Antiviral activity of small interfering RNAs: Specificity testing using heterologous virus reveals interferon-related effects overlooked by conventional mismatch controls

RNA interference by small interfering RNAs (siRNAs) is considered to be a highly specific method for knockdown of gene expression in eukaryotic cells via degradation of target mRNA. Mutated siRNA molecules with 1–4 mismatching nucleotides compared to the target mRNA are regularly used as specificity controls. Using siRNAs for inhibition of a fish-pathogenic rhabdovirus, we report that inclusion of a heterologous virus, as target control is essential for verification of the specificity of siRNA-induced interference with virus multiplication. Transfection with three different siRNAs specific to the viral glycoprotein gene of the target-virus efficiently inhibited viral multiplication in infected cell cultures, while two of three corresponding mismatched siRNAs did not have this effect. This suggested specific interference, but similar results were obtained when the same siRNAs were tested against a heterologous virus. Further analyses revealed that the siRNAs induced a non-target-specific anti-viral effect correlating with upregulation of the interferon induced Mx gene.