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Improving pandemic influenza risk assessment

Identifieur interne : 000A90 ( Ncbi/Merge ); précédent : 000A89; suivant : 000A91

Improving pandemic influenza risk assessment

Auteurs : Colin A. Russell [Royaume-Uni] ; Peter M. Kasson [États-Unis] ; Ruben O. Donis [États-Unis] ; Steven Riley [Royaume-Uni] ; John Dunbar [États-Unis] ; Andrew Rambaut [États-Unis] ; Jason Asher [États-Unis] ; Stephen Burke [États-Unis] ; C Todd Davis [États-Unis] ; Rebecca J. Garten [États-Unis] ; Sandrasegaram Gnanakaran [États-Unis] ; Simon I. Hay [Royaume-Uni] ; Sander Herfst [Pays-Bas] ; Nicola S. Lewis [Royaume-Uni] ; James O. Lloyd-Smith [États-Unis] ; Catherine A. Macken [États-Unis] ; Sebastian Maurer-Stroh [Singapour] ; Elizabeth Neuhaus [États-Unis] ; Colin R. Parrish [États-Unis] ; Kim M. Pepin [États-Unis] ; Samuel S. Shepard [États-Unis] ; David L. Smith [États-Unis] ; David L. Suarez [États-Unis] ; Susan C. Trock [États-Unis] ; Marc-Alain Widdowson [États-Unis] ; Dylan B. George [États-Unis] ; Marc Lipsitch [États-Unis] ; Jesse D. Bloom [États-Unis]

Source :

RBID : PMC:4199076

Abstract

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

DOI:http://dx.doi.org/10.7554/eLife.03883.001


Url:
DOI: 10.7554/eLife.03883
PubMed: 25321142
PubMed Central: 4199076

Links toward previous steps (curation, corpus...)

Links to Exploration step

PMC:4199076

Le document en format XML

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<addr-line>Washington, DC</addr-line>
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<addr-line>Boston</addr-line>
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<nlm:aff id="aff1">
<bold>Colin A Russell</bold>
<addr-line>Department of Veterinary Medicine</addr-line>
,
<institution>University of Cambridge</institution>
,
<addr-line>Cambridge</addr-line>
,
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Kasson, Peter M" sort="Kasson, Peter M" uniqKey="Kasson P" first="Peter M" last="Kasson">Peter M. Kasson</name>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<bold>Peter M Kasson</bold>
<addr-line>Department of Biomedical Engineering</addr-line>
,
<institution>University of Virginia</institution>
,
<addr-line>Charlottesville</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Donis, Ruben O" sort="Donis, Ruben O" uniqKey="Donis R" first="Ruben O" last="Donis">Ruben O. Donis</name>
<affiliation wicri:level="1">
<nlm:aff id="aff3">
<bold>Ruben O Donis</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Riley, Steven" sort="Riley, Steven" uniqKey="Riley S" first="Steven" last="Riley">Steven Riley</name>
<affiliation wicri:level="1">
<nlm:aff id="aff4">
<bold>Steven Riley</bold>
<addr-line>Department of Infectious Disease Epidemiology</addr-line>
,
<institution>School of Public Health, Imperial College London</institution>
,
<addr-line>London</addr-line>
,
<country>United Kingdom</country>
;
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Dunbar, John" sort="Dunbar, John" uniqKey="Dunbar J" first="John" last="Dunbar">John Dunbar</name>
<affiliation wicri:level="1">
<nlm:aff id="aff5">
<bold>John Dunbar</bold>
<addr-line>Bioscience Division</addr-line>
,
<institution>Los Alamos National Laboratory</institution>
,
<addr-line>Los Alamos</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name>
<affiliation wicri:level="1">
<nlm:aff id="aff6">
<bold>Andrew Rambaut</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Institute of Evolutionary Biology</addr-line>
,
<institution>University of Edinburgh</institution>
,
<addr-line>Edinburgh</addr-line>
,
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Asher, Jason" sort="Asher, Jason" uniqKey="Asher J" first="Jason" last="Asher">Jason Asher</name>
<affiliation wicri:level="1">
<nlm:aff id="aff7">
<bold>Jason Asher</bold>
<addr-line>Leidos contract support to the Division of Analytic Decision Support</addr-line>
,
<institution>Biomedical Advanced Research and Development Authority, Department of Health and Human Services</institution>
,
<addr-line>Washington</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Burke, Stephen" sort="Burke, Stephen" uniqKey="Burke S" first="Stephen" last="Burke">Stephen Burke</name>
<affiliation wicri:level="1">
<nlm:aff id="aff8">
<bold>Stephen Burke</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C Todd" last="Davis">C Todd Davis</name>
<affiliation wicri:level="1">
<nlm:aff id="aff9">
<bold>C Todd Davis</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Garten, Rebecca J" sort="Garten, Rebecca J" uniqKey="Garten R" first="Rebecca J" last="Garten">Rebecca J. Garten</name>
<affiliation wicri:level="1">
<nlm:aff id="aff10">
<bold>Rebecca J Garten</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Gnanakaran, Sandrasegaram" sort="Gnanakaran, Sandrasegaram" uniqKey="Gnanakaran S" first="Sandrasegaram" last="Gnanakaran">Sandrasegaram Gnanakaran</name>
<affiliation wicri:level="1">
<nlm:aff id="aff11">
<bold>Sandrasegaram Gnanakaran</bold>
<addr-line>Bioscience Division</addr-line>
,
<institution>Los Alamos National Laboratory</institution>
,
<addr-line>Los Alamos</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Hay, Simon I" sort="Hay, Simon I" uniqKey="Hay S" first="Simon I" last="Hay">Simon I. Hay</name>
<affiliation wicri:level="1">
<nlm:aff id="aff12">
<bold>Simon I Hay</bold>
<addr-line>Spatial Ecology and Epidemiology Group, Department of Zoology</addr-line>
,
<institution>University of Oxford</institution>
,
<addr-line>Oxford</addr-line>
,
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Herfst, Sander" sort="Herfst, Sander" uniqKey="Herfst S" first="Sander" last="Herfst">Sander Herfst</name>
<affiliation wicri:level="1">
<nlm:aff id="aff13">
