Efficiently Mining the B cell Repertoire for Cross-Reactive Coronavirus Antibodies

Abstract

Coronaviruses (CoVs) are single-stranded, positive-sense RNA viruses that infect a wide variety of species including birds, reptiles, and mammals. SARS-CoV-2 is only the latest coronavirus to jump from animals into humans in the last 20 years, and it has highlighted the necessity of developing our defenses against these threats before the next pandemic emerges. Antibodies are one of the most promising therapeutic and prophylactic drugs that we have against viruses, and they have been utilized extensively throughout the COVID-19 pandemic, however due to the rapid evolution of SARS-CoV-2, many lost effectiveness. This emphasizes the need for antibodies that are more cross-reactive and target more conserved epitopes of the spike protein. This dissertation contains my research efforts in characterizing novel, cross-reactive coronavirus antibodies, as well as developing techniques that will allow for the efficient discovery of rare, epitope-specific antibodies. In chapter 2, I characterize cross-reactive, potently neutralizing antibodies isolated from children, highlighting that antibodies from children may be an underutilized source for the discovery of cross-reactive CoV antibodies. In chapter 3, I present the discovery, characterization, and structure of an S2-specific, pan-betacoronavirus antibody to a novel epitope. Finally, I detail my work developing LIBRA-seq with antibody blocking, a high-throughput antibody discovery technology that will allow for the enrichment of antibodies that target rare epitopes that are difficult to identify through currently available technologies. Overall, my thesis work will contribute to the discovery and development of protective coronavirus antibodies, and epitope-specific antibody discovery tools in general.