A multilocus perspective on the evolutionary dynamics of multistrain pathogens

Abstract

Understanding the evolution of multistrain pathogens is of critical importance for forecasting epidemics and predicting the consequences of vaccination. One factor believed to play an important role is naturally-acquired immunity, and this has motivated a large-body of research seeking to understand how acquired immunity can mold the genomics of pathogen populations (pathogen strain structure). However, the diversity of existing models makes understanding the evolutionary connections between predictions difficult, leading to confusion about those that are broadly applicable and those that are not. Here we adopt a multilocus population genetics perspective to unify the evolutionary predictions of existing models, and provide insight on the role of naturally-acquired immunity in the evolution of pathogen strain structure. We identify three key factors: (i) the strength and specificity of immune protections, (ii) the dynamic immunological landscape, and (iii) the number of loci coding for the antigens of the pathogen. We use these three factors to clarify the relationship among previous models of multistrain dynamics and to establish solid theoretical foundations for the study of the evolutionary epidemiology of multitrain pathogens.