Accounting for population structure reveals ambiguity in the zaire ebolavirus reservoir dynamics

Bram Vranckenid; Tony Wawina-Bokalanga; Bert Vanmechelen; Joan Martí-Carreras; Miles W. Carroll; Justus Nsio; Jimmy Kapetshi; Sheila Makiala-Mandanda; Jean Jacques Muyembe-Tamfum; Guy Baeleid; Kurt Vermeire; Valentijn Vergote; Steve Ahuka-Mundeke; Piet Maesid

doi:10.1371/journal.pntd.0008117

Accounting for population structure reveals ambiguity in the zaire ebolavirus reservoir dynamics

Bram Vranckenid^*, Tony Wawina-Bokalanga, Bert Vanmechelen, Joan Martí-Carreras, Miles W. Carroll, Justus Nsio, Jimmy Kapetshi, Sheila Makiala-Mandanda, Jean Jacques Muyembe-Tamfum, Guy Baeleid, Kurt Vermeire, Valentijn Vergote, Steve Ahuka-Mundeke, Piet Maesid

^*Corresponding author for this work

Research & Development Institute Divisional Office

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Abstract

Ebolaviruses pose a substantial threat to wildlife populations and to public health in Africa. Evolutionary analyses of virus genome sequences can contribute significantly to elucidate the origin of new outbreaks, which can help guide surveillance efforts. The reconstructed between-outbreak evolutionary history of Zaire ebolavirus so far has been highly consistent. By removing the confounding impact of population growth bursts during local outbreaks on the free mixing assumption that underlies coalescent-based demographic reconstructions, we find—contrary to what previous results indicated—that the circulation dynamics of Ebola virus in its animal reservoir are highly uncertain. Our findings also accentuate the need for a more fine-grained picture of the Ebola virus diversity in its reservoir to reliably infer the reservoir origin of outbreak lineages. In addition, the recent appearance of slower-evolving vari-ants is in line with latency as a survival mechanism and with bats as the natural reservoir host.

Original language	English
Article number	e0008117
Journal	PLoS Neglected Tropical Diseases
Volume	14
Issue number	3
Early online date	4 Mar 2020
DOIs	https://doi.org/10.1371/journal.pntd.0008117
Publication status	E-pub ahead of print - 4 Mar 2020

Bibliographical note

Funding Information: TWB is supported by the Special Research Fund, KU Leuven (Bijzonder Onderzoeksfonds, KU Leuven, 3M170314 C14/17/ 100). BVr is supported by a postdoctoral grant (12U7118N) and BVa is supported by a doctoral grant (1S28617N) from the Research Foundation Flanders-Fonds voor Wetenschappelijk OnderzoeVlaanderen (FWO, Flanders, Belgium). JMC is supported by a doctoral grant from HONOURs Marie-Sklodowska-Curie training network (721367). GB acknowledges support from the Interne Fondsen KU Leuven / Internal Funds KU Leuven under grant agreement C14/18/094. This work is supported by the Special Research Fund, KU Leuven (Bijzonder Onderzoeksfonds, KU Leuven, C14/17/100). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Open Access: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publisher Copyright: © 2020 Vrancken et al.

Citation: Vrancken B, Wawina-Bokalanga T, Vanmechelen B, Martı´-Carreras J, Carroll MW, Nsio J, et al. (2020) Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics. PLoS Negl Trop Dis 14(3): e0008117.

DOI: https://doi.org/10.1371/journal.pntd.0008117

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Vrancken2020AccountingForPopulationStructureRevealsAmbiguityPLoSNeglTropDisFinal published version, 1.96 MBLicence: CC BY

Cite this

Vranckenid, B., Wawina-Bokalanga, T., Vanmechelen, B., Martí-Carreras, J., Carroll, M. W., Nsio, J., Kapetshi, J., Makiala-Mandanda, S., Muyembe-Tamfum, J. J., Baeleid, G., Vermeire, K., Vergote, V., Ahuka-Mundeke, S., & Maesid, P. (2020). Accounting for population structure reveals ambiguity in the zaire ebolavirus reservoir dynamics. PLoS Neglected Tropical Diseases, 14(3), [e0008117]. https://doi.org/10.1371/journal.pntd.0008117

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abstract = "Ebolaviruses pose a substantial threat to wildlife populations and to public health in Africa. Evolutionary analyses of virus genome sequences can contribute significantly to elucidate the origin of new outbreaks, which can help guide surveillance efforts. The reconstructed between-outbreak evolutionary history of Zaire ebolavirus so far has been highly consistent. By removing the confounding impact of population growth bursts during local outbreaks on the free mixing assumption that underlies coalescent-based demographic reconstructions, we find—contrary to what previous results indicated—that the circulation dynamics of Ebola virus in its animal reservoir are highly uncertain. Our findings also accentuate the need for a more fine-grained picture of the Ebola virus diversity in its reservoir to reliably infer the reservoir origin of outbreak lineages. In addition, the recent appearance of slower-evolving vari-ants is in line with latency as a survival mechanism and with bats as the natural reservoir host.",

author = "Bram Vranckenid and Tony Wawina-Bokalanga and Bert Vanmechelen and Joan Mart{\'i}-Carreras and Carroll, {Miles W.} and Justus Nsio and Jimmy Kapetshi and Sheila Makiala-Mandanda and Muyembe-Tamfum, {Jean Jacques} and Guy Baeleid and Kurt Vermeire and Valentijn Vergote and Steve Ahuka-Mundeke and Piet Maesid",

note = "Funding Information: TWB is supported by the Special Research Fund, KU Leuven (Bijzonder Onderzoeksfonds, KU Leuven, 3M170314 C14/17/ 100). BVr is supported by a postdoctoral grant (12U7118N) and BVa is supported by a doctoral grant (1S28617N) from the Research Foundation Flanders-Fonds voor Wetenschappelijk OnderzoeVlaanderen (FWO, Flanders, Belgium). JMC is supported by a doctoral grant from HONOURs Marie-Sklodowska-Curie training network (721367). GB acknowledges support from the Interne Fondsen KU Leuven / Internal Funds KU Leuven under grant agreement C14/18/094. This work is supported by the Special Research Fund, KU Leuven (Bijzonder Onderzoeksfonds, KU Leuven, C14/17/100). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Open Access: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Publisher Copyright: {\textcopyright} 2020 Vrancken et al. Citation: Vrancken B, Wawina-Bokalanga T, Vanmechelen B, Martı´-Carreras J, Carroll MW, Nsio J, et al. (2020) Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics. PLoS Negl Trop Dis 14(3): e0008117. DOI: https://doi.org/10.1371/journal.pntd.0008117",

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Vranckenid, B, Wawina-Bokalanga, T, Vanmechelen, B, Martí-Carreras, J, Carroll, MW, Nsio, J, Kapetshi, J, Makiala-Mandanda, S, Muyembe-Tamfum, JJ, Baeleid, G, Vermeire, K, Vergote, V, Ahuka-Mundeke, S & Maesid, P 2020, 'Accounting for population structure reveals ambiguity in the zaire ebolavirus reservoir dynamics', PLoS Neglected Tropical Diseases, vol. 14, no. 3, e0008117. https://doi.org/10.1371/journal.pntd.0008117

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Accounting for population structure reveals ambiguity in the zaire ebolavirus reservoir dynamics

Abstract

Bibliographical note

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