<bold>Sander Herfst</bold>
<addr-line>Department of Viroscience</addr-line>
,
<institution>Postgraduate School of Molecular Medicine, Erasmus Medical Center</institution>
,
<addr-line>Rotterdam</addr-line>
,
<country>Netherlands</country>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Lewis, Nicola S" sort="Lewis, Nicola S" uniqKey="Lewis N" first="Nicola S" last="Lewis">Nicola S. Lewis</name>
<affiliation wicri:level="1">
<nlm:aff id="aff14">
<bold>Nicola S Lewis</bold>
<addr-line>Department of Zoology</addr-line>
,
<institution>University of Cambridge</institution>
,
<addr-line>Cambridge</addr-line>
,
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Lloyd Smith, James O" sort="Lloyd Smith, James O" uniqKey="Lloyd Smith J" first="James O" last="Lloyd-Smith">James O. Lloyd-Smith</name>
<affiliation wicri:level="1">
<nlm:aff id="aff15">
<bold>James O Lloyd-Smith</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Department of Ecology and Evolutionary Biology</addr-line>
,
<institution>University of California, Los Angeles</institution>
,
<addr-line>Los Angeles</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Macken, Catherine A" sort="Macken, Catherine A" uniqKey="Macken C" first="Catherine A" last="Macken">Catherine A. Macken</name>
<affiliation wicri:level="1">
<nlm:aff id="aff16">
<bold>Catherine A Macken</bold>
<addr-line>Bioscience Division</addr-line>
,
<institution>Los Alamos National Laboratory</institution>
,
<addr-line>Los Alamos</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Maurer Stroh, Sebastian" sort="Maurer Stroh, Sebastian" uniqKey="Maurer Stroh S" first="Sebastian" last="Maurer-Stroh">Sebastian Maurer-Stroh</name>
<affiliation wicri:level="1">
<nlm:aff id="aff17">
<bold>Sebastian Maurer-Stroh</bold>
<addr-line>Bioinformatics Institute</addr-line>
,
<institution>Agency for Science Technology and Research</institution>
,
<addr-line>Singapore</addr-line>
,
<country>Singapore</country>
;
<addr-line>National Public Health Laboratory, Communicable Diseases Division</addr-line>
,
<institution>Ministry of Health</institution>
,
<addr-line>Singapore</addr-line>
,
<country>Singapore</country>
;
<addr-line>School of Biological Sciences</addr-line>
,
<institution>Nanyang Technological University</institution>
,
<addr-line>Singapore</addr-line>
,
<country>Singapore</country>
</nlm:aff>
<country xml:lang="fr">Singapour</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Neuhaus, Elizabeth" sort="Neuhaus, Elizabeth" uniqKey="Neuhaus E" first="Elizabeth" last="Neuhaus">Elizabeth Neuhaus</name>
<affiliation wicri:level="1">
<nlm:aff id="aff18">
<bold>Elizabeth Neuhaus</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Parrish, Colin R" sort="Parrish, Colin R" uniqKey="Parrish C" first="Colin R" last="Parrish">Colin R. Parrish</name>
<affiliation wicri:level="1">
<nlm:aff id="aff19">
<bold>Colin R Parrish</bold>
<addr-line>James A Baker Institute</addr-line>
,
<institution>College of Veterinary Medicine, Cornell University</institution>
,
<addr-line>Ithaca</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Pepin, Kim M" sort="Pepin, Kim M" uniqKey="Pepin K" first="Kim M" last="Pepin">Kim M. Pepin</name>
<affiliation wicri:level="1">
<nlm:aff id="aff20">
<bold>Kim M Pepin</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>National Wildlife Research Center</addr-line>
,
<institution>United States Department of Agriculture</institution>
,
<addr-line>Fort Collins</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Shepard, Samuel S" sort="Shepard, Samuel S" uniqKey="Shepard S" first="Samuel S" last="Shepard">Samuel S. Shepard</name>
<affiliation wicri:level="1">
<nlm:aff id="aff21">
<bold>Samuel S Shepard</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Smith, David L" sort="Smith, David L" uniqKey="Smith D" first="David L" last="Smith">David L. Smith</name>
<affiliation wicri:level="1">
<nlm:aff id="aff22">
<bold>David L Smith</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Spatial Ecology and Epidemiology Group, Department of Zoology</addr-line>
,
<institution>University of Oxford</institution>
,
<addr-line>Oxford</addr-line>
,
<country>United Kingdom</country>
;
<institution>Sanaria Institute for Global Health and Tropical Medicine</institution>
,
<addr-line>Rockville</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Suarez, David L" sort="Suarez, David L" uniqKey="Suarez D" first="David L" last="Suarez">David L. Suarez</name>
<affiliation wicri:level="1">
<nlm:aff id="aff23">
<bold>David L Suarez</bold>
<addr-line>Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratories</addr-line>
,
<institution>United States Department of Agriculture</institution>
,
<addr-line>Athens</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Trock, Susan C" sort="Trock, Susan C" uniqKey="Trock S" first="Susan C" last="Trock">Susan C. Trock</name>
<affiliation wicri:level="1">
<nlm:aff id="aff24">
<bold>Susan C Trock</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Widdowson, Marc Alain" sort="Widdowson, Marc Alain" uniqKey="Widdowson M" first="Marc-Alain" last="Widdowson">Marc-Alain Widdowson</name>
<affiliation wicri:level="1">
<nlm:aff id="aff25">
<bold>Marc-Alain Widdowson</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="George, Dylan B" sort="George, Dylan B" uniqKey="George D" first="Dylan B" last="George">Dylan B. George</name>
<affiliation wicri:level="1">
<nlm:aff id="aff26">
<bold>Dylan B George</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Division of Analytic Decision Support, Biomedical Advanced Research and Development Authority</addr-line>
,
<institution>Assistant Secretary for Preparedness and Response, Department of Health and Human Services</institution>
,
