Identifying host and viral correlates for coronavirus pathogenesis

AbstractThe coronavirus (CoV) spike protein is a key viral determinant responsible for receptor binding andfusion/entry. The spike protein has also been predicted to be the major factor driving cross-speciestransmission, allowing the emergence of epidemic strains like SARS- and MERS-CoV. In the first decade afterSARS-CoV emergence, changes to the epidemic spike that allowed binding to a new host receptor werethought to underlie this zoonotic emergence. However, our work has shown that bat species already harborSARS-like CoVs with spike proteins capable of infecting human cells. These results argue that for a subset ofbat CoVs, receptor binding and infection of human cells is not the major barrier for emergence.We found that despite equivalent replication in vitro, chimeric viruses containing bat CoV spikes have reducedvirulence in vivo. Mice infected with a chimeric SARS-CoV expressing the bat derived SHC014-CoV spike hadreduced weight loss and lethality compared to SARS-CoV controls. Importantly, this attenuation occurs despiteequivalent replication to SARS-CoV in the lung. The results indicate that virulence is dictated by more thanjust the ability to infect host cells in vitro. Notably, we also found that the SHC014 spike chimera has reducedinfection of the large airways of the lung. These preliminary data shaped our central hypothesis that SARS-CoV virulence is predicated on both host interactions with and viral motifs in the CoV spike protein.Understanding the host and viral mechanisms that drive reduced airway infection may predict in vivopathogenesis and have critical implications for zoonotic emergence.In this proposal, we explore the host factors and CoV spike changes that attenuate the zoonotic SHC014 spikein vivo. In part one, we examine tropism changes finding that the zoonotic SHC014 spike has impaired upperairway infection. We predict that this incompatibility relates to differences in host protease activity. Wesubsequently define the specific host proteases that mediate this attenuation using both in vitro and in vivoapproaches. In part two, we use mouse-adaptation and structural analysis to predict spike changesresponsible for attenuation of the SHC014 spike. We subsequently generate mutant viruses and restore theSHC014 spike or attenuate the SARS spike in vivo. Finally, we evaluate the mechanism of attenuationfocusing on spike interactions with host proteases. Together, the proposal identifies host proteases and spikeinteractions that alter airway infection and dictate virulence following coronavirus infection. These findingsprovide critical insights for understanding virulence as well as have important implications for emergence andtransmission of coronaviruses.