Fig. 1: Schematic for discovery of vRNA-interacting proteins and functional host factors for SARS-CoV-2, ZIKV and EBOV.

a ChIRP-MS was performed to identify human proteins that interact with viral RNA genomes in cells infected with the indicated RNA viruses. Human cells were infected with SARS-CoV-2, ZIKV or EBOV. Two types of control were used to specifically enrich vRNA-interacting proteins in infected samples: mock (cells without infection) and the “segment transfection” (cells expressing vRNA segments of the SARS-CoV-2, ZIKV, or EBOV genomes by plasmid transfection). Virus-infected, mock, and vRNA segment-transfected cells were crosslinked using formaldehyde and then sonicated to release RNA–protein complexes. For each virus, the vRNA–human protein complexes were purified using biotinylated oligos specifically tiling the viral RNA genome, and the co-purified human proteins were identified using mass spectrometry. FA, formaldehyde. b Comparison of the different vRNA interactomes identified the common and the virus-specific interactors. c Gene loss-of-function screen for functional interactors that affect virus infection. d Antiviral drug discovery informed by the comparative interactomes. We developed an antiviral drug screening workflow based on repurposing of FDA-approved drugs that targeting the vRNA-interacting proteins. Then the antiviral activities of the repurposing drugs against the infections of SARS-CoV-2, ZIKV, and EBOV were experimentally confirmed in this study. e Focusing on COVID-19, antiviral activities of the selected repurposing drugs were evaluated in a mouse model challenged with SARS-CoV-2.