Reconstructing unseen transmission events to infer dengue dynamics from viral sequences

Henrik Salje (), Amy Wesolowski, Tyler S. Brown, Mathew V. Kiang, Irina Maljkovic Berry, Noemie Lefrancq, Stefan Fernandez, Richard G. Jarman, Kriangsak Ruchusatsawat, Sopon Iamsirithaworn, Warunee P. Vandepitte, Piyarat Suntarattiwong, Jonathan M. Read, Chonticha Klungthong, Butsaya Thaisomboonsuk, Kenth Engø-Monsen, Caroline Buckee, Simon Cauchemez and Derek A. T. Cummings
Additional contact information
Henrik Salje: University of Cambridge
Amy Wesolowski: Johns Hopkins Bloomberg School of Public Health
Tyler S. Brown: Harvard T.H. Chan School of Public Health
Mathew V. Kiang: Harvard T.H. Chan School of Public Health
Irina Maljkovic Berry: Viral Diseases Branch, Walter Reed Army Institute of Research
Noemie Lefrancq: University of Cambridge
Stefan Fernandez: Armed Forces Research Institute of Medical Sciences
Richard G. Jarman: Viral Diseases Branch, Walter Reed Army Institute of Research
Kriangsak Ruchusatsawat: Ministry of Public Health
Sopon Iamsirithaworn: Ministry of Public Health
Warunee P. Vandepitte: Queen Sirikit National Institute of Child Health
Piyarat Suntarattiwong: Queen Sirikit National Institute of Child Health
Jonathan M. Read: Lancaster University
Chonticha Klungthong: Armed Forces Research Institute of Medical Sciences
Butsaya Thaisomboonsuk: Armed Forces Research Institute of Medical Sciences
Kenth Engø-Monsen: Telenor Research
Caroline Buckee: Harvard T.H. Chan School of Public Health
Simon Cauchemez: Institut Pasteur, CNRS
Derek A. T. Cummings: University of Florida

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21888-9

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DOI: 10.1038/s41467-021-21888-9

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