Abstract

Influenza has large antigenic diversity and rapid evolution, and it can keep escaping from host immunity. To understand the evolutionary dynamics of influenza with host immune reaction, we developed two models : i) a deterministic epidemiological model with discrete epidemic seasons used to study the initial phase of the evolutionary branching process associated with two antigenic escape mutants derived from a common ancestral strain ii) a multi-strain SIR individual based model. With these models we found that: (1). The time at which a new strain appears relative to the epidemic peak of an existing strain is important because it determines the environment the emergent mutant experiences in terms of the short term immune profile of the host population. Strains are more likely to coexist, and hence to establish a new clade in the viral phylogeny, when there is a significant time overlap between their epidemics. (2) In a year, the most frequent emergence time of successful strain (the strain will produce new mutant strain) is early stage of epidemic season. The duration from emergence time to maximum prevalence is over one year. This has implication for the prediction of epidemic strain in future.