Discovery of potently-neutralizing antibodies against SARS-CoV-2 using Barcode Enabled Antigen Mapping (BEAM)

Abstract Humans who have recovered from infectious disease possess a memory B cell pool that contains highly-potent antibodies against the cleared pathogenic agent. This pool is a valuable source of therapeutic antibodies but identifying these requires a method that can screen a large number of cells rapidly to identify promising candidates. We used Barcode Enabled Antigen Mapping (BEAM) to screen 100 million peripheral blood mononuclear cells (PBMCs) from a donor who had recovered from COVID-19. This method labels antigens of interest with unique reporter oligonucleotides and uses these labeled antigens to stain lymphocytes according to the binding specificity of their antigen receptors. Individual antigen-bound cells are then captured and analysed using the 10x Genomics Single Cell Immune Profiling Solution. This allows us to identify the antigen-specific cells while also generating transcriptomic profiles and natively paired, heavy and light chain full-length B-cell receptor sequences from each cell. We used BEAM to identify B cells that bound to the spike protein of SARS-CoV-2 and discovered 222 antibodies with high binding affinity confirmed by SPR. The majority of these antibodies bound to multiple variants of concern with some also recognising endemic coronaviruses. We then investigated the potential for these antibodies to neutralize live SARS-CoV-2 and confirmed that 55 exhibited potent neutralization activity. Finally, we performed epitope binning and discovered that the collection of antibodies bound to multiple different epitopes on the spike protein. Compared with hybridoma or other approaches, single cell methods have the potential to discover therapeutic antibodies more rapidly and with a higher diversity of leads.