Fig. 4: Immune-cell dynamics before, during, and after rDEN2Δ30 infection.

a Deconvolution of gene expression using a leukocyte gene signatures matrix to obtain median proportions of select adaptive and innate white blood cells at each timepoint. Center lines show the medians; box limits indicate the 25th and 75th percentiles; whiskers represent 95% confidence interval. Kruskal–Wallis one-way ANOVA was used to determine P values. ^*P < 0.05; ^#P < 0.1. b–g Flow cytometric analysis of peripheral blood mononuclear cells from rDEN2Δ30-infected subjects. Data are expressed as fold change in cell frequency at days 8, and 28 after infection relative to day 0 baseline. Center lines show the medians; box limits indicate the 25th and 75th percentiles and all data points are shown. Kruskal–Wallis one-way ANOVA was used to determine P values indicated as ^*P < 0.05 and ^#P < 0.1. b Lineage-negative (CD3⁻CD19⁻CD56⁻CD14⁻CD16⁻) HLA-DR+ dendritic cells (DC), HLA-DR^hi activated DC (DC_act); c monocytes: classical (c_mono), intermediate (i_mono), and non-classical (nc_mono); d natural killer T cells (nkt), NK1-5 populations (defined by CD56 and CD16 staining as outlined in Supplementary Fig. 4); e CD3⁺ T cells (t cells), CD4⁺ T cells (cd4), and CD8⁺ T cells (cd8); f CD8⁺ T-cell populations: activated CD279⁺ (cd8_act), cytotoxic CD57⁺ (cd8_cyto), CCR7⁻CD45RA⁺ T-effector re-expressing CD45RA (cd8t_emra), CCR7⁺CD45RA⁺ naive (cd8t_naive), CCR7⁻CD45RA⁻ effector memory (cd8t_em), CCR7⁺CD45RA⁻ central memory (cd8t_cm), and homeostatic CD127⁺ (cd8_homeo); g CD4⁺ T-cell populations: activated CD279⁺ (cd4_act), cytotoxic CD57⁺ (cd4_cyto), activation-induced marker (AIM)-positive CD154⁺CD134⁺(cd4_AIM), CD25⁺CD134⁺ (cd4_AIM_old), regulatory T cells CD127^–CD25⁺ (t_regs), homeostatic CD127⁺ (cd4_homeo), CCR7^–CD45RA⁺ T effector re-expressing CD45RA (cd4t_emra), CCR7⁺CD45RA⁺ naive (cd4t_naive), CCR7^–CD45RA^– effector memory (cd4t_em), CCR7⁺CD45RA^– central memory (cd4t_cm); h CD19⁺ B cells (bcells), plasmablasts CD19⁺ CD38^hiCD27^hi (pb), IgM⁺CD27^– naïve B cells (naive_b), and IgM^–CD27+ switched memory B cells (s_mbc). See Fig. S4 for gating. Source data are provided as a Source Data file.