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Project

A phylogeographic approach to test and quantify the effect of environmental factors on biological dispersion: computational developments and applications

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 analysing 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 a methodology to formally test the effect of environmental factors on pathogen transmission and evolution. The present post-doctoral project presents three specific aims: (1) to develop such a methodology made of two alternative but complementary methods, (2) to test and validate these two methods with artificial datasets simulated under different epidemiological scenarios, and (3) to apply both methods on the study of environmental factors impacting the dispersal rate of rabies epidemics and avian influenza (H5N1).

Date:1 Oct 2015 →  30 Sep 2018
Keywords:applications, computational developments, biological dispersion, environmental factors, phylogeographic approach
Disciplines:Microbiology, Systems biology, Laboratory medicine