Pathogen diversity from an ecological perspective: case studies on H3N2 influenza and Plasmodium falciparum malaria
Sequence data is becoming increasingly available for many pathogens in both time and space. This creates the extraordinary opportunity to address whether pathogen populations are structured into strains, and if so, what are the connections between strain structure and the population dynamics of infectious diseases. In particular, the genetic diversity associated with antigenic phenotypes, the variation recognized by the immune system is of interest. Here, conceptual models with a basis in competitive ecological interactions provide a basis to understand whether and how immune selection (competitive interactions between strains mediated by cross-immunity) structures pathogen populations and how this structure influences in turn the transmission dynamics of pathogens. In this talk, I present two examples, from our work on Plasmodium falciparum malaria and H3N2 influenza, with individual-based models of transmission that track the history of infection of individual hosts and the genetic relatedness of the pathogen. Conceptual connections of ‘strain theory’ to the broader subject of diversity in ecological communities are discussed.