<addr-line>Washington, DC</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Lipsitch, Marc" sort="Lipsitch, Marc" uniqKey="Lipsitch M" first="Marc" last="Lipsitch">Marc Lipsitch</name>
<affiliation wicri:level="1">
<nlm:aff id="aff27">
<bold>Marc Lipsitch</bold>
<addr-line>Center for Communicable Disease Dynamics, Department of Epidemiology</addr-line>
,
<institution>Harvard School of Public Health</institution>
,
<addr-line>Boston</addr-line>
,
<country>United States</country>
;
<addr-line>Department of Immunology and Infectious Diseases</addr-line>
,
<institution>Harvard School of Public Health</institution>
,
<addr-line>Boston</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Bloom, Jesse D" sort="Bloom, Jesse D" uniqKey="Bloom J" first="Jesse D" last="Bloom">Jesse D. Bloom</name>
<affiliation wicri:level="1">
<nlm:aff id="aff28">
<bold>Jesse D Bloom</bold>
<addr-line>Division of Basic Sciences</addr-line>
,
<institution>Fred Hutchinson Cancer Research Center</institution>
,
<addr-line>Seattle</addr-line>
,
<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series>
<title level="j">eLife</title>
<idno type="eISSN">2050-084X</idno>
<imprint>
<date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.</p>
<p>
<bold>DOI:</bold>
<ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03883.001">http://dx.doi.org/10.7554/eLife.03883.001</ext-link>
</p>
</div>
</front>
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</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">eLife</journal-id>
<journal-id journal-id-type="iso-abbrev">Elife</journal-id>
<journal-id journal-id-type="hwp">eLife</journal-id>
<journal-id journal-id-type="publisher-id">eLife</journal-id>
<journal-title-group>
<journal-title>eLife</journal-title>
</journal-title-group>
<issn pub-type="epub">2050-084X</issn>
<publisher>
<publisher-name>eLife Sciences Publications, Ltd</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">25321142</article-id>
<article-id pub-id-type="pmc">4199076</article-id>
<article-id pub-id-type="publisher-id">03883</article-id>
<article-id pub-id-type="doi">10.7554/eLife.03883</article-id>
<article-categories>
<subj-group subj-group-type="display-channel">
<subject>Feature Article</subject>
</subj-group>
<subj-group subj-group-type="heading">
<subject>Genomics and Evolutionary Biology</subject>
</subj-group>
<subj-group subj-group-type="heading">
<subject>Microbiology and Infectious Disease</subject>
</subj-group>
<subj-group subj-group-type="sub-display-channel">
<subject>Science Forum</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Improving pandemic influenza risk assessment</article-title>
</title-group>
<contrib-group>
<contrib id="author-4919" contrib-type="author">
<name>
<surname>Russell</surname>
<given-names>Colin A</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con1"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-4526" contrib-type="author">
<name>
<surname>Kasson</surname>
<given-names>Peter M</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con2"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16013" contrib-type="author">
<name>
<surname>Donis</surname>
<given-names>Ruben O</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con3"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-9283" contrib-type="author">
<name>
<surname>Riley</surname>
<given-names>Steven</given-names>
</name>
<xref ref-type="aff" rid="aff4">4</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con4"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16014" contrib-type="author">
<name>
<surname>Dunbar</surname>
<given-names>John</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con5"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-4769" contrib-type="author">
<name>
<surname>Rambaut</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="aff6">6</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con6"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16015" contrib-type="author">
<name>
<surname>Asher</surname>
<given-names>Jason</given-names>
</name>
<xref ref-type="aff" rid="aff7">7</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con7"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16016" contrib-type="author">
<name>
<surname>Burke</surname>
<given-names>Stephen</given-names>
</name>
<xref ref-type="aff" rid="aff8">8</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con8"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16017" contrib-type="author">
<name>
<surname>Davis</surname>
<given-names>C Todd</given-names>
</name>
<xref ref-type="aff" rid="aff9">9</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con9"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16018" contrib-type="author">
<name>
<surname>Garten</surname>
<given-names>Rebecca J</given-names>
</name>
<xref ref-type="aff" rid="aff10">10</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con10"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16019" contrib-type="author">
<name>
<surname>Gnanakaran</surname>
<given-names>Sandrasegaram</given-names>
</name>
<xref ref-type="aff" rid="aff11">11</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con11"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-4122" contrib-type="author">
<name>
<surname>Hay</surname>
<given-names>Simon I</given-names>
</name>
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-0611-7272</contrib-id>
<xref ref-type="aff" rid="aff12">12</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con12"></xref>
<xref ref-type="fn" rid="conf1"></xref>
</contrib>
<contrib id="author-16020" contrib-type="author">
<name>
<surname>Herfst</surname>
<given-names>Sander</given-names>
</name>
<xref ref-type="aff" rid="aff13">13</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con13"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16021" contrib-type="author">
