Many viruses affecting human populations, including serious respiratory illnesses such as influenza and SARS-CoV-2, evolve rapidly over time scales of months or years. This evolution is driven in part by the pressure exerted by host immune systems, which upon infection or vaccination acquire protection against circulating strains of the virus, giving a selective advantage to strains that can escape immunity. Viral evolution, in turn, drives shifts in both individual and population-wide host immune repertoires, which are composed of large repertoires of lymphocytes with specific antigenic targets that can evolve in a Darwinian fashion within each host. This gives rise to a complex pattern of co-evolution between viruses and immune systems, occurring at multiple scales. Understanding this coevolutionary process is key to interpreting and predicting future viral evolution, to decoding the immune repertoire, and to designing efficient vaccination strategies.

This program aims to cover various aspects of these questions, from the molecular, physiological and organismal level of the immune response, to the population and epidemiological levels of viral-host dynamics. Specifically, we will discuss current and future efforts to better map out the molecular recognition landscape between viral antigens and immune receptors; understand how this recognition triggers and modifies the immune system, preparing it for future infections including with different strains, and how it drives viral evolution; and discuss how multi-scale co-evolutionary models can integrate this information to make better epidemiological predictions.