A protease activity profiling strategy to inhibit cell-to-cell transmission of SARS-CoV-2

This COVID-19 Rapid Response award is jointly funded (50:50) between the Medical Research Council and the National Institute for Health Research. The figure displayed is the total award amount of the two funders combined, with each partner contributing equally towards the project. This proposal focuses on the molecular underpinning of enhanced transmissibility of SARS-CoV-2, and develop strategies to attenuate it to arrest viral spread. Viral infections spread based on their ability to overcome multiple barriers and move from cell to cell, tissue to tissue, person to person and even across species. Host expansion, transmissibility and tissue tropism of coronaviruses are primarily determined by host adaptations of the viral Spike. Alignment with related coronaviruses has revealed that SARS-CoV-2 Spike carries additional protease-cleavage sites. However, whether the SARS-CoV-2 Spike undergoes additional processing, the identity of cellular proteases involved and whether they confer enhanced transmissibility to SARS-CoV-2 is currently not known. To arrest the chain of transmission, we will determine: (i) the identity of the cellular proteases, (ii) whether inhibiting the proteases blocks virus transmission, (iii) whether blocking cleavage of the viral Spike itself blocks transmission. Using activity-based protein profiling we have captured serine-proteases that are specifically activated in SARS-CoV-2 infected samples but not in SARS- or MERS-CoV. We have already identified two such proteases and will scale-up to identify the others. We aim to inhibit these proteases both genetically and pharmacologically, to test functional consequences on virus transmission and tissue tropism. Additionally, we aim to mutate the proteolytic processing sites on the viral Spike itself, to assess effects on tissue tropism and transmission. Our unique combination of tools and expertise, puts us in an excellent position to study and inhibit transmission of SARS-CoV-2.