VIRADAPT

Vaccination protects individuals against viral infections and limits the spread of epidemics. But the effectiveness of vaccines is threatened by viral adaptation, which can bypass host immune defenses and/or increase virus transmission. The aim of the VIRADAPT project is to better understand this adaptation, identify the most sustainable vaccine strategies, and develop new methods for characterizing variant phenotypes. In a first step (Work Package 1, WP1), we will develop a theoretical framework at the interface between population genetics and mathematical epidemiology, taking into account the different stages in the adaptation of a virus propagating in a heterogeneous host population (naïve, naturally immunized or vaccinated). These models will enable us to identify vaccination strategies that limit the risks of adaptation. In a second phase (WP2), we will use the theoretical framework developed in WP1 to characterize the phenotypes that govern viral propagation (transmission, immune evasion). We will develop a new statistical inference method for estimating these phenotypes from the temporal and spatial dynamics of the variants. This analysis of the dynamics of viral evolution in different countries (France, United Kingdom, Canada) will enable us to quantify the phenotypic adaptation of the main SARS-CoV-2 variants that emerged during the first three years of the pandemic. This combination of theoretical approach and data analysis will enable us to better understand the emergence and spread of viral adaptation. VIRADAPT will thus contribute to the optimization of public health policies (1) by making recommendations on more sustainable vaccine deployment strategies, and (2) by developing a new method for rapidly characterizing the phenotypes of new variants.