A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death

West Nile virus (WNV) causes an acute neurological infection attended by massive neuronal cell death. However, the mechanism(s) behind the virus-induced cell death is poorly understood. Using a library containing 77,406 sgRNAs targeting 20,121 genes, we performed a genome-wide screen followed by a second screen with a sub-library. Among the genes identified, seven genes, EMC2, EMC3, SEL1L, DERL2, UBE2G2, UBE2J1, and HRD1, stood out as having the strongest phenotype, whose knockout conferred strong protection against WNV-induced cell death with two different WNV strains and in three cell lines. Interestingly, knockout of these genes did not block WNV replication. Thus, these appear to be essential genes that link WNV replication to downstream cell death pathway(s). In addition, the fact that all of these genes belong to the ER-associated protein degradation (ERAD) pathway suggests that this might be the primary driver of WNV-induced cell death. [Display omitted] •A knockout screening method based on CRISPR-Cas9•Two rounds of screening improve sensitivity and specificity•Seven genes of the ERAD pathway are essential for WNV-induced cell death•These genes connect WNV replication to ensuing cell death Ma et al. use a CRISPR-based genome-wide knockout screening method to identify seven genes linked to ER-associated degradation (ERAD) as factors involved in West Nile virus (WNV)-induced cell death.