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A simple approach to measure transmissibility and forecast incidence

Identifieur interne : 002D77 ( Ncbi/Merge ); précédent : 002D76; suivant : 002D78

A simple approach to measure transmissibility and forecast incidence

Auteurs : Pierre Nouvellet [Royaume-Uni] ; Anne Cori [Royaume-Uni] ; Tini Garske [Royaume-Uni] ; Isobel M. Blake [Royaume-Uni] ; Ilaria Dorigatti [Royaume-Uni] ; Wes Hinsley [Royaume-Uni] ; Thibaut Jombart [Royaume-Uni] ; Harriet L. Mills [Royaume-Uni] ; Gemma Nedjati-Gilani [Royaume-Uni] ; Maria D. Van Kerkhove [Royaume-Uni, France] ; Christophe Fraser [Royaume-Uni] ; Christl A. Donnelly [Royaume-Uni] ; Neil M. Ferguson [Royaume-Uni] ; Steven Riley [Royaume-Uni]

Source :

RBID : PMC:5871640

Abstract

Highlights

Our simple approach relies on very few parameters and minimal assumptions

Subjective choice of best training period improved forecasts

Despites its simplicity, our model forecasted well under a range scenarios.

This approach can be a natural 'null model' for comparison with methods.


Url:
DOI: 10.1016/j.epidem.2017.02.012
PubMed: 28351674
PubMed Central: 5871640

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PMC:5871640

Le document en format XML

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</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff0015">Center for Global Health, Institute Pasteur, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
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<placeName>
<region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
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<author>
<name sortKey="Fraser, Christophe" sort="Fraser, Christophe" uniqKey="Fraser C" first="Christophe" last="Fraser">Christophe Fraser</name>
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<author>
<name sortKey="Donnelly, Christl A" sort="Donnelly, Christl A" uniqKey="Donnelly C" first="Christl A." last="Donnelly">Christl A. Donnelly</name>
<affiliation wicri:level="3">
<nlm:aff id="aff0005">MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK</nlm:aff>
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<nlm:aff id="aff0010">National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London</wicri:regionArea>
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<settlement type="city">Londres</settlement>
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<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Ferguson, Neil M" sort="Ferguson, Neil M" uniqKey="Ferguson N" first="Neil M." last="Ferguson">Neil M. Ferguson</name>
<affiliation wicri:level="3">
<nlm:aff id="aff0005">MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London</wicri:regionArea>
<placeName>
<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff0010">National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London</wicri:regionArea>
<placeName>
<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Riley, Steven" sort="Riley, Steven" uniqKey="Riley S" first="Steven" last="Riley">Steven Riley</name>
<affiliation wicri:level="3">
<nlm:aff id="aff0005">MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London</wicri:regionArea>
<placeName>
<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="aff0010">National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London</wicri:regionArea>
<placeName>
<settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
</analytic>
<series>
<title level="j">Epidemics</title>
<idno type="ISSN">1755-4365</idno>
<idno type="eISSN">1878-0067</idno>
<imprint>
<date when="2018">2018</date>
</imprint>
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<div type="abstract" xml:lang="en">
<title>Highlights</title>
<p>
<list list-type="simple" id="lis0005">
<list-item id="lsti0005">
<label></label>
<p id="par0005">Our simple approach relies on very few parameters and minimal assumptions</p>
</list-item>
<list-item id="lsti0010">
<label></label>
<p id="par0010">Subjective choice of best training period improved forecasts</p>
</list-item>
<list-item id="lsti0015">
<label></label>
<p id="par0015">Despites its simplicity, our model forecasted well under a range scenarios.</p>
</list-item>
<list-item id="lsti0020">
<label></label>
<p id="par0020">This approach can be a natural 'null model' for comparison with methods.</p>
</list-item>
</list>
</p>
</div>
</front>
<back>
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</back>
</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Epidemics</journal-id>
<journal-id journal-id-type="iso-abbrev">Epidemics</journal-id>
<journal-title-group>
<journal-title>Epidemics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1755-4365</issn>
<issn pub-type="epub">1878-0067</issn>
