On a model of neuroblastoma cells and mouse brains, NS3 is shown to suppress the expression of mature RNAs miR-466d-3p, which are found to regulate JEV-induced inflammation in the CNS. The helicase region of NS3 binds specifically to miRNA precursors and can lead to incorrect unwinding of miRNA precursors, thereby reducing the expression of mature miRNAs. MiR-466d-3p degradation induced by NS3, promotes IL-1β expression and JEV replication. Arginine molecules of NS3 are the main miRNA-binding sites. NS3 proteins of ZIKV, WNV, DENV1, and DENV2 can also degrade miRNAs. This evidence concerns the gene IL1B and neuroblastoma.