Host and viral determinants for efficient SARS-CoV-2 infection

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, is a novel lineage b betacoronavirus first identified in patients with unexplained pneumonia in Wuhan, China, in late 2019. Although less pathogenic than SARS-CoV, SARS-CoV-2 is highly transmissible among humans. Moreover, the continuous mutation of SARS-CoV-2 is associated with the emergence of new variants which may be less susceptible to available vaccines and/or antivirals. In-depth investigations on the basic virology and the determinants that contribute to efficient SARS-CoV-2 infection are important to provide novel understanding on SARS-CoV-2 virology and to facilitate the development of novel treatment options.

In Chapter 2, I aimed to identify the host and viral determinants that are essential for efficient SARS-CoV-2 infection in human lung epithelial cells and ex vivo human lung tissues. My findings identified heparan sulfate as an important attachment factor for SARS-CoV-2 infection. Additionally, I found that sialic acids on angiotensin-converting enzyme 2 (ACE2) hinder efficient SARS-CoV-2 and SARS-CoV infections by preventing spike-ACE2 interaction. While sialic acid-mediated restriction significantly limits SARS-CoV infection in both human lung epithelial cells and ex vivo human lung tissues, it has a weaker restraint on SARS-CoV-2 infection. I further demonstrated that the furin-like cleavage site, which is distinct in the spike protein of SARS-CoV-2 compared to that of SARS-CoV, is required for efficient virus replication in human lung but not intestinal tissues. These findings add to our understanding of the host and viral factors involved in efficient SARS-CoV-2 infection in human lung tissues and help to identify additional candidate intervention targets.

Besides ACE2 and other attachment factors, proteolytic cleavage of the viral spike protein is necessary for successful SARS-CoV-2 infection. While the host protease transmembrane protease serine 2 (TMPRSS2) is well-known for its proteolytic cleavage roles in SARS-CoV-2 infection, the involvement of other proteases capable of facilitating SARS-CoV-2 entry remains incompletely explored. In Chapter 3 of this thesis, I demonstrated that multiple members of the membrane-type matrix metalloproteinase (MT-MMP) and a disintegrin and metalloproteinase (ADAM) families can mediate SARS-CoV-2 entry. SARS-CoV-2 replication is significantly reduced by MT-MMP inhibition in both human lung epithelial Calu-3 cells and in the lung of golden Syrian hamsters, indicating that MT-MMPs play a physiologically relevant role during SARS-CoV-2 infection. Mechanistically, I demonstrated that MT-MMPs mediate the cleavage of the SARS-CoV-2 spike protein and ACE2, and promote spike-mediated fusion. Furthermore, I showed that Omicron BA.1 (B.1.1.529.1) has an increased efficiency on MT-MMP usage while an altered efficiency on transmembrane serine protease usage for virus entry compared with that of the ancestral wild-type SARS-CoV-2. These findings reveal additional proteases that can facilitate SARS-CoV-2 infection and new host-based treatment options for SARS-CoV-2 infection.

Taken together, the novel findings in this thesis revealed novel host and viral determinants that are essential for efficient viral infection and new intervention targets for SARS-CoV-2.