Rapid discovery of monoclonal antibodies via high-throughput single BCR affinity sequencing

Abstract

Abstract To jointly capture antigen-binding affinity and paired heavy–light-chain sequences at scale has remained a bottleneck for monoclonal antibody discovery. Here, we present Antigen Affinity BCR-seq (AAB-seq), a high-throughput single-cell sequencing platform that can obtain the relative antibody–antigen affinity of thousands of paired native BCR sequences. AAB-seq employs dual-labeled antigens and DNA-barcoded anti-light-chain antibodies to compute an AAB score that is proportional to antibody–antigen binding strength. Integrated with a rapid, low-cost direct cloning workflow, it enables affinity-guided antibody retrieval without de novo antibody gene synthesis. Validated against ovalbumin and SARS–COV–2 RBD, AAB-seq discovered potent antibodies whose AAB score correlates strongly with ELISA, including novel SARS–COV–2 neutralizing antibodies with potent effector functions. Together, AAB-seq accelerates antibody screening and potentially provides large-scale sequence-affinity datasets for machine learning-driven therapeutic antibody design and development.