Abstract
Recent advances in genomics, mathematical modelling and computational biology have enabled evolutionary approaches to become a key component in studying of viral infectious diseases. The use of evolutionary approaches offers many advantages compared to traditional epidemiological methods; for example, they can reconstruct the demographic history of an entire epidemic even when surveillance data are sparse or non-existent, they require only a small number of sampled pathogens, and they can detect linkages among infections in time and space that may not be evident otherwise. Even over short time scales, viruses can accumulate significant diversity, resulting a genomic imprint of the ecological impact on transmission dynamics. By statistically analyzing the genetic differences among viruses sampled from a population, we can reveal the underlying processes that govern viral transmission. Yet, a major challenge in this field is to develop methodologies to formally test the effect of environmental factors on pathogen transmission and evolution. Over the last years, we have addressed this challenge by developing tools in landscape phylogeography, a field at the interface between spatial and molecular epidemiology and that aims to relate phylogenetic informed movements to environmental factors. Specifically, we here present new methods that we developed and applied to investigate the impact of environmental factors on the dispersal velocity, dispersal direction, or dispersal frequency of viral lineages. In particular, we have applied those new analytical approaches to investigate the external factors having impacted several epidemics of public and one health importance like, e.g., the Ebola virus outbreak in West Africa (2014-16; Dellicour et al. 2018), the circulation of Rabies virus in different regions and host species (Dellicour et al., 2019), and the West Nile virus invasion in North America (Dellicour et al., 2020). For instance, our analyses have demonstrated that announcements of border closures were followed by a significant but transient effect on international virus dispersal during the 2014-16 Ebola virus outbreak, and that West Nile virus lineages tended to disperse faster in areas associated with higher temperatures. With our latest developments in the field of landscape phylogeography, we illustrate how to go beyond historical reconstructions and exploit spatially-explicit phylogeographic reconstructions to formally test epidemiological hypotheses.
References
Dellicour, S., Lequime, S., Vrancken, B., Gill, M. S., Bastide, P., Gangavarapu, K., Matteson, N. L., Tan, Y., du Plessis, L., Fisher, A. A., Nelson, M. I., Gilbert, M., Suchard, M. A., Andersen, K. G., Grubaugh, N. D., Pybus, O. G., & Lemey, P. (2020). Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature communications, 11(1), 5620. https://doi.org/10.1038/s41467-020-19122-z
Dellicour, S., Troupin, C., Jahanbakhsh, F., Salama, A., Massoudi, S., Moghaddam, M. K., Baele, G., Lemey, P., Gholami, A., & Bourhy, H. (2019). Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran. Molecular ecology, 28(18), 4335–4350. https://doi.org/10.1111/mec.15222
Dellicour, S., Baele, G., Dudas, G., Faria, N. R., Pybus, O. G., Suchard, M. A., Rambaut, A., & Lemey, P. (2018). Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nature communications, 9(1), 2222. https://doi.org/10.1038/s41467-018-03763-2