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Reconstructing unseen transmission events to infer dengue dynamics from viral sequences.

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cam.issuedOnline2021-03-22
dc.contributor.authorSalje, Henrik
dc.contributor.authorWesolowski, Amy
dc.contributor.authorBrown, Tyler S
dc.contributor.authorKiang, Mathew V
dc.contributor.authorBerry, Irina Maljkovic
dc.contributor.authorLefrancq, Noemie
dc.contributor.authorFernandez, Stefan
dc.contributor.authorJarman, Richard G
dc.contributor.authorRuchusatsawat, Kriangsak
dc.contributor.authorIamsirithaworn, Sopon
dc.contributor.authorVandepitte, Warunee P
dc.contributor.authorSuntarattiwong, Piyarat
dc.contributor.authorRead, Jonathan M
dc.contributor.authorKlungthong, Chonticha
dc.contributor.authorThaisomboonsuk, Butsaya
dc.contributor.authorEngø-Monsen, Kenth
dc.contributor.authorBuckee, Caroline
dc.contributor.authorCauchemez, Simon
dc.contributor.authorCummings, Derek AT
dc.contributor.orcidWesolowski, Amy [0000-0001-6320-3575]
dc.contributor.orcidKiang, Mathew V [0000-0001-9198-150X]
dc.contributor.orcidBerry, Irina Maljkovic [0000-0001-8555-5352]
dc.contributor.orcidLefrancq, Noemie [0000-0001-5991-6169]
dc.contributor.orcidJarman, Richard G [0000-0002-5765-0173]
dc.contributor.orcidEngø-Monsen, Kenth [0000-0003-1618-7597]
dc.contributor.orcidBuckee, Caroline [0000-0002-8386-5899]
dc.contributor.orcidCauchemez, Simon [0000-0001-9186-4549]
dc.contributor.orcidCummings, Derek AT [0000-0002-9437-1907]
dc.date.accessioned2021-11-25T00:31:17Z
dc.date.available2021-11-25T00:31:17Z
dc.date.issued2021-03-22
dc.description.abstractFor most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogenetic framework that addresses these limitations by considering individual transmission events, reconstructed across spatial scales. We apply it to geocoded dengue virus sequences from Thailand (N = 726 over 18 years). We find infected individuals spend 96% of their time in their home community compared to 76% for the susceptible population (mainly children) and 42% for adults. Dynamic pockets of local immunity make transmission more likely in places with high heterotypic immunity and less likely where high homotypic immunity exists. Age-dependent mixing of individuals and vector distributions are not important in determining spread. This approach provides previously unknown insights into one of the most complex disease systems known and will be applicable to other pathogens.
dc.format.mediumElectronic
dc.identifier.doi10.17863/CAM.78520
dc.identifier.eissn2041-1723
dc.identifier.issn2041-1723
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/331075
dc.languageeng
dc.language.isoeng
dc.publisherSpringer Science and Business Media LLC
dc.publisher.urlhttp://dx.doi.org/10.1038/s41467-021-21888-9
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAdult
dc.subjectAedes
dc.subjectAlgorithms
dc.subjectAnimals
dc.subjectChild
dc.subjectDengue
dc.subjectDengue Virus
dc.subjectGenome, Viral
dc.subjectHost-Pathogen Interactions
dc.subjectHumans
dc.subjectModels, Theoretical
dc.subjectMosquito Vectors
dc.subjectPhylogeny
dc.subjectPhylogeography
dc.subjectPopulation Dynamics
dc.subjectThailand
dc.titleReconstructing unseen transmission events to infer dengue dynamics from viral sequences.
dc.typeArticle
dcterms.dateAccepted2021-02-18
prism.issueIdentifier1
prism.publicationDate2021
prism.publicationNameNat Commun
prism.startingPage1810
prism.volume12
pubs.funder-project-idEuropean Commission Horizon 2020 (H2020) ERC (804744)
rioxxterms.licenseref.startdate2021-03-22
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.typeJournal Article/Review
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1038/s41467-021-21888-9

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