Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection

Abstract

Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here, we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, MERS-CoV, bat coronavirus HKU5 expressing the SARS-CoV-1 spike, and VSV expressing the SARS-CoV-2 spike. We identify known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways including HMGB1 and the SWI/SNF chromatin remodeling complex that are SARS-lineage and pan-coronavirus specific, respectively. We show HMGB1 regulates ACE2 expression and is critical for viral entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. Together this identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS-lineage specific and pan-coronavirus host factors that regulate susceptibility to highly pathogenic coronaviruses.

Highlights

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  Developed monkey CRISPR library to screen pathogenic coronaviruses in Vero-E6 cells.

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  Screens identified genes that are SARS-CoV-2-, MERS-CoV-, and pan-coronavirus-specific.

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  Therapeutic targets including SMARCA4 identified for SARS-CoV-2 infection.

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  HMGB1 is novel regulator of ACE2 expression and critical for viral entry.

Abstract

To identify potential therapeutic targets for SARS-CoV-2 and related pathogenic coronaviruses, Wei et al. conduct genome-wide CRISPR screens in Vero-E6 cells using SARS-CoV-2, MERS-CoV or pseudoviruses presenting SARS-CoV-1 or -2 spike proteins. They identify pro-viral genes and pathways including HMGB1 and the SWI/SNF chromatin remodeling complex that are SARS-lineage and pan-coronavirus specific, respectively, and demonstrate that HMGB1 is critical for SARS-lineage viral entry because it plays a critical role in ACE2 expression.