Alphaviruses are mosquito-transmitted viruses that can cause severe disease in both animals and humans. The host type I Interferon (IFN) response plays a critical role in limiting alphavirus infections. However, the specific interactions of type I IFN with that of the alphaviruses remain largely uncharacterized. Therefore, to gain insight into these early interactions, this study addresses the role of genetic virulence determinants in modulating the host type I IFN response. These analyses are based upon previous detailed mapping studies that identified a virulence determinant within the nsP1/nsP2 cleavage domain of the mouse adapted, neurovirulent Sindbis AR86 alphavirus that is critical for AR86 pathogenesis in vivo. We demonstrate that a Threonine to Isoleucine change at this position, leads to a mutant virus that robustly induces IFN independently of effects on viral replication or viral mediated shutoff of host macromolecular syntheses. Furthermore, we demonstrate that the modulation in type I IFN induction is not specific to the Sindbis AR86 virus, as a similar mutation within the Ross River Virus, also leads to robust type I IFN responses, suggesting that the nsP1/nsP2 determinant may be fundamentally important for all alphaviruses. Additional work has established that the nsP1/nsP2 determinant modulates type I IFN induction through the IPS-1 signaling pathway, primarily mediated by the RIG-I and PKR receptors. As RIG-I and PKR recognize specific RNA ligands, such as free 5' triphosphates on uncapped viral RNAs, we next determined whether the nsP1/nsP2 determinant would disrupt the viral capping apparatus. We found increased synthesis of uncapped viral 26S subgenomic RNAs made within infected cells containing the nsP1/nsP2 mutation. Furthermore, the uncapped 26S RNAs differentially activated RIG-I which was phosphatase dependent. Therefore, altogether, our data presents a novel mechanism in which a genetic determinant specifically enhances the viral capping apparatus in order to evade the host type I IFN receptors. And disruption of the capping apparatus leads to the synthesis of uncapped RNAs that are efficiently recognized by the RIG-I and PKR host sensors to induce IFN to aid in the clearance of the viral infection