<publisher>
<publisher-name>Elsevier</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">28351674</article-id>
<article-id pub-id-type="pmc">5871640</article-id>
<article-id pub-id-type="publisher-id">S1755-4365(17)30024-5</article-id>
<article-id pub-id-type="doi">10.1016/j.epidem.2017.02.012</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>A simple approach to measure transmissibility and forecast incidence</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Nouvellet</surname>
<given-names>Pierre</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0010" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cori</surname>
<given-names>Anne</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Garske</surname>
<given-names>Tini</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Blake</surname>
<given-names>Isobel M.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Dorigatti</surname>
<given-names>Ilaria</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Hinsley</surname>
<given-names>Wes</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jombart</surname>
<given-names>Thibaut</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0010" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mills</surname>
<given-names>Harriet L.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Nedjati-Gilani</surname>
<given-names>Gemma</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Van Kerkhove</surname>
<given-names>Maria D.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0015" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Fraser</surname>
<given-names>Christophe</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0010" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Donnelly</surname>
<given-names>Christl A.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0010" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ferguson</surname>
<given-names>Neil M.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0010" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Riley</surname>
<given-names>Steven</given-names>
</name>
<email>s.riley@imperial.ac.uk</email>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="aff0010" ref-type="aff">b</xref>
<xref rid="cor0005" ref-type="corresp"></xref>
</contrib>
</contrib-group>
<aff id="aff0005">
<label>a</label>
MRC Centre for Outbreak Analysis and Modelling, Imperial College London, Faculty of Medicine, London, UK</aff>
<aff id="aff0010">
<label>b</label>
National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, Faculty of Medicine, London, UK</aff>
<aff id="aff0015">
<label>c</label>
Center for Global Health, Institute Pasteur, Paris, France</aff>
<author-notes>
<corresp id="cor0005">
<label></label>
Corresponding author at: MRC Centre for Outbreak Analysis and Modelling, Imperial College London, St Mary’s Campus, Norfolk Place, London W2 1PG, UK.MRC Centre for Outbreak Analysis and ModellingImperial College LondonFaculty of MedicineLondonUK
<email>s.riley@imperial.ac.uk</email>
</corresp>
</author-notes>
<pub-date pub-type="pmc-release">
<day>1</day>
<month>3</month>
<year>2018</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub">
<month>3</month>
<year>2018</year>
</pub-date>
<volume>22</volume>
<fpage>29</fpage>
<lpage>35</lpage>
<history>
<date date-type="received">
<day>14</day>
<month>6</month>
<year>2016</year>
</date>
<date date-type="rev-recd">
<day>1</day>
<month>2</month>
<year>2017</year>
</date>
<date date-type="accepted">
<day>17</day>
<month>2</month>
<year>2017</year>
</date>
</history>
<permissions>
<copyright-statement>© 2017 The Authors</copyright-statement>
<copyright-year>2017</copyright-year>
<license license-type="CC BY" xlink:href="http://creativecommons.org/licenses/by/4.0/">
<license-p>This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).</license-p>
</license>
</permissions>
<abstract abstract-type="author-highlights" id="abs0005">
<title>Highlights</title>
<p>
<list list-type="simple" id="lis0005">
<list-item id="lsti0005">
<label></label>
<p id="par0005">Our simple approach relies on very few parameters and minimal assumptions</p>
</list-item>
<list-item id="lsti0010">
<label></label>
<p id="par0010">Subjective choice of best training period improved forecasts</p>
</list-item>
<list-item id="lsti0015">
<label></label>
<p id="par0015">Despites its simplicity, our model forecasted well under a range scenarios.</p>
</list-item>
<list-item id="lsti0020">
<label></label>
<p id="par0020">This approach can be a natural 'null model' for comparison with methods.</p>
</list-item>
</list>
</p>
</abstract>
<abstract id="abs0010">
