High-throughput specificity profiling of antibody libraries using ribosome display and microfluidics

High-throughput methods for pair-wise mapping of protein-protein interactions would enable deeper understanding of biological processes, such as natural antibody responses, however current techniques are limited by the number of interactions that can be screened at once. To overcome this, we have developed PolyMap (polyclonal mapping), a system based on bulk binding of a ribosome-displayed antibody library to a library of cell-surface expressed antigens, combined with single cell analysis using droplet microfluidics. We demonstrate the mapping of thousands of antigen-antibody interactions between diverse antibody libraries isolated from convalescent and vaccinated COVID-19 donors and a set of clinically relevant SARS-CoV-2 spike variants. We identify over 150 antibodies with a variety of distinctive binding patterns towards the antigen variants, and find a broader binding profile, including targeting of the Omicron variant, in the antibody repertoires of more recent donors. We then use this data to select mixtures of a small number of clones with complementary reactivity that together provide strong potency and broad neutralization. PolyMap is a generalizable platform that can be used for one-pot epitope mapping, immune repertoire profiling, and therapeutic design, and in the future could be expanded to other families of interacting proteins.