Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics

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 variants is in line with latency as a survival mechanism and with bats as the natural reservoir host. Author summary Because of its implications for awareness, surveillance and risk assessment of EBOV transmission to humans, the origin of emerging Zaire ebolavirus is investigated at each outbreak. To reliably do so requires a good understanding of the circulation dynamics of Zaire ebolavirus in its reservoir, which has yet to be determined. Here, we analyzed available full-length Zaire ebolavirus genomes from past and current outbreaks to infer the between-outbreak circulation dynamics while avoiding model misspecification by downsampling the data.