Splenic and central nervous system T-cell responses correlate with increased disease outcomes after West Nile virus (WNV) infection. F1 crosses of Collaborative Cross strains were grouped into neuroinvasion, no disease (NND) and neuroinvasion with disease (ND) categories as defined in “Results” and Table 1. Cohorts of mice were infected with 100 plaque-forming units of WNV by subcutaneous injection in the rear footpad. At day 7 or 12 after infection, age-matched male mice were euthanized, and spleens and brains were harvested and prepared for flow cytometry staining to determine the frequency of splenic regulatory T cells (Tregs) expressing CD44, CXCR3, or ICOS on day 7 after infection (A), the frequency of splenic Tregs expressing CD73 on day 7 after infection (B), the frequency of splenic CD8+ T cells expressing tetramer on day 7 after infection (C), the frequency of splenic CD4+ T cells expressing CXCR3 on day 7 after infection (D), the frequency of brain Tregs expressing β1-integrin on day 7 after infection (E), and the frequency of brain CD8+ T cells expressing tetramer on day 7 (F) and day 12 after infection (G). Statistical significance was determined by the unpaired t test. *P ≤ .05, **P ≤ .01, ***P ≤ .001, and ****P ≤ .0001.