Bayesian inference for an emerging arboreal epidemic in the presence of control
Identifieur interne : 000D38 ( Pmc/Curation ); précédent : 000D37; suivant : 000D39Bayesian inference for an emerging arboreal epidemic in the presence of control
Auteurs : Matthew Parry [Nouvelle-Zélande, Royaume-Uni] ; Gavin J. Gibson [Royaume-Uni] ; Stephen Parnell [Royaume-Uni] ; Tim R. Gottwald ; Michael S. Irey ; Timothy C. Gast ; Christopher A. Gilligan [Royaume-Uni]Source :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2014.
Abstract
Fast-moving and destructive emerging epidemics are seldom left to run their course because of the imperative to control further spread. Contemporaneous control measures, however, greatly complicate the characterization of the disease transmission process and the extraction of the epidemiological parameters of interest. The spread of Huanglongbing on orchard scales is used as a case study for modeling an emerging epidemic in the presence of control. We show that even with missing and censored data, and with seasonal and host age dependencies, it is possible to infer the parameters of a fully spatiotemporal stochastic model of disease spread. The value of the fitted model is to provide an engine for simulation studies of the costs and benefits of proposed disease control strategies.
Url:
DOI: 10.1073/pnas.1310997111
PubMed: 24711393
PubMed Central: 4035939
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000D39
Links to Exploration step
PMC:4035939Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Bayesian inference for an emerging arboreal epidemic in the presence of control</title><author><name sortKey="Parry, Matthew" sort="Parry, Matthew" uniqKey="Parry M" first="Matthew" last="Parry">Matthew Parry</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Mathematics and Statistics,<institution>University of Otago</institution>, Dunedin 9054,<country>New Zealand</country>;</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">Epidemiology and Modelling Group, Department of Plant Sciences,<institution>University of Cambridge</institution>, Cambridge CB2 3EA,<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="Gibson, Gavin J" sort="Gibson, Gavin J" uniqKey="Gibson G" first="Gavin J." last="Gibson">Gavin J. Gibson</name><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Actuarial Mathematics and Statistics and the Maxwell Institute for Mathematical Sciences,<institution>Heriot-Watt University</institution>, Edinburgh EH14 4AS,<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="Parnell, Stephen" sort="Parnell, Stephen" uniqKey="Parnell S" first="Stephen" last="Parnell">Stephen Parnell</name><affiliation wicri:level="1"><nlm:aff id="aff4">Department of Computational and Systems Biology,<institution>Rothamsted Research</institution>, Harpenden AL5 2JQ,<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="Gottwald, Tim R" sort="Gottwald, Tim R" uniqKey="Gottwald T" first="Tim R." last="Gottwald">Tim R. Gottwald</name><affiliation><nlm:aff wicri:cut="; and" id="aff5">US Department of Agriculture,<institution>Agricultural Research Service</institution>, Fort Pierce,<addr-line>FL</addr-line> 34945</nlm:aff></affiliation></author><author><name sortKey="Irey, Michael S" sort="Irey, Michael S" uniqKey="Irey M" first="Michael S." last="Irey">Michael S. Irey</name><affiliation><nlm:aff id="aff6">Southern Gardens Citrus,<institution>US Sugar Corporation</institution>, Clewiston,<addr-line>FL</addr-line> 33440</nlm:aff></affiliation></author><author><name sortKey="Gast, Timothy C" sort="Gast, Timothy C" uniqKey="Gast T" first="Timothy C." last="Gast">Timothy C. Gast</name><affiliation><nlm:aff id="aff6">Southern Gardens Citrus,<institution>US Sugar Corporation</institution>, Clewiston,<addr-line>FL</addr-line> 33440</nlm:aff></affiliation></author><author><name sortKey="Gilligan, Christopher A" sort="Gilligan, Christopher A" uniqKey="Gilligan C" first="Christopher A." last="Gilligan">Christopher A. Gilligan</name><affiliation wicri:level="1"><nlm:aff id="aff2">Epidemiology and Modelling Group, Department of Plant Sciences,<institution>University of Cambridge</institution>, Cambridge CB2 3EA,<country>United Kingdom</country>;</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24711393</idno><idno type="pmc">4035939</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035939</idno><idno type="RBID">PMC:4035939</idno><idno type="doi">10.1073/pnas.1310997111</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000D39</idno><idno type="wicri:Area/Pmc/Curation">000D38</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Bayesian inference for an emerging arboreal epidemic in the presence of control</title><author><name sortKey="Parry, Matthew" sort="Parry, Matthew" uniqKey="Parry