Genome-wide Screening Identifies Unique Host-Directed Drugs and Pro-viral Signalling Pathways for SARS-CoV-2

Khan, j. Q.; Rajamanickam, K.; Vizeacoumar, F. S.; Balouchi, M.; Zhang, Y.; Elhasasna, H.; Rohamare, M.; Dong, H.; Glover, K.; Anderson-Woodsworth, T.; Bhanumathy, K.; Lew, J.; Kumar, A.; Vizeacoumar, F. J.; Falzarano, D.; Wilson, J. A.

doi:10.1101/2025.10.15.682635

bioRxiv · 10.1101/2025.10.15.682635

Genome-wide Screening Identifies Unique Host-Directed Drugs and Pro-viral Signalling Pathways for SARS-CoV-2

Khan, j. Q.·Rajamanickam, K.·Vizeacoumar, F. S.·Balouchi, M.·Zhang, Y.·Elhasasna, H.·Rohamare, M.·Dong, H.·Glover, K.·Anderson-Woodsworth, T.·Bhanumathy, K.·Lew, J.·Kumar, A.·Vizeacoumar, F. J.·Falzarano, D.·Wilson, J. A.

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Abstract

SARS-CoV-2 is a positive-sense RNA virus and was responsible for the devastating COVID-19 pandemic. Although the current disease burden is less severe, there are limited treatment options, significant gaps in knowledge, and a looming threat of the emergence of variants and future pandemics. To address these challenges, we performed genome-wide CRISPR knockout screens in a novel human lung cell line NCI-H23ACE2, as well as in HEK293TACE2 cells, with SARS-CoV-2 Wuhan virus, with the aim of identifying host-dependency factors that could predict effective antivirals. We identified four host-directed drugs, donepezil, dH-ergocristine, trametinib and sorafenib, that could potentially be repurposed to treat coronavirus infections. Three of the drugs inhibited SARS-CoV-2, HCoV-229E, and HCoV-OC43, suggesting they could be used as pan-coronavirus antivirals. We also confirmed that SARS-CoV-2 relies on the NRAS/Raf/MEK/ERK signaling pathway for its replication. Our study highlights the robustness and efficiency of a bilateral approach of gene silencing and antiviral screening to identify host-dependency factors and effective antivirals.

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Khan, j. Q., Rajamanickam, K., Vizeacoumar, F. S., Balouchi, M., Zhang, Y., Elhasasna, H., Rohamare, M., Dong, H., Glover, K., Anderson-Woodsworth, T., Bhanumathy, K., Lew, J., Kumar, A., Vizeacoumar, F. J., Falzarano, D., Wilson, J. A.. 2025-10-17. Genome-wide Screening Identifies Unique Host-Directed Drugs and Pro-viral Signalling Pathways for SARS-CoV-2. https://doi.org/10.1101/2025.10.15.682635

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