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Reconstructing unseen transmission events to infer dengue dynamics from viral sequences

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Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. / Salje, H.; Wesolowski, A.; Brown, T.S.; Kiang, M.V.; Berry, I.M.; Lefrancq, N.; Fernandez, S.; Jarman, R.G.; Ruchusatsawat, K.; Iamsirithaworn, S.; Vandepitte, W.P.; Suntarattiwong, P.; Read, J.M.; Klungthong, C.; Thaisomboonsuk, B.; Engø-Monsen, K.; Buckee, C.; Cauchemez, S.; Cummings, D.A.T.

In: Nature Communications, Vol. 12, No. 1, 1810, 22.03.2021.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Salje, H, Wesolowski, A, Brown, TS, Kiang, MV, Berry, IM, Lefrancq, N, Fernandez, S, Jarman, RG, Ruchusatsawat, K, Iamsirithaworn, S, Vandepitte, WP, Suntarattiwong, P, Read, JM, Klungthong, C, Thaisomboonsuk, B, Engø-Monsen, K, Buckee, C, Cauchemez, S & Cummings, DAT 2021, 'Reconstructing unseen transmission events to infer dengue dynamics from viral sequences', Nature Communications, vol. 12, no. 1, 1810. https://doi.org/10.1038/s41467-021-21888-9

APA

Salje, H., Wesolowski, A., Brown, T. S., Kiang, M. V., Berry, I. M., Lefrancq, N., Fernandez, S., Jarman, R. G., Ruchusatsawat, K., Iamsirithaworn, S., Vandepitte, W. P., Suntarattiwong, P., Read, J. M., Klungthong, C., Thaisomboonsuk, B., Engø-Monsen, K., Buckee, C., Cauchemez, S., & Cummings, D. A. T. (2021). Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. Nature Communications, 12(1), [1810]. https://doi.org/10.1038/s41467-021-21888-9

Vancouver

Salje H, Wesolowski A, Brown TS, Kiang MV, Berry IM, Lefrancq N et al. Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. Nature Communications. 2021 Mar 22;12(1). 1810. https://doi.org/10.1038/s41467-021-21888-9

Author

Salje, H. ; Wesolowski, A. ; Brown, T.S. ; Kiang, M.V. ; Berry, I.M. ; Lefrancq, N. ; Fernandez, S. ; Jarman, R.G. ; Ruchusatsawat, K. ; Iamsirithaworn, S. ; Vandepitte, W.P. ; Suntarattiwong, P. ; Read, J.M. ; Klungthong, C. ; Thaisomboonsuk, B. ; Engø-Monsen, K. ; Buckee, C. ; Cauchemez, S. ; Cummings, D.A.T. / Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. In: Nature Communications. 2021 ; Vol. 12, No. 1.

Bibtex

@article{71885beaef01431ea3e29922a8e8acce,
title = "Reconstructing unseen transmission events to infer dengue dynamics from viral sequences",
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. ",
keywords = "dengue fever, disease vector, immunity, pathogen, phylogenetics, reconstruction, virus, Thailand, Dengue virus",
author = "H. Salje and A. Wesolowski and T.S. Brown and M.V. Kiang and I.M. Berry and N. Lefrancq and S. Fernandez and R.G. Jarman and K. Ruchusatsawat and S. Iamsirithaworn and W.P. Vandepitte and P. Suntarattiwong and J.M. Read and C. Klungthong and B. Thaisomboonsuk and K. Eng{\o}-Monsen and C. Buckee and S. Cauchemez and D.A.T. Cummings",
year = "2021",
month = mar,
day = "22",
doi = "10.1038/s41467-021-21888-9",
language = "English",
volume = "12",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

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 -