Alphavirus Pathogenesis and Immunity

Chikungunya (CHIKV) and Ross River (RRV) viruses are mosquito-transmitted RNA viruses that cause explosive epidemics of debilitating acute and chronic polyarthralgia/polyarthritis. Although CD8+ T cells recognize and eliminate virus-infected cells, their role in arthritogenic alphavirus infection has remained enigmatic. Remarkably, in mouse models of CHIKV and RRV infection, viral burden in joint tissues is equivalent in congenic wild-type and CD8α-/- mice, and priming of CD8+ T cells after CHIKV and RRV infection is delayed and dampened. The mechanistic basis for how arthritogenic alphaviruses evade CD8+ T cell immunity is unknown. scRNAseq analysis of CD8+ T cells in the draining lymph node of RRV-infected mice revealed reduced maturation and proliferation in contrast to CD8+ T cells from LCMV-infected mice, which show a rapid conversion to effector T cells. The impaired CD8+ T cell priming was reversed by loss of type I IFN signaling in DCs, which increased viral infection and antigen in DCs; this result suggests that type I IFN paradoxically impairs CD8+ T cell priming by limiting alphavirus infection of key antigen (Ag)-presenting cells (APCs). Separately, we found that viral Ag presentation by CHIKV-infected or nsP2-transfected joint tissue fibroblasts was inefficient. Primary ankle fibroblasts infected ex vivo failed to activate Ag-specific CD8+ T cells, and mutations in the CHIKV nsP2 protein restored Ag presentation and CD8+ T cell activation. Finally, using intravital microscopy (IVM), we observed that viral epitope-specific CD8+ T cells do not durably engage or kill RRV-infected cells. Our primary goal is to define mechanisms by which arthritogenic alphaviruses evade CD8+ T cell-mediated clearance. In Aim 1, we hypothesize that type I IFN restricts infection of myeloid cells which limits direct antigen presentation and the timely priming of anti-alphavirus CD8+ T cells. We will determine the phenotype and infection status of APCs that intrinsically can or cannot respond to type I IFN during alphavirus infection versus immunization. In addition, we will determine how type I IFN signaling directly affects CD8+ T cell responses during alphavirus infection and test if improved priming enhances clearance of alphavirus infection. In Aim 2, we hypothesize that alphavirus- infected cells in joint tissue are inefficiently targeted by CD8+ T cells because the viral nsP2 protein disrupts MHC-I Ag presentation. We will determine mechanisms by which CHIKV infection and nsP2 protein impair MHC-I Ag presentation and define the extent to which this is a generalizable alphavirus immune evasion mechanism. In Aim 3, we hypothesize that virus-infected cells in joint-associated tissues are inefficiently targeted by CD8+ T cells because the priming environment generates CD8+ T cells that poorly engage virus-infected cells. We will define how the intrinsic absence of type I IFN signaling in APCs regulates the differentiation and maturation of CD8+ T cells during alphavirus infection and immunization. We also will use IVM to determine the impact of APC- and CD8+ T cell-intrinsic type I IFN signaling on viral antigen-specific CD8+ T cell migration and homing. We will define the frequency, duration, and outcome of interactions between CD8+ T cells and virus-infected cells. Project Number: 1R01AI185051-01A1 | Fiscal Year: 2025 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Thomas Morrison (+1 co-PI) | Institution: UNIVERSITY OF COLORADO DENVER, Aurora, CO | Award Amount: $782,871 | Activity Code: R01 | Study Section: Viral Pathogenesis and Immunity Study Section [VPI] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R01AI18505101A1