<name>
<surname>Lewis</surname>
<given-names>Nicola S</given-names>
</name>
<xref ref-type="aff" rid="aff14">14</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con14"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16022" contrib-type="author">
<name>
<surname>Lloyd-Smith</surname>
<given-names>James O</given-names>
</name>
<xref ref-type="aff" rid="aff15">15</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con15"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16023" contrib-type="author">
<name>
<surname>Macken</surname>
<given-names>Catherine A</given-names>
</name>
<xref ref-type="aff" rid="aff16">16</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con16"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16024" contrib-type="author">
<name>
<surname>Maurer-Stroh</surname>
<given-names>Sebastian</given-names>
</name>
<xref ref-type="aff" rid="aff17">17</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con17"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16025" contrib-type="author">
<name>
<surname>Neuhaus</surname>
<given-names>Elizabeth</given-names>
</name>
<xref ref-type="aff" rid="aff18">18</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con18"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16026" contrib-type="author">
<name>
<surname>Parrish</surname>
<given-names>Colin R</given-names>
</name>
<xref ref-type="aff" rid="aff19">19</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con19"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16027" contrib-type="author">
<name>
<surname>Pepin</surname>
<given-names>Kim M</given-names>
</name>
<xref ref-type="aff" rid="aff20">20</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con20"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16028" contrib-type="author">
<name>
<surname>Shepard</surname>
<given-names>Samuel S</given-names>
</name>
<xref ref-type="aff" rid="aff21">21</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con21"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-9945" contrib-type="author">
<name>
<surname>Smith</surname>
<given-names>David L</given-names>
</name>
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-4367-3849</contrib-id>
<xref ref-type="aff" rid="aff22">22</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con22"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16029" contrib-type="author">
<name>
<surname>Suarez</surname>
<given-names>David L</given-names>
</name>
<xref ref-type="aff" rid="aff23">23</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con23"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16030" contrib-type="author">
<name>
<surname>Trock</surname>
<given-names>Susan C</given-names>
</name>
<xref ref-type="aff" rid="aff24">24</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con24"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16031" contrib-type="author">
<name>
<surname>Widdowson</surname>
<given-names>Marc-Alain</given-names>
</name>
<xref ref-type="aff" rid="aff25">25</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con25"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-12632" contrib-type="author">
<name>
<surname>George</surname>
<given-names>Dylan B</given-names>
</name>
<xref ref-type="aff" rid="aff26">26</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con26"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-16032" contrib-type="author">
<name>
<surname>Lipsitch</surname>
<given-names>Marc</given-names>
</name>
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-1504-9213</contrib-id>
<xref ref-type="aff" rid="aff27">27</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con27"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<contrib id="author-4031" contrib-type="author">
<name>
<surname>Bloom</surname>
<given-names>Jesse D</given-names>
</name>
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-1267-3408</contrib-id>
<xref ref-type="aff" rid="aff28">28</xref>
<xref ref-type="other" rid="par-1"></xref>
<xref ref-type="other" rid="par-2"></xref>
<xref ref-type="fn" rid="con28"></xref>
<xref ref-type="fn" rid="conf2"></xref>
</contrib>
<aff id="aff1">
<label>1</label>
<bold>Colin A Russell</bold>
<addr-line>Department of Veterinary Medicine</addr-line>
,
<institution>University of Cambridge</institution>
,
<addr-line>Cambridge</addr-line>
,
<country>United Kingdom</country>
</aff>
<aff id="aff2">
<label>2</label>
<bold>Peter M Kasson</bold>
<addr-line>Department of Biomedical Engineering</addr-line>
,
<institution>University of Virginia</institution>
,
<addr-line>Charlottesville</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff3">
<label>3</label>
<bold>Ruben O Donis</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff4">
<label>4</label>
<bold>Steven Riley</bold>
<addr-line>Department of Infectious Disease Epidemiology</addr-line>
,
<institution>School of Public Health, Imperial College London</institution>
,
<addr-line>London</addr-line>
,
<country>United Kingdom</country>
;
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff5">
<label>5</label>
<bold>John Dunbar</bold>
<addr-line>Bioscience Division</addr-line>
,
<institution>Los Alamos National Laboratory</institution>
,
<addr-line>Los Alamos</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff6">
<label>6</label>
<bold>Andrew Rambaut</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Institute of Evolutionary Biology</addr-line>
,
<institution>University of Edinburgh</institution>
,
<addr-line>Edinburgh</addr-line>
,
<country>United Kingdom</country>
</aff>
<aff id="aff7">
<label>7</label>
<bold>Jason Asher</bold>
<addr-line>Leidos contract support to the Division of Analytic Decision Support</addr-line>
