Integrated multi-omics analyses identify key anti-viral host factors and pathways controlling SARS-CoV-2 infection

Anti-viral host factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill this gap, we performed a genome-wide CRISPR dropout screen and integrated analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-seq, and host-host/viral protein-protein/RNA interactome. We identified many anti-viral host genes that were missed by previous studies, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that inhibited viral entry/replication. We also identified the cohesin complex as a novel antiviral pathway, supporting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discovered an anti-viral transcription factor KLF5, a regulator of sphingolipid metabolism, which was up-regulated and harbored genetic variations linked to COVID-19 patients with severe symptoms. Our analyses provide a resource for understanding the host antiviral network for combating SARS-CoV-2 and may help develop new therapeutic strategies. We performed a genome-wide LOF screen based on virus-induced cytopathic effect. Our LOF screen was optimized to identify depleted hits with potential anti-viral activities. This screen employed a SARS-CoV-2-permissive lung epithelial cell line, A549-AC, which constitutively expresses human ACE2 and Cas-9. Cells with gRNAs targeting anti-viral host factors would be significantly depleted after SARS-CoV-2 infection, whereas gRNAs targeting pro-viral host factors would be enriched.To achieve 50-80% of cell killing (an optimal selection condition for dropout screens), we infected A549-AC cells with MOI 5 for 48-hour (h) post infection. Cells with gRNA library without virus infection were used as the negative control.