Interferon inhibits a model RNA virus via a limited set of inducible effector genes

Abstract

Interferons control viral infection by inducing the expression of antiviral effector proteins encoded by interferon‐stimulated genes (ISGs). The field has mostly focused on identifying individual antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is not known how many ISGs are required to protect cells from a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, we used CRISPR‐based loss‐of‐function screens to identify a markedly limited set of ISGs that confer interferon‐mediated suppression of a model alphavirus, Venezuelan equine encephalitis virus (VEEV). We show via combinatorial gene targeting that three antiviral effectors—ZAP, IFIT3, and IFIT1—together constitute the majority of interferon‐mediated restriction of VEEV, while accounting for < 0.5% of the interferon‐induced transcriptome. Together, our data suggest a refined model of the antiviral interferon response in which a small subset of “dominant” ISGs may confer the bulk of the inhibition of a given virus. image ZAP, IFIT3, and IFIT1 are dominant effectors that restrict Venezuelan equine encephalitis virus, while comprising < 0.5% of the total interferon‐induced genes. Viruses may thus be suppressed by only a limited set of interferon‐stimulated genes. Screens identify three antiviral effectors required for IFN‐mediated restriction of Venezuelan equine encephalitis virus (VEEV). ZAP/IFIT3/IFIT1 triple knockout cells have impaired restriction of VEEV after treatment with Type I and Type III IFN. ISG effectors tetherin, viperin, ISG20, and IFITM3 do not significantly contribute to IFN‐mediated suppression of VEEV. IFN‐suppression can be mostly dependent (VEEV), moderately dependent (SINV, VSV), or largely independent (ZIKV, ONNV) of ZAP, IFIT3, and IFIT1.