Antibody Discovery for Non-Human Coronaviruses with the Potential for Human Emergence

The COVID-19 pandemic has emphasized the importance of developing effective countermeasures quickly. Through various pandemic preparedness initiatives, effective SARS-CoV-2-neutralizing antibodies were discovered and validated within months; and similarly for SARS-CoV-2 vaccines. However, even with such unprecedented speed of countermeasure development, the pandemic has had a devastating effect, resulting in the loss of millions of human lives, extreme potentially long-lasting burden on the health care system, and economic turmoil. The critical need for preemptive development of countermeasures that can counteract future coronavirus outbreaks is clear. To that end, here we propose to develop a program for the discovery of countermeasures against a broad diversity of coronaviruses, specifically focusing on coronaviruses that have not yet emerged in humans. In particular, we will focus on the discovery and characterization of coronavirus-specific antibodies, as potential therapeutic candidates and templates for broadly protective vaccines. A critical advantage of our efforts is our recently developed LIBRA-seq technology (LInking B-cell Receptor to Antigen specificity through sequencing) for antibody discovery and characterization of antigen-specific antibody repertoires. Unlike other antibody discovery approaches, LIBRA-seq is the first to enable the simultaneous determination of B-cell receptor (BCR) sequence and antigen specificity for a large number of B cells against a theoretically unlimited number of diverse antigens, at the single-cell level. LIBRA-seq therefore provides a unique opportunity for screening for antigen-specific B cells that are capable of recognizing a wide range of coronaviruses. Overall, the discovery of antibodies against diverse coronaviruses will become a first line of defense against new outbreaks with previously unencountered coronaviruses. Our proposed efforts fall within the Infectious Diseases Peer Reviewed Medical Research Program (PRMRP) Portfolio, Viral Diseases Fiscal Year 2022 (FY22) PRMRP Topic Area, with a focus on the following FY22 PRMRP Strategic Goal: "Develop or optimize vaccine strategies, platforms, or compounds, to include active or passive immunoprophylaxis, especially for Dengue, Lassa, and Crimean-Congo Hemorrhagic fever viruses, beta-coronaviruses." In general, we hypothesize that even though the human immune system has not been exposed specifically to non-human coronaviruses, we will still be able to identify effective antibodies against such coronaviruses. This hypothesis is supported by the preliminary data included in our application that highlights the identification of exceptionally broadly reactive coronavirus antibodies, including against a wide range of non-human coronaviruses, from human samples using the LIBRA-seq technology. The efforts in this proposal will directly address an important FY22 PRMRP Strategic Goal within a significant Topic Area, leading to the identification of novel monoclonal antibody candidates against a wide range of beta-, and potentially other, coronaviruses that have the potential to emerge in humans. In essence, this proposal will ultimately result in a repository of antibodies against diverse coronaviruses that can be used as part of ultra-rapid response strategies to prevent future coronavirus pandemics. While the antibody discovery efforts in the context of SARS-CoV-2 showed that effective antibodies can be identified efficiently within a couple of months with appropriate antigen and human infection sample availability, the work we propose here will help avoid that initial discovery period. As we now know, even 1-2 months can make an enormous difference in an exponentially evolving pandemic, especially at the early stages of infection spread. Therefore, in this application we are proposing the proactive development of a coronavirus repository, in contrast to the generally reactive current antibody discovery strategies for pandemic preparedness. We note that this proposed project is a first step toward the creation of pan-beta-coronavirus, and even more broadly - pan-coronavirus, antibody repository. In our efforts here, we will perform initial characterization of the LIBRA-seq-identified antibodies against a set of diverse coronaviruses. These initial results will show the feasibility of the proposed approach and will motivate a subsequent significant expansion of these efforts, both toward further validation of the identified antibodies (e.g., in therapeutic and prophylactic experiments in animal models), as well as toward screening against a larger number of additional diverse non-human coronaviruses. Overall, our results will provide unparalleled levels of information linking antibody sequence to antigen specificity in the context of coronaviruses. The transformative potential of the proposed efforts is high both with respect to developing a specific coronavirus antibody repository, as well as from the perspective of establishing a novel platform for pandemic preparedness against infectious diseases in general. Indeed, the antibody discovery platform that we are proposing here will also be readily generalizable to other zoonotic diseases, and as such, will have a broad and lasting impact on our path to pandemic preparedness against established and emerging infectious diseases. The work in this project is therefore of high translational and clinical significance. Less