CD4 T cell functionality distinguishes NCan mice at multiple stages during infection. (A) Scores plot of selected lung features for PLS-DA model comparing canonical mice (blue) and NCan mice (purple) at 5 wk after infection (same mice from Fig. 2, n = 2–4 mice per sex per strain per time point from one experiment). Each dot represents an individual mouse, and the ellipse marks the 95% group confidence interval. (B) Bar plot depicting the ARI for indicated lung feature groups. Bars are colored by ARI value. (C) Scatter plots depicting indicated lung features measured by flow cytometry at 2 or 5 wk after infection. Canonical mice are represented by blue symbols with solid connecting line. NCan mice are indicated by purple symbols with dotted connecting line. Each point is an individual mouse, and statistical significance was assessed via Mann–Whitney U test with Benjamini–Hochberg correction (ns = not significant [P > 0.05], *P < 0.05, **P < 0.01, ***P < 0.001). (D–F) Representative flow plots (log₁₀ fluorescence) of lung CD4 T cells staining for (D) T-bet versus Foxp3, (E) RORγt versus GATA3, and (F) CCR6 versus CXCR3 at 5 wk after infection. In each panel, the left plot is a representative canonical strain (B6) and the right plot is a representative NCan strain (CC024). Numbers in each quadrant indicate the percent of CD4 T cells staining positive for the respective marker. NK, natural killer cell; DN, double negative (CD4⁻ CD8α⁻); LV, latent variable.