Data integration in pathogen phylodynamics : from ancient epidemic histories to recent viral outbreaks
Thursday 21 March 2019 (12h15 - 13h00) - Génopode - Auditoire A
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Abstract of the talk
The field of phylodynamics has witnessed a rich development of statistical inference tools with increasing levels of sophistication that can be applied to address a variety of questions about the evolution and epidemiology of viruses. A Bayesian phylogenetic framework that focuses on time-measured trees has proven fertile ground for integrating approaches that aim at uncovering pathogen evolution and spread.
First, I will focus on the need for new molecular clock models that can accommodate various sources of evolutionary rate heterogeneity to adequately estimate the time-scale of epidemic histories. Among others, I will illustrate this for Hepatitis B virus (HBV), which represents an example of a deep evolutionary history that has been difficult to date accurately using sequences sampled over the last decades. Recent ancient DNA work has now resulted in the first HBV genomes from samples dating back thousands of years. This provides invaluable calibration information provided time-dependent evolutionary rates are accounted for.
The next focus will be on integrating location data to estimate spatiotemporal histories of viral spread. Specifically, I will illustrate how simple generalised linear modelling can be implemented in phylogenetic diffusion models in order to test and quantify the contribution of covariates in spatial spread. Applications involve reconstructing the spatial spread of Ebola virus during the 2013-2016 West African epidemic.
To meet with Dr. Lemey during the day, please register for the Doodle