Strain competition dynamics in an evolutionary context: H3N2 influenza as a case study

Mercedes Pascual

Short Abstract
Mathematical models for the population dynamics of pathogens that take into consideration their antigenic variation (the variation seen by the immune system) in a finite space, can exhibit an array of nonlinear behavior including periodic or chaotic cycles in the successive replacement of strains. These are essentially competitive systems in which strains compete for hosts at the population level. These models have been proposed as one possible explanation for the patterns of genetic and antigenic diversity observed in H3N2 influenza, and in particular, for the limited standing diversity at any given point in time (Recker et al., PNAS 2007). We extend these deterministic models to incorporate explicit evolution in the form of mutations in antigenic space, with an individual-based and stochastic implementation that also tracks the genealogy of the virus. Parameter space is explored between the two extremes of dynamics dominated respectively by the opening of niches (frequency-dependent competition) and by the arrival of new types (innovation). The resulting patterns of pathogen diversity and population dynamics are discussed in the context of H3N2 influenza, as well as of competitive systems in general.