Fig. 1

Single-cell transcriptomics of immune responses to SIV pathogenic variants. A Schematic of sample collection strategy. Pig-tailed macaques were infected with CL8 (shades of blue) or 170 (red/orange) and PBMCs sampled at the indicated time points. B Virological and pathological characteristics of SIV pathogenic variants. C Plasma viral loads of CL8- and 170-infected animals at the profiled time points. Animal 170 B died at 31 weeks post-infection from simian AIDS-related complications. D UMAP projections of full scRNA-seq dataset colored by animal (left), time point (middle), and coarse cell type annotation (right). E Heatmap of whole transcriptome perturbation score per cell type per animal, as described by [38]. F Bar plot depicting cell type proportions of cells with SIV-aligned reads. G Scatter plot depicting association between plasma viral load and the percentage of SIV⁺ cells in the scRNA-seq dataset.