Distinct pathways for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses.

Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014-CoV, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the S1 N–terminal domain, uncovered through the rescue and serial passage of a virus bearing the FPPR substitution, further enhanced spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles' heels that could be targeted with countermeasures. Author summary: The recent emergence of several highly virulent human coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2, underscores the risk coronaviruses can pose to the human population. Bat coronaviruses (CoVs) are of particular concern due to their potential to adapt to new hosts. Here, we attempted to generate recombinant vesicular stomatitis viruses (rVSVs) bearing the spike glycoproteins from several SARS-like bat CoVs to study their cell entry mechanisms. We identified two mutations in the SHC014-CoV spike that afforded successful recovery of an rVSV bearing this spike by greatly increasing viral entry. Interestingly, these mutations occur outside the receptor-binding domain (RBD) but enhance spike-receptor interaction nevertheless. These and other results herein establish that these mutations serve to "open" the spike and thereby augment virus-receptor engagement. Our work uncovers new genetic pathways that could contribute to the adaptation of bat CoVs during host spillover. However, these mutations also render the spike more susceptible to neutralizing antibodies that recognize the RBD, pointing to fitness tradeoffs associated with these pathways. [ABSTRACT FROM AUTHOR]