A biophysical model of viral escape from polyclonal antibodies

Abstract

A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes. Here we introduce a biophysical model of this process that partitions the total polyclonal antibody activity by epitope, and then quantifies how each viral mutation affects the antibody activity against each epitope. We develop software that can use deep mutational scanning data to infer these properties for polyclonal antibody mixtures. We validate this software using a computationally simulated deep mutational scanning experiment, and demonstrate that it enables the prediction of escape by arbitrary combinations of mutations. The software described in this paper is available at https://jbloomlab.github.io/polyclonal.

Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning

“…To directly quantify how mutations affected neutralization, we included a non-neutralized “standard” virus pseudotyped with VSV-G to enable conversion of relative sequencing counts to absolute neutralization measurements 23 . To estimate the effects of individual mutations from our library measurements (which include both singly and multiply mutated Envs), we fit a biophysical model where antibody neutralization at each epitope has a Hill-curve dependence on antibody concentration and mutations within a given epitope have additive effects on antibody affinity 22 . This model, which is implemented in the polyclonal software (https://jbloomlab.github.io/polyclonal/), utilizes information from both singly and multiply mutated Env variants under realistic assumptions about how mutations combine to escape antibody binding.…”

“…The escape map for the final serum, IDC508, revealed neutralization escape at two distinct antibody epitopes (Figure 6A,C,D, and interactive escape maps linked in figure legend). The existence of two epitopes was inferred by fitting the biophysical model 22 to the deep mutational scanning measurements and finding that escape in multiply mutated variants was best explained by mutations affecting antibody binding at two distinct regions. Note that identification of two separate epitopes is crucially enabled by the ability of our deep mutational scanning system to quantify escape by Envs with multiple mutations 22 .…”

“…We modeled the effects of mutations on antibody and serum escape as described previously in Dadonaite et al 23 Briefly, we calculated the non-neutralized fraction of each variant at each antibody calculation to get the probability of escape of each variant at each concentration. We then used the software package polyclonal 22 version 4.1 (see https://jbloomlab.github.io/polyclonal/ for documentation) to estimate the effects of each individual mutation on escape using a biophysical model. Under this model, antibodies, mixtures of antibodies, or polyclonal serum can target Env at one or more epitopes.…”

“…A goal of our experiments is to map escape from polyclonal serum antibodies as well as monoclonal antibodies. Since polyclonal serum is composed of multiple antibodies that can target different epitopes [30][31][32] , mapping escape from serum requires libraries that contain Envs with mutations in multiple epitopes 22 . However, about half of all possible amino-acid mutations to proteins are highly deleterious, 29,[33][34][35] so a library of multiply mutated Envs with random mutations would contain a high fraction of non-functional proteins.…”

“…Here we use an improved deep mutational scanning system to measure how mutations affect neutralization of Env by human anti-HIV sera that target the CD4-binding site. This new system can measure the effects of combinations of mutations, enabling quantitative deconvolution of how mutations mediate escape at distinct antibody epitopes 22 . We find that several sera have neutralizing activities that resemble monoclonal antibodies, but one sera has neutralizing activity targeting two distinct epitopes.…”