Interferon-Associated Antiviral Programs Define LAG-3+ Exhaustion-Like CD8+ T-Cell Remodeling in Influenza a Virus Infection: An Integrative Single-Cell and Multi-Cohort Analysis

BACKGROUND: Influenza A virus (IAV) infection induces complex antiviral immune responses, yet how innate sensing, host genetic susceptibility, and adaptive immune dysfunction converge remains incompletely understood. This study investigated peripheral immune remodeling during IAV infection, focusing on LAG-3-expressing CD8+ T cells and their transcriptional and genetic signatures. METHODS: Single-cell and bulk transcriptomics, genetic analyses, Mendelian randomization, network modeling, and machine learning were integrated. Flow cytometry was used to validate LAG-3 expression and CD8+ T-cell dysfunction in healthy controls and children with IAV infection. RESULTS: IAV infection caused marked immune remodeling and expansion of LAG-3+ exhaustion-like CD8+ T cells spanning naïve, effector, and exhaustion-associated states. Interferon-stimulated genes dominated differential expression, co-expression modules, and pathway enrichment. Ten influenza-exhaustion signature genes were identified, with Mendelian randomization prioritizing IFI44, IFIT3, MX2, ZBP1, IFIT1, and HES4 as genetically associated with IAV susceptibility. Gene-based classifiers achieved AUCs up to 0.886 across three independent cohorts. Flow cytometry confirmed increased LAG-3 expression and reduced CD107a activity in pediatric IAV infection. CONCLUSIONS: IAV infection is characterized by an interferon-dominated program and expansion of dysfunctional LAG-3+ CD8+ T cells, highlighting candidate biomarkers for immune remodeling.