title: Epidemic dynamics and antigenic evolution in a single season of influenza A.
abstract: We use a mathematical model to study the evolution of influenza A during the epidemic dynamics of a single season. Classifying strains by their distance from the epidemic-originating strain, we show that neutral mutation yields a constant rate of antigenic evolution, even in the presence of epidemic dynamics. We introduce host immunity and viral immune escape to construct a non-neutral model. Our population dynamics can then be framed naturally in the context of population genetics, and we show that departure from neutrality is governed by the covariance between a strain's fitness and its distance from the original epidemic strain. We quantify the amount of antigenic evolution that takes place in excess of what is expected under neutrality and find that this excess amount is largest under strong host immunity and long epidemics.
authors.affiliation: Department of Biological Sciences, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA. maciek@charles.stanford.edu
authors.forename: Maciej F
authors.initials: MF
authors.lastname: Boni
authors.forename: Julia R
authors.initials: JR
authors.lastname: Gog
authors.forename: Viggo
authors.initials: V
authors.lastname: Andreasen
authors.forename: Marcus W
authors.initials: MW
authors.lastname: Feldman
mesh_terms: D000940:Antigenic Variation; D004196:Disease Outbreaks; D019143:Evolution, Molecular; D040961:Genetic Drift; D006801:Humans; D009980:Influenza A virus / Q000235:genetics / Q000276:immunology*; D007251:Influenza, Human / Q000453:epidemiology* / Q000276:immunology; D008954:Models, Biological; D017354:Point Mutation; D011157:Population Dynamics; D012621:Seasons; D020539:Sequence Analysis, Protein