Poliovirus Escape from RNA Interference: Short Interfering RNA-Target Recognition and Implications for Therapeutic Approaches

TLDR

siRNAs can potently inhibit poliovirus replication, yet the limits of RNAi as an antiviral remain poorly understood. The authors performed competitive analyses of escape mutants to dissect how siRNA recognition occurs. Poliovirus evades siRNA inhibition through point mutations, especially G:U mismatches in the central and 3′ target regions, but simultaneous targeting of multiple sites with a siRNA pool blocks resistance, underscoring the precision of RNAi recognition and informing therapeutic design.

Abstract

Short interfering RNAs (siRNAs) directed against poliovirus and other viruses effectively inhibit viral replication. Although RNA interference (RNAi) may provide the basis for specific antiviral therapies, the limitations of RNAi antiviral strategies are ill defined. Here, we show that poliovirus readily escapes highly effective siRNAs through unique point mutations within the targeted regions. Competitive analysis of the escape mutants provides insights into the basis of siRNA recognition. The RNAi machinery can tolerate mismatches but is exquisitely sensitive to mutations within the central region and the 3' end of the target sequence. Indeed, specific mutations in the target sequence resulting in G:U mismatches are sufficient for the virus to escape siRNA inhibition. However, using a pool of siRNAs to simultaneously target multiple sites in the viral genome prevents the emergence of resistant viruses. Our study uncovers the elegant precision of target recognition by the RNAi machinery and provides the basis for the development of effective RNAi-based therapies that prevent viral escape.