Innate Immunity to West Nile Virus

West Nile virus (WNV) is a flavivirus of global concern and serves as model flavivirus. WNV is transmitted to humans via the bite of an infected mosquito, and infection is accurately modeled in immunocompetent mice. During acute infection, WNV replicates in short-lived peripheral myeloid cells and can spread to long-lived parenchymal cells of many tissues unless restricted by the innate immune response. Those who recover from infection often experience long-term sequelae including persistent inflammation and cognitive decline. WNV can invade the central nervous system (CNS) and cause death. Both innate and adaptive immunity are essential for control of WNV and CNS invasion, but how these responses are initiated and programmed following myeloid cell acute infection are not well understood. Our studies show that the RIG-I-like receptors (RLRs), RIG-I and MDA5, play essential roles in recognition of WNV in myeloid cells. Our preliminary studies now indicate that RIG-I and MDA5 sense and bind to specific pathogen associated molecular pattern (PAMP) motifs within WNV genomic and replication strand RNA products to trigger the innate immune response in myeloid cells. Using novel RIG-I and MDA5 conditional knockout mice lacking either factor in myeloid cells, we reveal that the RLRs direct a myeloid cell response that serves to restrict systemic virus replication; myeloid cell signaling by RLRs directs an innate immune response that serves to suppress virus spread, induce type I and III interferons, and protect against CNS invasion. Immunological analyses indicate that RLR signaling in myeloid cells plays an impotent role to program the adaptive immune response for clearance of infection. Using an infected cell-reporter mouse model we have identified previously infected WNV-experienced cells including CNS neurons, following virus clearance. Functional genomics analyses of WNV-infected myeloid cells, and spatial transcriptional profiling of tissue regions of the WNV-experienced cells, show signatures of innate and adaptive immune programming that precede long-term inflammatory signatures of WNV sequelae. Thus, WNV PAMP sensing and innate and adaptive immune actions lead to outcomes of virus control and infection sequelae but the molecular mechanisms programming these outcomes are not defined. The proposed studies will investigate the hypothesis that RLR- mediated sensing of WNV within short-lived, replaceable myeloid cells initiates innate immune response that prevents viral spread and neuroinvasion, which parenchymal cells that survive viral infection can drive long-term inflammatory sequelae due to unresolved inflammatory signaling that remains after viral clearance. We will conduct the following Specific Aims: 1: Define the WNV PAMP ligands of RIG-I and MDA5, and determine PAMP- induced innate immune activation programs; 2: Determine the myeloid cell-specific role of RLRs in innate immune protection and immune programming against WNV infection. 3: Identify the determinants by which WNV infection promotes sequelae across tissues. This work will provide important insight into the virus and host features of immune programming and post-infection sequelae from infection by WNV and other flaviviruses.