<p>Outbreaks of novel pathogens such as SARS, pandemic influenza and Ebola require substantial investments in reactive interventions, with consequent implementation plans sometimes revised on a weekly basis. Therefore, short-term forecasts of incidence are often of high priority. In light of the recent Ebola epidemic in West Africa, a forecasting exercise was convened by a network of infectious disease modellers. The challenge was to forecast unseen “future” simulated data for four different scenarios at five different time points. In a similar method to that used during the recent Ebola epidemic, we estimated current levels of transmissibility, over variable time-windows chosen in an ad hoc way. Current estimated transmissibility was then used to forecast near-future incidence. We performed well within the challenge and often produced accurate forecasts. A retrospective analysis showed that our subjective method for deciding on the window of time with which to estimate transmissibility often resulted in the optimal choice. However, when near-future trends deviated substantially from exponential patterns, the accuracy of our forecasts was reduced. This exercise highlights the urgent need for infectious disease modellers to develop more robust descriptions of processes – other than the widespread depletion of susceptible individuals – that produce non-exponential patterns of incidence.</p>
</abstract>
<kwd-group id="kwd0005">
<title>Keywords</title>
<kwd>Forecasting</kwd>
<kwd>Rapid response</kwd>
<kwd>Branching process</kwd>
<kwd>Renewal equation</kwd>
<kwd>MCMC</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>France</li>
<li>Royaume-Uni</li>
</country>
<region>
<li>Angleterre</li>
<li>Grand Londres</li>
<li>Île-de-France</li>
</region>
<settlement>
<li>Londres</li>
<li>Paris</li>
</settlement>
</list>
<tree>
<country name="Royaume-Uni">
<region name="Angleterre">
<name sortKey="Nouvellet, Pierre" sort="Nouvellet, Pierre" uniqKey="Nouvellet P" first="Pierre" last="Nouvellet">Pierre Nouvellet</name>
</region>
<name sortKey="Blake, Isobel M" sort="Blake, Isobel M" uniqKey="Blake I" first="Isobel M." last="Blake">Isobel M. Blake</name>
<name sortKey="Cori, Anne" sort="Cori, Anne" uniqKey="Cori A" first="Anne" last="Cori">Anne Cori</name>
<name sortKey="Donnelly, Christl A" sort="Donnelly, Christl A" uniqKey="Donnelly C" first="Christl A." last="Donnelly">Christl A. Donnelly</name>
<name sortKey="Donnelly, Christl A" sort="Donnelly, Christl A" uniqKey="Donnelly C" first="Christl A." last="Donnelly">Christl A. Donnelly</name>
<name sortKey="Dorigatti, Ilaria" sort="Dorigatti, Ilaria" uniqKey="Dorigatti I" first="Ilaria" last="Dorigatti">Ilaria Dorigatti</name>
<name sortKey="Ferguson, Neil M" sort="Ferguson, Neil M" uniqKey="Ferguson N" first="Neil M." last="Ferguson">Neil M. Ferguson</name>
<name sortKey="Ferguson, Neil M" sort="Ferguson, Neil M" uniqKey="Ferguson N" first="Neil M." last="Ferguson">Neil M. Ferguson</name>
<name sortKey="Fraser, Christophe" sort="Fraser, Christophe" uniqKey="Fraser C" first="Christophe" last="Fraser">Christophe Fraser</name>
<name sortKey="Fraser, Christophe" sort="Fraser, Christophe" uniqKey="Fraser C" first="Christophe" last="Fraser">Christophe Fraser</name>
<name sortKey="Garske, Tini" sort="Garske, Tini" uniqKey="Garske T" first="Tini" last="Garske">Tini Garske</name>
<name sortKey="Hinsley, Wes" sort="Hinsley, Wes" uniqKey="Hinsley W" first="Wes" last="Hinsley">Wes Hinsley</name>
<name sortKey="Jombart, Thibaut" sort="Jombart, Thibaut" uniqKey="Jombart T" first="Thibaut" last="Jombart">Thibaut Jombart</name>
<name sortKey="Jombart, Thibaut" sort="Jombart, Thibaut" uniqKey="Jombart T" first="Thibaut" last="Jombart">Thibaut Jombart</name>
<name sortKey="Mills, Harriet L" sort="Mills, Harriet L" uniqKey="Mills H" first="Harriet L." last="Mills">Harriet L. Mills</name>
<name sortKey="Nedjati Gilani, Gemma" sort="Nedjati Gilani, Gemma" uniqKey="Nedjati Gilani G" first="Gemma" last="Nedjati-Gilani">Gemma Nedjati-Gilani</name>
<name sortKey="Nouvellet, Pierre" sort="Nouvellet, Pierre" uniqKey="Nouvellet P" first="Pierre" last="Nouvellet">Pierre Nouvellet</name>
<name sortKey="Riley, Steven" sort="Riley, Steven" uniqKey="Riley S" first="Steven" last="Riley">Steven Riley</name>
<name sortKey="Riley, Steven" sort="Riley, Steven" uniqKey="Riley S" first="Steven" last="Riley">Steven Riley</name>
<name sortKey="Van Kerkhove, Maria D" sort="Van Kerkhove, Maria D" uniqKey="Van Kerkhove M" first="Maria D." last="Van Kerkhove">Maria D. Van Kerkhove</name>
</country>
<country name="France">
<region name="Île-de-France">
<name sortKey="Van Kerkhove, Maria D" sort="Van Kerkhove, Maria D" uniqKey="Van Kerkhove M" first="Maria D." last="Van Kerkhove">Maria D. Van Kerkhove</name>
</region>
</country>
</tree>
</affiliations>
</record>

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