,
<institution>Biomedical Advanced Research and Development Authority, Department of Health and Human Services</institution>
,
<addr-line>Washington</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff8">
<label>8</label>
<bold>Stephen Burke</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff9">
<label>9</label>
<bold>C Todd Davis</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff10">
<label>10</label>
<bold>Rebecca J Garten</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff11">
<label>11</label>
<bold>Sandrasegaram Gnanakaran</bold>
<addr-line>Bioscience Division</addr-line>
,
<institution>Los Alamos National Laboratory</institution>
,
<addr-line>Los Alamos</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff12">
<label>12</label>
<bold>Simon I Hay</bold>
<addr-line>Spatial Ecology and Epidemiology Group, Department of Zoology</addr-line>
,
<institution>University of Oxford</institution>
,
<addr-line>Oxford</addr-line>
,
<country>United Kingdom</country>
</aff>
<aff id="aff13">
<label>13</label>
<bold>Sander Herfst</bold>
<addr-line>Department of Viroscience</addr-line>
,
<institution>Postgraduate School of Molecular Medicine, Erasmus Medical Center</institution>
,
<addr-line>Rotterdam</addr-line>
,
<country>Netherlands</country>
</aff>
<aff id="aff14">
<label>14</label>
<bold>Nicola S Lewis</bold>
<addr-line>Department of Zoology</addr-line>
,
<institution>University of Cambridge</institution>
,
<addr-line>Cambridge</addr-line>
,
<country>United Kingdom</country>
</aff>
<aff id="aff15">
<label>15</label>
<bold>James O Lloyd-Smith</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Department of Ecology and Evolutionary Biology</addr-line>
,
<institution>University of California, Los Angeles</institution>
,
<addr-line>Los Angeles</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff16">
<label>16</label>
<bold>Catherine A Macken</bold>
<addr-line>Bioscience Division</addr-line>
,
<institution>Los Alamos National Laboratory</institution>
,
<addr-line>Los Alamos</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff17">
<label>17</label>
<bold>Sebastian Maurer-Stroh</bold>
<addr-line>Bioinformatics Institute</addr-line>
,
<institution>Agency for Science Technology and Research</institution>
,
<addr-line>Singapore</addr-line>
,
<country>Singapore</country>
;
<addr-line>National Public Health Laboratory, Communicable Diseases Division</addr-line>
,
<institution>Ministry of Health</institution>
,
<addr-line>Singapore</addr-line>
,
<country>Singapore</country>
;
<addr-line>School of Biological Sciences</addr-line>
,
<institution>Nanyang Technological University</institution>
,
<addr-line>Singapore</addr-line>
,
<country>Singapore</country>
</aff>
<aff id="aff18">
<label>18</label>
<bold>Elizabeth Neuhaus</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff19">
<label>19</label>
<bold>Colin R Parrish</bold>
<addr-line>James A Baker Institute</addr-line>
,
<institution>College of Veterinary Medicine, Cornell University</institution>
,
<addr-line>Ithaca</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff20">
<label>20</label>
<bold>Kim M Pepin</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>National Wildlife Research Center</addr-line>
,
<institution>United States Department of Agriculture</institution>
,
<addr-line>Fort Collins</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff21">
<label>21</label>
<bold>Samuel S Shepard</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff22">
<label>22</label>
<bold>David L Smith</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Spatial Ecology and Epidemiology Group, Department of Zoology</addr-line>
,
<institution>University of Oxford</institution>
,
<addr-line>Oxford</addr-line>
,
<country>United Kingdom</country>
;
<institution>Sanaria Institute for Global Health and Tropical Medicine</institution>
,
<addr-line>Rockville</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff23">
<label>23</label>
<bold>David L Suarez</bold>
<addr-line>Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratories</addr-line>
,
<institution>United States Department of Agriculture</institution>
,
<addr-line>Athens</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff24">
<label>24</label>
<bold>Susan C Trock</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff25">
<label>25</label>
<bold>Marc-Alain Widdowson</bold>
<addr-line>Influenza Division</addr-line>
,
<institution>Centers for Disease Control and Prevention</institution>
,
<addr-line>Atlanta</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff26">
<label>26</label>
<bold>Dylan B George</bold>
<addr-line>Fogarty International Center</addr-line>
,
<institution>National Institutes of Health</institution>
,
<addr-line>Bethesda</addr-line>
,
<country>United States</country>
;
<addr-line>Division of Analytic Decision Support, Biomedical Advanced Research and Development Authority</addr-line>
,
<institution>Assistant Secretary for Preparedness and Response, Department of Health and Human Services</institution>
,
<addr-line>Washington, DC</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff27">
<label>27</label>
<bold>Marc Lipsitch</bold>
<addr-line>Center for Communicable Disease Dynamics, Department of Epidemiology</addr-line>
,
<institution>Harvard School of Public Health</institution>
,
<addr-line>Boston</addr-line>
,
<country>United States</country>
;
<addr-line>Department of Immunology and Infectious Diseases</addr-line>
,
<institution>Harvard School of Public Health</institution>
,
<addr-line>Boston</addr-line>
,
<country>United States</country>
</aff>
<aff id="aff28">
<label>28</label>
<bold>Jesse D Bloom</bold>
<addr-line>Division of Basic Sciences</addr-line>
,
