Discovery of genes that modulate flavivirus replication in an interferon-dependent manner

Summary Establishment of the interferon (IFN)-mediated antiviral state provides a crucial initial line of defense against viral infection. Numerous genes that contribute to this antiviral state remain to be identified. Using a loss-of-function strategy, we screened an original library of 1156 siRNAs targeting 386 individual curated human genes in stimulated microglial cells infected with Zika virus (ZIKV), an emerging RNA virus that belongs to the flavivirus genus. The screen recovered twenty-one potential host proteins that modulate ZIKV replication in an IFN-dependent manner, including the previously known IFITM3 and LY6E. Further characterization contributed to delineate the spectrum of action of these genes towards other pathogenic RNA viruses, including Hepatitis C virus and SARS-CoV-2. Our data revealed that APOL3 acts as a proviral factor for ZIKV and several other related and unrelated RNA viruses. In addition, we showed that MTA2, a chromatin remodeling factor, possesses potent flavivirus-specific antiviral functions. Our work identified previously unrecognized genes that modulate the replication of RNA viruses in an IFN-dependent way, opening new perspectives to target weakness points in the life cycle of these viruses. Author summary The interferon (IFN) response, which is a powerful arm of the antiviral immune program, protects cells from invading viral pathogens by transcriptionally inducing the expression of interferon-stimulated genes (ISGs). ISGs effectively establish the antiviral state by directly blocking the viral life cycle by targeting specific stages of replication. Some ISGs are specific to a virus or a viral family, while others are broad-spectrum. Identifying which ISGs exert antiviral function against which virus is crucial because it enables the subsequent understanding of weakness points in the life cycle of viruses. Using a loss-of-fonction screening strategy, we investigated the ability of 386 unique ISGs to inhibit the replication of Zika virus (ZIKV), a virus that recently emerged in the Pacific and the Americas. Using this approach, we identified novel modulators of ZIKV replication in IFN-treated human cells. Our work contributes to a better understanding of the molecular basis behind the complexity the antiviral program. Furthermore, taking advantage of naturally occurring viral inhibitors may be an effective strategy for the development of novel drugs that activate, amplify or mimic their action.