Recombinant human B cell repertoires enable screening for rare, specific and natively-paired antibodies

The human antibody repertoire is increasingly being recognized as a valuable source of therapeutic grade antibodies. However, methods for mining primary antibody-expressing B cells are limited in their ability to rapidly isolate rare and functionally-relevant binders. Here we show the capture of two million primary B cells into natively-paired expressible libraries that can be directly enriched and screened for function. We achieve this by encapsulating B cells into picoliter-sized droplets, in which their cognate V genes are fused in frame to form an scFv cassette. We demonstrate the power of this approach by constructing the first natively-paired phage-display libraries from the peripheral blood cells of two healthy donors, which allowed us to drive selection towards antibodies cross-reactive to different influenza hemagglutinin (HA) subtypes. Within four weeks we progressed from whole blood isolation to 18 unique anti-HA monoclonal antibodies, six of which were cross-reactive to multiple HA subtypes, including one that showed cross-reactivity to 10 different subtypes from influenza A (Group 1 and 2) and B lineages. The vast majority of these antibody sequences were not detected by next-generation sequencing of the paired repertoire, illustrating how this method can isolate extremely rare leads not likely found by existing technologies.