<institution>Fred Hutchinson Cancer Research Center</institution>
,
<addr-line>Seattle</addr-line>
,
<country>United States</country>
</aff>
</contrib-group>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Sgaier</surname>
<given-names>Sema</given-names>
</name>
<role>Reviewing editor</role>
<aff>
<institution>Bill & Melinda Gates Foundation</institution>
,
<country>India</country>
</aff>
</contrib>
</contrib-group>
<author-notes>
<corresp id="cor1">
<label>*</label>
For correspondence:
<email>car44@cam.ac.uk</email>
</corresp>
</author-notes>
<pub-date pub-type="epub">
<day>16</day>
<month>10</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection">
<year>2014</year>
</pub-date>
<volume>3</volume>
<elocation-id>e03883</elocation-id>
<history>
<date date-type="received">
<day>04</day>
<month>7</month>
<year>2014</year>
</date>
<date date-type="accepted">
<day>29</day>
<month>9</month>
<year>2014</year>
</date>
</history>
<permissions>
<license license-type="open-access" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">
<license-p>This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the
<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0">Creative Commons CC0 public domain dedication</ext-link>
.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="elife03883.pdf"></self-uri>
<abstract>
<p>Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.</p>
<p>
<bold>DOI:</bold>
<ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03883.001">http://dx.doi.org/10.7554/eLife.03883.001</ext-link>
</p>
</abstract>
<kwd-group kwd-group-type="author-keywords">
<title>Author keywords</title>
<kwd>influenza</kwd>
<kwd>pandemic</kwd>
<kwd>emergence</kwd>
</kwd-group>
<kwd-group kwd-group-type="research-organism">
<title>Research organism</title>
<kwd>human</kwd>
<kwd>viruses</kwd>
</kwd-group>
<funding-group>
<award-group id="par-1">
<funding-source>U.S. Department of Homeland Security
<ext-link ext-link-type="uri" xlink:href="http://www.crossref.org/fundref/">FundRef identification ID: </ext-link>
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100000180</named-content>
</funding-source>
<award-id>Research and Policy for Infectious Disease Dynamics</award-id>
<principal-award-recipient>
<name>
<surname>Russell</surname>
<given-names>Colin A</given-names>
</name>
<name>
<surname>Kasson</surname>
<given-names>Peter M</given-names>
</name>
<name>
<surname>Donis</surname>
<given-names>Ruben O</given-names>
</name>
<name>
<surname>Riley</surname>
<given-names>Steven</given-names>
</name>
<name>
<surname>Dunbar</surname>
<given-names>John</given-names>
</name>
<name>
<surname>Rambaut</surname>
<given-names>Andrew</given-names>
</name>
<name>
<surname>Asher</surname>
<given-names>Jason</given-names>
</name>
<name>
<surname>Burke</surname>
<given-names>Stephen</given-names>
</name>
<name>
<surname>Davis</surname>
<given-names>C Todd</given-names>
</name>
<name>
<surname>Garten</surname>
<given-names>Rebecca J</given-names>
</name>
<name>
<surname>Gnanakaran</surname>
<given-names>Sandrasegaram</given-names>
</name>
<name>
<surname>Hay</surname>
<given-names>Simon I</given-names>
</name>
<name>
<surname>Herfst</surname>
<given-names>Sander</given-names>
</name>
<name>
<surname>Lewis</surname>
<given-names>Nicola S</given-names>
</name>
<name>
<surname>Lloyd-Smith</surname>
<given-names>James O</given-names>
</name>
<name>
<surname>Macken</surname>
<given-names>Catherine A</given-names>
</name>
<name>
<surname>Maurer-Stroh</surname>
<given-names>Sebastian</given-names>
</name>
<name>
<surname>Neuhaus</surname>
<given-names>Elizabeth</given-names>
</name>
<name>
<surname>Parrish</surname>
<given-names>Colin R</given-names>
</name>
<name>
<surname>Pepin</surname>
<given-names>Kim M</given-names>
</name>
<name>
<surname>Shepard</surname>
<given-names>Samuel S</given-names>
</name>
<name>
<surname>Smith</surname>
<given-names>David L</given-names>
</name>
<name>
<surname>Suarez</surname>
<given-names>David L</given-names>
</name>
<name>
<surname>Trock</surname>
<given-names>Susan C</given-names>
</name>
<name>
<surname>Widdowson</surname>
<given-names>Marc-Alain</given-names>
</name>
<name>
<surname>George</surname>
<given-names>Dylan B</given-names>
</name>
<name>
<surname>Lipsitch</surname>
<given-names>Marc</given-names>
</name>
<name>
<surname>Bloom</surname>
<given-names>Jesse D</given-names>
</name>
</principal-award-recipient>
</award-group>
<award-group id="par-2">
<funding-source>Fogarty International Center
<ext-link ext-link-type="uri" xlink:href="http://www.crossref.org/fundref/">FundRef identification ID: </ext-link>
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100000061</named-content>
</funding-source>
<award-id>Research and Policy for Infectious Disease Dynamics</award-id>
<principal-award-recipient>
<name>
<surname>Russell</surname>
<given-names>Colin A</given-names>
</name>
<name>
<surname>Kasson</surname>
<given-names>Peter M</given-names>
</name>
<name>
<surname>Donis</surname>
<given-names>Ruben O</given-names>
</name>
<name>
<surname>Riley</surname>
<given-names>Steven</given-names>
</name>
<name>
<surname>Dunbar</surname>
<given-names>John</given-names>
</name>
<name>
<surname>Rambaut</surname>
<given-names>Andrew</given-names>
</name>
<name>
<surname>Asher</surname>
<given-names>Jason</given-names>
</name>
<name>
<surname>Burke</surname>
<given-names>Stephen</given-names>
</name>
<name>
<surname>Davis</surname>
<given-names>C Todd</given-names>
</name>
<name>
<surname>Garten</surname>
<given-names>Rebecca J</given-names>
</name>
<name>
<surname>Gnanakaran</surname>
<given-names>Sandrasegaram</given-names>
</name>
<name>
<surname>Hay</surname>
<given-names>Simon I</given-names>
</name>
<name>
<surname>Herfst</surname>
<given-names>Sander</given-names>
