Identifying host and viral correlates for coronavirus pathogenesis

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Abstract The coronavirus (CoV) spike protein is a key viral determinant responsible for receptor binding and fusion/entry. The spike protein has also been predicted to be the major factor driving cross-species transmission, allowing the emergence of epidemic strains like SARS- and MERS-CoV. In the first decade after SARS-CoV emergence, changes to the epidemic spike that allowed binding to a new host receptor were thought to underlie this zoonotic emergence. However, our work has shown that bat species already harbor SARS-like CoVs with spike proteins capable of infecting human cells. These results argue that for a subset of bat 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 reduced virulence in vivo. Mice infected with a chimeric SARS-CoV expressing the bat derived SHC014-CoV spike had reduced weight loss and lethality compared to SARS-CoV controls. Importantly, this attenuation occurs despite equivalent replication to SARS-CoV in the lung. The results indicate that virulence is dictated by more than just the ability to infect host cells in vitro. Notably, we also found that the SHC014 spike chimera has reduced infection 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 vivo pathogenesis and have critical implications for zoonotic emergence. In this proposal, we explore the host factors and CoV spike changes that attenuate the zoonotic SHC014 spike in vivo. In part one, we examine tropism changes finding that the zoonotic SHC014 spike has impaired upper airway infection. We predict that this incompatibility relates to differences in host protease activity. We subsequently define the specific host proteases that mediate this attenuation using both in vitro and in vivo approaches. In part two, we use mouse-adaptation and structural analysis to predict spike changes responsible for attenuation of the SHC014 spike. We subsequently generate mutant viruses and restore the SHC014 spike or attenuate the SARS spike in vivo. Finally, we evaluate the mechanism of attenuation focusing on spike interactions with host proteases. Together, the proposal identifies host proteases and spike interactions that alter airway infection and dictate virulence following coronavirus infection. These findings provide critical insights for understanding virulence as well as have important implications for emergence and transmission of coronaviruses.