Clade-3 Bat Sarbecovirus PRD0038 Reveals Constraints on Coronavirus Emergence and Immune Sensitivity.

Zoonotic Sarbecoviruses present a documented threat to global health. Here, we report the recovery of an African clade-3 recombinant Sarbecovirus, PRD0038, and derivatives encoding reporter genes. Cryo-EM structural analyses of rPRD0038 revealed spike glycoprotein sites that facilitate the receptor-binding domain (RBD)-up conformation, enhancing replication in R. affinis but not human ACE2 expressing cells. Host range analysis of rPRD0038 identified civets, rabbits, camels, and cows as potential intermediate hosts, while confirming the lack of human ACE2 usage and replication in primary human airway epithelial cells. Despite significant divergence from SARS-CoV-2, PRD0038 remains susceptible to FDA-approved nucleoside and mPro-targeted antivirals as well as some monoclonal antibodies that target select conserved spike epitopes. Pre-existing SARS-CoV-2 immune memory conferred reduced cross-neutralizing activity against PRD0038. Finally, we present an R. affinis ACE2-expressing mouse model for assessing PRD0038 in vivo replication and pathogenesis, and testing countermeasures. Together, these data illustrate functional and immunological constraints that regulate the emergence potential of clade-3 bat Sarbecoviruses while identifying protective therapeutics.