Evolutionary dynamics of a virus in a vaccinated population

Bell, G.

The progress of an epidemic in a small closed community is simulated by an agent-based model which allows vaccination and variation. The attributes of the virus are governed by two genetic loci: the P-locus, which determines growth, and the M-locus, which determines immune characteristics. Mutation at either locus modifies the attributes of the virus and leads to evolution through natural selection. For both loci the crucial variable is the potential mutation supply UPot, because evolution is likely to happen when UPot > 1. Mutation at the P-locus causes a limited increase in virulence, which may be affected by vaccine design. Mutation at the M-locus may cause a qualitative shift of dynamic regime from a simple limited epidemic to a perennial endemic disease by giving rise to escape mutants which may themselves mutate. A broad vaccine that remains efficacious despite several mutations at the M-locus prevents this shift and provides protection despite the evolution of the virus. Escape variants may nevertheless arise through recombination after coinfection, and can be suppressed by timely revaccination, using the prevalent strain to design the vaccine.