Xin Yin, Yuan Pu, Shuofeng Yuan , Lars Pache , Christopher Churas , Stuart Weston , Laura Riva , Lacy M Simons , William J Cisneros , Thomas Clausen , Grace Biddle , Simon Doss-Gollin , Meagan Deming , Paul D De Jesus, Ha Na Kim , Daniel Fuentes, John M Whitelock , Jeffrey D Esko , Megan S Lord , Ignacio Mena, Adolfo García-Sastre , Judd F Hultquist , Matthew B Frieman , Trey Ideker , Dexter Pratt , Laura Martin-Sancho , Sumit K Chanda 

PLoS Biol. 2025 Jun 12;23(6):e3002738. doi: 10.1371/journal.pbio.3002738. Online ahead of print.

Abstract

Defining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, most of these approaches relied on utilizing pooled genome-scale CRISPR libraries, which are biased toward the discovery of host proteins impacting early stages of viral replication. To identify host factors involved throughout the SARS-CoV-2 infectious cycle, we conducted an arrayed genome-scale siRNA screen. Resulting data were integrated with published functional screens and proteomics data to reveal (i) common pathways that were identified in all OMICs datasets-including regulation of Wnt signaling and gap junctions, (ii) pathways uniquely identified in this screen-including NADH oxidation, or (iii) pathways supported by this screen and proteomics data but not published functional screens-including arachionate production and MAPK signaling. The identified proviral host factors were mapped into the SARS-CoV-2 infectious cycle, including 32 proteins that were determined to impact viral replication and 27 impacting late stages of infection, respectively. Additionally, a subset of proteins was tested across other coronaviruses revealing a subset of proviral factors that were conserved across pandemic SARS-CoV-2, epidemic SARS-CoV-1 and MERS-CoV, and the seasonal coronavirus OC43-CoV. Further studies illuminated a role for the heparan sulfate proteoglycan perlecan in SARS-CoV-2 viral entry and found that inhibition of the non-canonical NF-kB pathway through targeting of BIRC2 restricts SARS-CoV-2 replication both in vitro and in vivo. These studies provide critical insight into the landscape of virus-host interactions driving SARS-CoV-2 replication as well as valuable targets for host-directed antivirals.