Fig. 7: Potently activated specific T cells contribute to viral clearance.
a,b, Kinetics (a) and summary (b) of specific T cells in BALF over the sampling time (dpo) during viral shedding (RNA+, red, ns/np: 61/60) and after viral clearance (RNA−, blue, ns/np: 52/51). Data are presented as the mean ± s.e.m., with the number of samples (ns) and patients (np) indicated. Statistical comparisons were performed using a linear mixed-effects model fit by REML, with two-tailed t-tests based on Satterthwaite’s method. c, Clonality analysis of specific T cells in BALF at the RNA+ (n = 8) and RNA− (n = 8) stages. d, Distribution (left) and clone size (right) of persistent specific T cell clones from RNA+ to RNA− stages in the BALF samples. e, Volcano plot of DEGs in specific CD4+ and CD8+ T cells in BALF comparing the RNA+ and RNA− stages. Horizontal black dashed line: Benjamini–Hochberg Padj = 0.05. f, GSEA analysis of specific CD4+ (top) and CD8+ (bottom) T cells in BALF comparing RNA+ (n = 8) versus RNA− (n = 8) stages. g, Comparison of immune function-associated scoring modules between specific T cells during the RNA+ (n = 8) and RNA− (n = 8) stages. The scoring methods are detailed in the Methods. Data are presented as the mean ± s.d.; a two-tailed Mann–Whitney U-test was used. h, Proportion of cell subclusters (clustered in Extended Data Fig. 3a) in BALF during the RNA+ and RNA− stages. i, Proportion of the AM population in leukocytes (CD45+) in BALF samples between the RNA+ (n = 56) and RNA− (n = 50) stages based on flow data. Each dot represents one sample. Data are shown as the mean ± s.e.m.; a two-tailed Mann–Whitney U-test was used. j, Circos plot depicting prioritized ligand–receptor interactions between T cells and other cell types in BALF. The outer ring shows the color-coded cell types, while the inner ring highlights the ligand–receptor pairs. The line and arrow widths are proportional to the log fold change between the RNA− and RNA+ progression stages in ligands and receptors, respectively. Different colors and line types denote several types of interactions, as outlined in the legend. FDR, false discovery rate.
