Reconstructing unseen transmission events to infer dengue dynamics from viral sequences

Salje, H. and Wesolowski, A. and Brown, T.S. and Kiang, M.V. and Berry, I.M. and Lefrancq, N. and Fernandez, S. and Jarman, R.G. and Ruchusatsawat, K. and Iamsirithaworn, S. and Vandepitte, W.P. and Suntarattiwong, P. and Read, J.M. and Klungthong, C. and Thaisomboonsuk, B. and Engø-Monsen, K. and Buckee, C. and Cauchemez, S. and Cummings, D.A.T. (2021) Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. Nature Communications, 12 (1). ISSN 2041-1723

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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.

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Journal Article
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Nature Communications
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Deposited On:
13 Apr 2021 15:30
Last Modified:
22 Nov 2022 10:09