</name>
<name>
<surname>Lewis</surname>
<given-names>Nicola S</given-names>
</name>
<name>
<surname>Lloyd-Smith</surname>
<given-names>James O</given-names>
</name>
<name>
<surname>Macken</surname>
<given-names>Catherine A</given-names>
</name>
<name>
<surname>Maurer-Stroh</surname>
<given-names>Sebastian</given-names>
</name>
<name>
<surname>Neuhaus</surname>
<given-names>Elizabeth</given-names>
</name>
<name>
<surname>Parrish</surname>
<given-names>Colin R</given-names>
</name>
<name>
<surname>Pepin</surname>
<given-names>Kim M</given-names>
</name>
<name>
<surname>Shepard</surname>
<given-names>Samuel S</given-names>
</name>
<name>
<surname>Smith</surname>
<given-names>David L</given-names>
</name>
<name>
<surname>Suarez</surname>
<given-names>David L</given-names>
</name>
<name>
<surname>Trock</surname>
<given-names>Susan C</given-names>
</name>
<name>
<surname>Widdowson</surname>
<given-names>Marc-Alain</given-names>
</name>
<name>
<surname>George</surname>
<given-names>Dylan B</given-names>
</name>
<name>
<surname>Lipsitch</surname>
<given-names>Marc</given-names>
</name>
<name>
<surname>Bloom</surname>
<given-names>Jesse D</given-names>
</name>
</principal-award-recipient>
</award-group>
<funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement>
</funding-group>
<custom-meta-group>
<custom-meta>
<meta-name>elife-xml-version</meta-name>
<meta-value>0.7</meta-value>
</custom-meta>
<custom-meta specific-use="meta-only">
<meta-name>Author impact statement</meta-name>
<meta-value>Predicting the pandemic potential of influenza viruses from genetic sequence data could transform pandemic risk assessment but progress towards this goal will require the integration of experimental work, computational tools, and virus surveillance.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
<sub-article id="SA1" article-type="article-commentary">
<front-stub>
<article-id pub-id-type="doi">10.7554/eLife.03883.005</article-id>
<title-group>
<article-title>Decision letter</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Sgaier</surname>
<given-names>Sema</given-names>
</name>
<role>Reviewing editor</role>
<aff>
<institution>Bill & Melinda Gates Foundation</institution>
,
<country>India</country>
</aff>
</contrib>
</contrib-group>
</front-stub>
<body>
<boxed-text position="float" orientation="portrait">
<p>eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see
<ext-link ext-link-type="uri" xlink:href="http://elifesciences.org/review-process">review process</ext-link>
). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.</p>
</boxed-text>
<p>Thank you for sending your work entitled “Improving pandemic influenza risk assessment” for consideration at eLife. Your article has been favorably evaluated by Prabhat Jha (Senior editor), Sema Sgaier (Reviewing editor), and two peer reviewers. There are only a few minor comments from the reviewers that we would like for you to address before publication.</p>
<p>1) Author contributions: there are currently 25+ authors listed. One suggestion for you to consider is listing a few as main others and others as a group.</p>
<p>2) Provide more references for the statements made throughout the paper; there are many statements where references would be helpful. Please review the text and address this where possible.</p>
<p>3)
<xref ref-type="fig" rid="fig2">Figure 2</xref>
: Please change the label “Level of overall concern” to “Level of public health concern/pandemic risk” to be consistent with the figure legend.</p>
<p>4) Abstract suggested change: “it should become possible to predict pandemic potential from sequence data.”</p>
</body>
</sub-article>
<sub-article id="SA2" article-type="reply">
<front-stub>
<article-id pub-id-type="doi">10.7554/eLife.03883.006</article-id>
<title-group>
<article-title>Author response</article-title>
</title-group>
</front-stub>
<body>
<p>
<italic>1) Author contributions: there are currently 25+ authors listed. One suggestion for you to consider is listing a few as main others and others as a group</italic>
.</p>
<p>This paper was born out of a workshop-based meeting on assessing the pandemic risk of influenza viruses. The level of interaction and discussion at the meeting was truly fantastic and it was the quality of the meeting that led us to writing the paper. Everyone at the meeting genuinely contributed to the production of the paper; there are no honorary authors here.</p>
<p>While we appreciate that the author list is somewhat lengthy, 28 authors to be exact, the group that produced this paper comprises opinion leaders in basic science and public health from diverse backgrounds. We feel that consensus from such a diverse group makes a powerful statement and would like to keep the author list as originally submitted.</p>
<p>
<italic>2) Provide more references for the statements made throughout the paper; there are many statements where references would be helpful. Please review the text and address this where possible</italic>
.</p>
<p>We have carefully gone through the text and added 20 new references.</p>
<p>
<italic>3)</italic>
<xref ref-type="fig" rid="fig2">
<italic>Figure 2</italic>
</xref>
<italic>: Please change the label “Level of overall concern” to “Level of public health concern/pandemic risk” to be consistent with the figure legend</italic>
.</p>
<p>Due to the length of the phrase “Level of public health concern/pandemic risk”, making this change to
<xref ref-type="fig" rid="fig2">Figure 2</xref>
would require restructuring the figure. We have changed the label to read “Level of pandemic risk”, which we feel links well with the figure caption.</p>
<p>
<italic>4) Abstract suggested change: “it should become possible to predict pandemic potential from sequence data</italic>
.
