGroup><title type="main">Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees</title><title type="shortAuthors"><i>R. Hovmöller et al.</i></title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1 #a2" corresponding="yes"><personName><givenNames>Rasmus</givenNames><familyName>Hovmöller</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a2"><personName><givenNames>Boyan</givenNames><familyName>Alexandrov</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a2"><personName><givenNames>Jori</givenNames><familyName>Hardman</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a2" corresponding="yes"><personName><givenNames>Daniel</givenNames><familyName>Janies</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="US"><unparsedAffiliation>Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="US"><unparsedAffiliation>Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA</unparsedAffiliation></affiliation></affiliationGroup><supportingInformation><p><link href="http://routemap.osu.edu/publications">http://routemap.osu.edu/publications</link></p><p>Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:07483007:media:cla297:CLA_297_sm_HA1646"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:07483007:media:cla297:CLA_297_sm_NA1335"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:07483007:media:cla297:CLA_297_sm_WF482"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high‐quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum‐length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled “Routemap” (<url href="http://routemap.osu.edu">http://routemap.osu.edu</url>). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data.</p><p>© The Willi Hennig Society 2009.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Tracking the geographical spread of avian influenza (H5N1) with multiple phylogenetic trees</title></titleInfo><name type="personal"><namePart type="given">Rasmus</namePart><namePart type="family">Hovmöller</namePart><affiliation>Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA</affiliation><affiliation>Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA</affiliation><affiliation>E-mail: Daniel.Janies@osumc.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Boyan</namePart><namePart type="family">Alexandrov</namePart><affiliation>Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jori</namePart><namePart type="family">Hardman</namePart><affiliation>Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Daniel</namePart><namePart type="family">Janies</namePart><affiliation>Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA</affiliation><affiliation>E-mail: Daniel.Janies@osumc.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2010-02</dateIssued><edition>Accepted 6 October 2009</edition><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">4</extent><extent unit="tables">0</extent></physicalDescription><abstract lang="en">Avian influenza (H5N1) has been of great social and economic importance since it first infected humans in Hong Kong in 1997. A highly pathogenic strain has spread from China and has killed humans in east Asia, west Africa, south Asia, and the Middle East. Recently, several molecular phylogenetic studies have focused on the relationships of various clades of H5N1 and their spread over time, space, and various hosts. These studies examining the geographical spread of H5N1 have based their conclusions on a single tree. This tree often results from the analysis of the genomic segment coding for the haemagglutinin (HA) or neuraminidase (NA) proteins and a limited sample of viral isolates. Here we present the first study using multiple candidate trees to estimate geographical transmission routes of H5N1. In addition, we use all high‐quality HA and NA sequences available to the public as of June 2008. We estimated geographical transmission routes of H5N1 by optimizing multistate characters with states representing different geographical regions over a pool of presumed minimum‐length trees. We also developed means to visualize our results in Keyhole Markup Language (KML) for virtual globes. We provide these methods as a web application entitled “Routemap” (http://routemap.osu.edu). The resulting visualizations are akin to airline route maps but they depict the routes of spread of viral lineages. We compare our results with the results of previous studies. We focus on the sensitivity of results to sampling of tree space, character coding schemes, optimization methods, and taxon sampling. In conclusion, we find that using one tree and a single character optimization method will ignore many of the transmission routes indicated by genetic sequence and geographical data. © The Willi Hennig Society 2009.</abstract><relatedItem type="host"><titleInfo><title>Cladistics</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><note type="content"> http://routemap.osu.edu/publications Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. http://routemap.osu.edu/publications Please note: Wiley‐Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. 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