Multilocus adaptation to vaccination

Pathogen adaptation to public health interventions, such as vaccination, may take tortuous routes and involve multiple mutations at distinct locations in the pathogen genome, acting on distinct phenotypic traits. Despite its importance for public health, how these multilocus adaptations jointly evolve is poorly understood. Here we consider the joint evolution of two adaptations: the pathogens ability to escape the vaccine-induced immune response and adjustments to the pathogens virulence and transmissi-bility. We elucidate the role played by epistasis and recombination, with an emphasis on the different protective effects of vaccination. We show that vaccines reducing transmission and/or increasing clearance generate positive epistasis between the vaccine-escape and virulence alleles, favouring strains that carry both mutations, whereas vaccines reducing virulence mortality generate negative epistasis, favouring strains that carry either mutation, but not both. High rates of recombination can affect these predictions. If epistasis is positive, frequent recombination can lead to the sequential fixation of the two mutations and prevent the transient build-up of more virulent escape strains. If epistasis is negative, frequent recombination between loci can create an evolutionary bistability, such that whichever adaptation is more accessible tends to be favoured in the long-term. Our work provides a timely alternative to the variant-centered perspective on pathogen adaptation and captures the effect of different types of vaccines on the interference between multiple adaptive mutations.