Fig. 2: GM discovery reveals ubiquitous response to IFN with cell-type-specific features.

a, Schema depicting temporal GM discovery (see Methods). This procedure was repeated for each major cell type (monocytes, CD4⁺ T cells, CTLs, proliferating T cells, NK cells, B cells, plasmablasts and mDCs) on a participant-by-participant basis, generating 0–8 GMs per cell type. Modules were arbitrarily numbered within a given cell type and participant. mDC, myeloid dendritic cell; PCA, principal-component analysis; PC, principal component; TOM, topological overlap matrix. b, In P1, six GMs across multiple cell types exhibited similar temporal expression profiles; each GM’s score (colored lines) peaked at the same timepoint as for peak viremia (line-and-dot plot). c, Number of occurrences of gene membership for all genes present across the six GMs in b. d, GM expression scores for IFN response modules in each participant. Normalized GM score is depicted by heat (black to orange), whereas raw module score is depicted by box size. The timepoint closest to peak viral load is indicated by a dotted line. e, Mean expression of ISG15 separated by timepoint and individual. Shaded area denotes 95% CI of the mean. See Supplementary Table 2 for the number of cells per timepoint per cell type. f, Luminex measurements of IP-10, MIG and IFN-γ and ELISA of soluble CD14 (sCD14) in matching plasma samples. Points are averages of duplicate measurements. PI, pre-infection; PV, peak viremia; 9 M, 9 months post-detection.