TY - JOUR
T1 - Reconstructing unseen transmission events to infer dengue dynamics from viral sequences
AU - Salje, Henrik
AU - Wesolowski, Amy
AU - Brown, Tyler S.
AU - Kiang, Mathew V.
AU - Berry, Irina Maljkovic
AU - Lefrancq, Noemie
AU - Fernandez, Stefan
AU - Jarman, Richard G.
AU - Ruchusatsawat, Kriangsak
AU - Iamsirithaworn, Sopon
AU - Vandepitte, Warunee P.
AU - Suntarattiwong, Piyarat
AU - Read, Jonathan M.
AU - Klungthong, Chonticha
AU - Thaisomboonsuk, Butsaya
AU - Engø-Monsen, Kenth
AU - Buckee, Caroline
AU - Cauchemez, Simon
AU - Cummings, Derek A.T.
N1 - Funding Information:
H.S. is funded by the European Research Council (No. 804744). H.S. and D.A.T.C. would like to recognise funding by The National Institutes of Health (R01AI114703). A.P.W. is funded by a Career Award at the Scientific Interface by the Burroughs Wellcome Fund, by the National Library of Medicine of the National Institutes of Health under Award Number DP2LM013102 and the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number R21Al151750. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
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.
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U2 - 10.1038/s41467-021-21888-9
DO - 10.1038/s41467-021-21888-9
M3 - Article
C2 - 33753725
AN - SCOPUS:85103219842
SN - 2041-1723
VL - 12
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 1810
ER -