Final published version
Licence: CC BY: Creative Commons Attribution 4.0 International License
Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
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TY - JOUR
T1 - Reconstructing unseen transmission events to infer dengue dynamics from viral sequences
AU - Salje, H.
AU - Wesolowski, A.
AU - Brown, T.S.
AU - Kiang, M.V.
AU - Berry, I.M.
AU - Lefrancq, N.
AU - Fernandez, S.
AU - Jarman, R.G.
AU - Ruchusatsawat, K.
AU - Iamsirithaworn, S.
AU - Vandepitte, W.P.
AU - Suntarattiwong, P.
AU - Read, J.M.
AU - Klungthong, C.
AU - Thaisomboonsuk, B.
AU - Engø-Monsen, K.
AU - Buckee, C.
AU - Cauchemez, S.
AU - Cummings, D.A.T.
PY - 2021/3/22
Y1 - 2021/3/22
N2 - For 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.
AB - For 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.
KW - dengue fever
KW - disease vector
KW - immunity
KW - pathogen
KW - phylogenetics
KW - reconstruction
KW - virus
KW - Thailand
KW - Dengue virus
U2 - 10.1038/s41467-021-21888-9
DO - 10.1038/s41467-021-21888-9
M3 - Journal article
VL - 12
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 1810
ER -