Figure 1. Discovery of host factors controlling SARS-CoV-2 infection.

(a) A schematic diagram of the functional CRISPR/Cas9 dropout screen based on virus-induced cytopathic effect (CPE). A549-AC cells were transduced with a genome-wide human gRNA library (five sgRNAs per gene) and followed by puromycin selection. After 3-day puromycin selection, 30 million pooled cells were collected as the reference sample. On day 7 after selection, pooled A549-AC cells were infected with recombinant SARS-CoV-2 at MOI=5 for 48 hours. Pooled A549-AC cells without viral treatment were severed as the controls. The changes in gRNA distribution between the viral infected samples and controls were determined. (b) A volcano plot showing top candidates for pro-viral and anti-viral host factors. The gene-level MAGeCK scores and the changes of gRNA distribution between A549-AC cells with and without viral infection were calculated. The log2 fold change of the second-best gRNA for each gene was selected for data representation. Genes whose gRNAs were significantly enriched or depleted in the infected group (p value <0.05 and |log₂FC| ≥0.5) were labeled as red and green dots, respectively. The top ten enriched/depleted (pro-viral/anti-viral) genes based on MAGeCK scores were indicated. (c) Ingenuity pathway analysis of identified host factors for SARS-CoV-2 infection. Enriched pathways for pro-viral factors (enriched, left panel) and anti-viral factors (depleted, right panel) with statistical significance (p value< 0.05) were illustrated.