Extended Data Fig. 6: Sustained B cell modules and shared genes and upstream drivers between participants.

a, B cell modules in MM1 with high cluster membership. b, Euler diagram of conserved overlapping genes between cell types from Fig. 3e–i, see Supplementary Table 8. c, Mean expression of ANXA1, HLA-DRA, CCL5, PRF1, and CD8A in CD4⁺ T cells, monocytes, CTLs, NK cells, and proliferating T cells, respectively. Shaded area denotes 95% confidence interval of the mean. Participants who did not have modules with shared temporal expression pattern as outlined in Fig. 3e–i are shown as dashed lines. See Supplementary Table 2 for cell numbers per timepoint per participant. d, Network of predicted upstream drivers of modules in Fig. 3e–i. Nodes are colored by significance in each cell-type. Edge width and color reflect the number of shared genes (width) in the gene sets of the upstream drivers for a given cell-type (color; see Methods). e, d displayed with only the edges from a given cell type. f, Luminex measurements of IP-10, MIG, IFN-γ, IL-12 in matching plasma samples. Points are averages of duplicate measurements. PI = pre-infection; 4W = 4 weeks post-detection; 9M = 9 months post-detection.