In summary, our findings suggested that JEV infection resulted in significant changes in the expression of multiple genes in mouse spleen and brain, including inflammatory cytokines, chemokines, IFN inducible genes, IFN regulators, and apoptosis related genes, etc. These genes may play a critical role on antiviral response of host against JEV infection but could also contribute to the pathogenesis of JEV resulting in encephalitis. Here, IFNA1 is linked to encephalitis.