M" first="Matthew" last="Parry">Matthew Parry</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Mathematics and Statistics,<institution>University of Otago</institution>, Dunedin 9054,<country>New Zealand</country>;</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">Epidemiology and Modelling Group, Department of Plant Sciences,<institution>University of Cambridge</institution>, Cambridge CB2 3EA,<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="Gibson, Gavin J" sort="Gibson, Gavin J" uniqKey="Gibson G" first="Gavin J." last="Gibson">Gavin J. Gibson</name><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Actuarial Mathematics and Statistics and the Maxwell Institute for Mathematical Sciences,<institution>Heriot-Watt University</institution>, Edinburgh EH14 4AS,<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="Parnell, Stephen" sort="Parnell, Stephen" uniqKey="Parnell S" first="Stephen" last="Parnell">Stephen Parnell</name><affiliation wicri:level="1"><nlm:aff id="aff4">Department of Computational and Systems Biology,<institution>Rothamsted Research</institution>, Harpenden AL5 2JQ,<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="Gottwald, Tim R" sort="Gottwald, Tim R" uniqKey="Gottwald T" first="Tim R." last="Gottwald">Tim R. Gottwald</name><affiliation><nlm:aff wicri:cut="; and" id="aff5">US Department of Agriculture,<institution>Agricultural Research Service</institution>, Fort Pierce,<addr-line>FL</addr-line> 34945</nlm:aff></affiliation></author><author><name sortKey="Irey, Michael S" sort="Irey, Michael S" uniqKey="Irey M" first="Michael S." last="Irey">Michael S. Irey</name><affiliation><nlm:aff id="aff6">Southern Gardens Citrus,<institution>US Sugar Corporation</institution>, Clewiston,<addr-line>FL</addr-line> 33440</nlm:aff></affiliation></author><author><name sortKey="Gast, Timothy C" sort="Gast, Timothy C" uniqKey="Gast T" first="Timothy C." last="Gast">Timothy C. Gast</name><affiliation><nlm:aff id="aff6">Southern Gardens Citrus,<institution>US Sugar Corporation</institution>, Clewiston,<addr-line>FL</addr-line> 33440</nlm:aff></affiliation></author><author><name sortKey="Gilligan, Christopher A" sort="Gilligan, Christopher A" uniqKey="Gilligan C" first="Christopher A." last="Gilligan">Christopher A. Gilligan</name><affiliation wicri:level="1"><nlm:aff id="aff2">Epidemiology and Modelling Group, Department of Plant Sciences,<institution>University of Cambridge</institution>, Cambridge CB2 3EA,<country>United Kingdom</country>;</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Significance</title><p>Fast-moving and destructive emerging epidemics are seldom left to run their course because of the imperative to control further spread. Contemporaneous control measures, however, greatly complicate the characterization of the disease transmission process and the extraction of the epidemiological parameters of interest. The spread of Huanglongbing on orchard scales is used as a case study for modeling an emerging epidemic in the presence of control. We show that even with missing and censored data, and with seasonal and host age dependencies, it is possible to infer the parameters of a fully spatiotemporal stochastic model of disease spread. The value of the fitted model is to provide an engine for simulation studies of the costs and benefits of proposed disease control strategies.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24711393</article-id><article-id pub-id-type="pmc">4035939</article-id><article-id pub-id-type="publisher-id">201310997</article-id><article-id pub-id-type="doi">10.1073/pnas.1310997111</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Agricultural Sciences</subject></subj-group></subj-group></article-categories><title-group><article-title>Bayesian inference for an emerging arboreal epidemic in the presence of control</article-title><alt-title alt-title-type="short">Inference for an emerging arboreal epidemic</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Parry</surname><given-names>Matthew</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gibson</surname><given-names>Gavin J.</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Parnell</surname><given-names>Stephen</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gottwald</surname><given-names>Tim R.</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Irey</surname><given-names>Michael S.</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gast</surname><given-names>Timothy C.</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gilligan</surname><given-names>Christopher A.