Host immunity and pathogen diversity: A computational study

Abstract

The distinctive features of human influenza A phylogeny have inspired many mathematical and computational studies of viral infections spreading in a host populationbut our understanding of the mechanisms that shape the coupled evolution of host immunitydisease incidence and viral antigenic properties is far from complete. In this paper we explore the epidemiology and the phylogeny of a rapidly mutating pathogen in a host population with a weak immune responsethat allows re-infection by the same strain and provides little cross-immunity. We find that mutation generates explosive diversity and thatas diversity growsthe system is driven to a very high prevalence level. This is in stark contrast with the behavior of similar models where mutation gives rise to a large epidemic followed by disease extinctionunder the assumption that infection with a strain provides lifelong immunity. For low mutation ratesthe behavior of the system shows the main qualitative features of influenza evolution. Our results highlight the importance of heterogeneity in the human immune response for understanding influenza A phenomenology. They are meant as a first step toward computationally affordableindividual based models including more complex host-pathogen interactions.