Functional and antigenic evolution of SARS-related coronaviruses

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PROJECT SUMMARY SARS-related coronaviruses (also known as sarbecoviruses) circulate in bat reservoirs, but two human spillovers in the past 20 years—SARS-CoV-1 in 2002 and SARS-CoV-2 in 2019—have caused globally devastating outbreaks. The emergence of SARS-CoV-2 from a previously unknown bat lineage highlights the pressing need to trace the evolutionary origins of viral properties that enable human spillover and develop therapeutic reagents that can broadly inhibit infection by diverse, potentially unsampled sarbecovirus lineages. Sarbecovirus zoonosis depends in part on the evolution of viruses to interact with ACE2 receptors on the surface of human and potential intermediate hosts’ cells, mediated by the viral spike receptor-binding domain (RBD). The RBD is also a key component to therapeutic control of SARS-CoV-2 and presumably other sarbecoviruses, as it is the target of the most potently neutralizing antibodies, including those in clinical development and in polyclonal human sera. Although I and others have begun surveying the impacts of mutations within SARS-CoV-2 itself on important biochemical phenotypes including binding to ACE2 receptor and antiviral antibodies, these studies have only limited utility in understanding the broader evolution of sarbecovirus RBDs, which exhibit considerable divergence in sequence and function. To characterize sarbecovirus functional and antigenic evolution, I propose to combine high-throughput protein binding experiments with computational evolutionary analyses, functional virology, and biochemistry: 1. I will profile the ACE2-binding specificities of all known sarbecovirus RBDs and their evolutionary precursors. I hypothesize that the ability to bind ACE2, including the human ACE2 ortholog, is more evolutionarily and geographically widespread than previously appreciated. 2. I will systematically characterize how diverse RBD mutations affect ACE2-binding phenotypes. I hypothesize that human ACE2 binding is an easily evolvable trait in sarbecovirus lineages where it has not been previously considered. I also hypothesize that divergence among sarbecovirus lineages shifts the genetic and biochemical determinants of ACE2 binding over evolutionary time. 3. I will identify RBD epitopes that are susceptible to broad pan-sarbecovirus antibody binding. By determining the relationship between breadth and other antibody properties across RBD epitopes, I highlight key features to target in the design of next-generation pan-sarbecovirus vaccines and antibody therapeutics. Identification of the evolutionary and biochemical basis for key sarbecovirus features enhances viral surveillance and therapeutic development, preparing for or even preventing future sarbecovirus spillovers. The new experimental expertise, broader training and mentorship, and research systems developed in this work will enable me to achieve my goal of leading an academic lab studying protein evolution at the host-virus interface.