Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron

Benlarbi, M.; Laroche, G.; Fink, C.; Fu, K.; Mulloy, R. P.; Phan, A.; Ariana, A.; Stewart, C. M.; Prevost, J.; Beaudoin-Bussieres, G.; Daniel, R.; Bo, Y.; Yockell-Lelievre, J.; Stanford, W. L.; Giguere, P. M.; Mubareka, S.; Finzi, A.; Dekaban, G. A.; Dikeakos, J. D.; Cote, M.

doi:10.1101/2022.02.19.481107

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bioRxiv · 10.1101/2022.02.19.481107

Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron

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Abstract

To infect cells, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds to angiotensin converting enzyme 2 (ACE2) via its spike glycoprotein (S), delivering its genome upon S-mediated membrane fusion. SARS-CoV-2 uses two distinct entry pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In investigating serine protease-independent cell-cell fusion, we found that the matrix metalloproteinases (MMPs), MMP2/9, can activate SARS-CoV-2 S fusion activity, but not that of SARS-CoV-1. Importantly, metalloproteinase activation of SARS-CoV-2 S represents a third entry pathway in cells expressing high MMP levels. This route of entry required cleavage at the S1/S2 junction in viral producer cells and differential processing of variants of concern S dictated its usage. In addition, metalloproteinase inhibitors reduced replicative Alpha infection and abrogated syncytia formation. Finally, we found that the Omicron S exhibit reduced metalloproteinase-dependent fusion and viral entry. Taken together, we identified a MMP2/9-dependent mode of activation of SARS-CoV-2 S. As MMP2/9 are released during inflammation and severe COVID-19, they may play important roles in SARS-CoV-2 S-mediated cytopathic effects, tropism, and disease outcome.

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Benlarbi, M., Laroche, G., Fink, C., Fu, K., Mulloy, R. P., Phan, A., Ariana, A., Stewart, C. M., Prevost, J., Beaudoin-Bussieres, G., Daniel, R., Bo, Y., Yockell-Lelievre, J., Stanford, W. L., Giguere, P. M., Mubareka, S., Finzi, A., Dekaban, G. A., Dikeakos, J. D., Cote, M.. 2022-02-22. Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron. https://doi.org/10.1101/2022.02.19.481107

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