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><sup>a</sup>Department of Mathematics and Statistics,<institution>University of Otago</institution>, Dunedin 9054,<country>New Zealand</country>;</aff><aff id="aff2"><sup>b</sup>Epidemiology and Modelling Group, Department of Plant Sciences,<institution>University of Cambridge</institution>, Cambridge CB2 3EA,<country>United Kingdom</country>;</aff><aff id="aff3"><sup>c</sup>Department of Actuarial Mathematics and Statistics and the Maxwell Institute for Mathematical Sciences,<institution>Heriot-Watt University</institution>, Edinburgh EH14 4AS,<country>United Kingdom</country>;</aff><aff id="aff4"><sup>d</sup>Department of Computational and Systems Biology,<institution>Rothamsted Research</institution>, Harpenden AL5 2JQ,<country>United Kingdom</country>;</aff><aff id="aff5"><sup>e</sup>US Department of Agriculture,<institution>Agricultural Research Service</institution>, Fort Pierce,<addr-line>FL</addr-line> 34945; and</aff><aff id="aff6"><sup>f</sup>Southern Gardens Citrus,<institution>US Sugar Corporation</institution>, Clewiston,<addr-line>FL</addr-line> 33440</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence should be addressed. E-mail: <email>cag1@cam.ac.uk</email>.</corresp><fn fn-type="edited-by"><p>Edited<xref ref-type="fn" rid="fn1">*</xref> by Burton H. Singer, University of Florida, Gainesville, FL, and approved March 4, 2014 (received for review September 16, 2013)</p></fn><fn fn-type="con"><p>Author contributions: M.P., G.J.G., T.R.G., and C.A.G. designed research; M.P., G.J.G., S.P., T.R.G., M.S.I., T.C.G., and C.A.G. performed research; M.P., S.P., and T.R.G. analyzed data; and M.P., G.J.G., T.R.G., and C.A.G. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>29</day><month>4</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>7</day><month>4</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>7</day><month>4</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>111</volume><issue>17</issue><fpage>6258</fpage><lpage>6262</lpage><permissions><license license-type="open-access"><license-p>Freely available online through the PNAS open access option.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201310997.pdf"></self-uri><abstract abstract-type="executive-summary"><title>Significance</title><p>Fast-moving and destructive emerging epidemics are seldom left to run their course because of the imperative to control further spread. Contemporaneous control measures, however, greatly complicate the characterization of the disease transmission process and the extraction of the epidemiological parameters of interest. The spread of Huanglongbing on orchard scales is used as a case study for modeling an emerging epidemic in the presence of control. We show that even with missing and censored data, and with seasonal and host age dependencies, it is possible to infer the parameters of a fully spatiotemporal stochastic model of disease spread. The value of the fitted model is to provide an engine for simulation studies of the costs and benefits of proposed disease control strategies.</p></abstract><abstract><p>The spread of Huanglongbing through citrus groves is used as a case study for modeling an emerging epidemic in the presence of a control. Specifically, the spread of the disease is modeled as a susceptible-exposed-infectious-detected-removed epidemic, where the exposure and infectious times are not observed, detection times are censored, removal times are known, and the disease is spreading through a heterogeneous host population with trees of different age and susceptibility. We show that it is possible to characterize the disease transmission process under these conditions. Two innovations in our work are (<italic>i</italic>) accounting for control measures via time dependence of the infectious process and (<italic>ii</italic>) including seasonal and host age effects in the model of the latent period. By estimating parameters in different subregions of a large commercially cultivated orchard, we establish a temporal pattern of invasion, host age dependence of the dispersal parameters, and a close to linear relationship between primary and secondary infectious rates. The model can be used to simulate Huanglongbing epidemics to assess economic costs and potential benefits of putative control scenarios.</p></abstract><kwd-group><kwd>spatiotemporal model</kwd><kwd>dispersal kernel</kwd><kwd>stochastic model</kwd></kwd-group><counts><page-count count="5"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000D38 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 000D38 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Pmc
|étape= Curation
|type= RBID
|clé= PMC:4035939
|texte= Bayesian inference for an emerging arboreal epidemic in the presence of control
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:24711393" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |