Fig. 1: Longitudinal profiling of peripheral immune cells in hyperacute and acute HIV infection by scRNA-seq.

a, Depiction of the typical trajectory of HIV viral load in the plasma during hyperacute and acute HIV infection adapted from Fiebig et al.⁸ and the timepoints sampled in this study. Since participants were tested twice weekly, there was an uncertainty of up to 3 d in where on the viral load curve the first detectable viremia occurred (error bar is representative). The exact days sampled are available in Supplementary Table 1. b, Viral load and CD4⁺ T cell count for four participants assayed in this study. Dotted lines indicate a missing data point for the metric. c, t-distributed stochastic neighbor embedding (tSNE) analysis of PBMCs from all participants and timepoints sampled (n = 59,162). Cells are annotated based on differential expression analysis on orthogonally discovered clusters. d, tSNE in c annotated by timepoint (top) and participant (bottom). e, Scatter-plot depicting the correlation between cell frequencies of CD4⁺ and CD8⁺ T cells measured by Seq-Well (n = 2 array replicates) and FACS (n = 1 flow replicate). R² values reflect variance described by an F-test for linear regression.