<italic>”</italic>
</p>
<p>We think the current wording, though longer, better reflects our thinking. We do not know if or when it will be possible to predict the total pandemic risk of a particular virus from sequence data – more work is needed first. In this sentence we want to speak to the potential utility of such predictions and push them as a direction for exploration.</p>
</body>
</sub-article>
</pmc>
<affiliations>
<list>
<country>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
<li>Singapour</li>
<li>États-Unis</li>
</country>
</list>
<tree>
<country name="Royaume-Uni">
<noRegion>
<name sortKey="Russell, Colin A" sort="Russell, Colin A" uniqKey="Russell C" first="Colin A" last="Russell">Colin A. Russell</name>
</noRegion>
<name sortKey="Hay, Simon I" sort="Hay, Simon I" uniqKey="Hay S" first="Simon I" last="Hay">Simon I. Hay</name>
<name sortKey="Lewis, Nicola S" sort="Lewis, Nicola S" uniqKey="Lewis N" first="Nicola S" last="Lewis">Nicola S. Lewis</name>
<name sortKey="Riley, Steven" sort="Riley, Steven" uniqKey="Riley S" first="Steven" last="Riley">Steven Riley</name>
</country>
<country name="États-Unis">
<noRegion>
<name sortKey="Kasson, Peter M" sort="Kasson, Peter M" uniqKey="Kasson P" first="Peter M" last="Kasson">Peter M. Kasson</name>
</noRegion>
<name sortKey="Asher, Jason" sort="Asher, Jason" uniqKey="Asher J" first="Jason" last="Asher">Jason Asher</name>
<name sortKey="Bloom, Jesse D" sort="Bloom, Jesse D" uniqKey="Bloom J" first="Jesse D" last="Bloom">Jesse D. Bloom</name>
<name sortKey="Burke, Stephen" sort="Burke, Stephen" uniqKey="Burke S" first="Stephen" last="Burke">Stephen Burke</name>
<name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C Todd" last="Davis">C Todd Davis</name>
<name sortKey="Donis, Ruben O" sort="Donis, Ruben O" uniqKey="Donis R" first="Ruben O" last="Donis">Ruben O. Donis</name>
<name sortKey="Dunbar, John" sort="Dunbar, John" uniqKey="Dunbar J" first="John" last="Dunbar">John Dunbar</name>
<name sortKey="Garten, Rebecca J" sort="Garten, Rebecca J" uniqKey="Garten R" first="Rebecca J" last="Garten">Rebecca J. Garten</name>
<name sortKey="George, Dylan B" sort="George, Dylan B" uniqKey="George D" first="Dylan B" last="George">Dylan B. George</name>
<name sortKey="Gnanakaran, Sandrasegaram" sort="Gnanakaran, Sandrasegaram" uniqKey="Gnanakaran S" first="Sandrasegaram" last="Gnanakaran">Sandrasegaram Gnanakaran</name>
<name sortKey="Lipsitch, Marc" sort="Lipsitch, Marc" uniqKey="Lipsitch M" first="Marc" last="Lipsitch">Marc Lipsitch</name>
<name sortKey="Lloyd Smith, James O" sort="Lloyd Smith, James O" uniqKey="Lloyd Smith J" first="James O" last="Lloyd-Smith">James O. Lloyd-Smith</name>
<name sortKey="Macken, Catherine A" sort="Macken, Catherine A" uniqKey="Macken C" first="Catherine A" last="Macken">Catherine A. Macken</name>
<name sortKey="Neuhaus, Elizabeth" sort="Neuhaus, Elizabeth" uniqKey="Neuhaus E" first="Elizabeth" last="Neuhaus">Elizabeth Neuhaus</name>
<name sortKey="Parrish, Colin R" sort="Parrish, Colin R" uniqKey="Parrish C" first="Colin R" last="Parrish">Colin R. Parrish</name>
<name sortKey="Pepin, Kim M" sort="Pepin, Kim M" uniqKey="Pepin K" first="Kim M" last="Pepin">Kim M. Pepin</name>
<name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name>
<name sortKey="Shepard, Samuel S" sort="Shepard, Samuel S" uniqKey="Shepard S" first="Samuel S" last="Shepard">Samuel S. Shepard</name>
<name sortKey="Smith, David L" sort="Smith, David L" uniqKey="Smith D" first="David L" last="Smith">David L. Smith</name>
<name sortKey="Suarez, David L" sort="Suarez, David L" uniqKey="Suarez D" first="David L" last="Suarez">David L. Suarez</name>
<name sortKey="Trock, Susan C" sort="Trock, Susan C" uniqKey="Trock S" first="Susan C" last="Trock">Susan C. Trock</name>
<name sortKey="Widdowson, Marc Alain" sort="Widdowson, Marc Alain" uniqKey="Widdowson M" first="Marc-Alain" last="Widdowson">Marc-Alain Widdowson</name>
</country>
<country name="Pays-Bas">
<noRegion>
<name sortKey="Herfst, Sander" sort="Herfst, Sander" uniqKey="Herfst S" first="Sander" last="Herfst">Sander Herfst</name>
</noRegion>
</country>
<country name="Singapour">
<noRegion>
<name sortKey="Maurer Stroh, Sebastian" sort="Maurer Stroh, Sebastian" uniqKey="Maurer Stroh S" first="Sebastian" last="Maurer-Stroh">Sebastian Maurer-Stroh</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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