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We introduce a multi-scale model for affinity maturation, which aims tocapture the intra-clonal, inter-clonal and epitope-specific organization of theB cell population in a germinal center. We apply the Eigen's model ofquasispecies evolution in a random fitness landscape, where the desiredmulti-scale structure is reflected in the mutational connectivity of the B cellreceptor (BCR) space, and on statistical characteristics of the fitnessensembles. Within this mathematical framework, we study the competition amongclasses of BCRs targeting different antigen epitopes, and construct aneffective immunogenic space where epitope immunodominance relations can beuniversally characterized. We study how varying the composition of a mixture ofantigens with variable and conserved domains allows for a parametricexploration of this space, and identify general principles for the rationaldesign of two-antigen cocktails. We find that optimization of the cocktailcomposition must take into account possible statistical asymmetries between thetwo classes of BCRs targeting the two variants of the mutated epitope, as wellas the evolutionary regime in which affinity maturation occurs.

Universal characterization of epitope immunodominance from a multi-scale model of clonal competition in germinal centers