Computing the inducibility of B cell lineages under a context-dependent model of affinity maturation: Applications to sequential vaccine design

A key challenge in B cell lineage-based vaccine design is understanding the inducibility of target neutralizing antibodies. We approach this problem through the use of detailed stochastic modeling of the somatic hypermutation process that occurs during affinity maturation. Under such a model, sequence mutation rates are context-dependent , rendering standard probability calculations for sequence evolution intractable. We develop an algorithmic approach to rapid, accurate approximation of key marginal sequence likelihoods required to inform modern sequential vaccine design strategies. These calculated probabilities are used to define an inducibility index for selecting among potential targets for immunogen design. We apply this approach to the problem of choosing targets for the design of boosting immunogens aimed at elicitation of the HIV broadly-neutralizing antibody DH270min11. Author summary Vaccine effectiveness relies on inducing the immune system to generate protective antibodies. Because antibodies are generated by random processes coupled to positive selection, the ability to induce certain rare but desirable antibodies can be limited by the inherent probability of occurrence. We use computational modeling to estimate the probability of antibody occurrence, and demonstrate the use of these estimates in designing vaccine regimens which maximize the probability of induction of broadly neutralizing antibodies.