(A) Overview of samples collected. Sampling time points are depicted across the timeline as days post inoculation (dpi). The colored arrows indicate sampling performed on animals necropsied at 7 dpi (pink) or animals necropsied at 21 dpi (orange). BALF = bronchoalveolar lavage fluid, IHC = immunohistochemistry. (B) Summary of age, weight and body condition score divided by sex. (C, D, E, F) Baselines of total lipid signal by lipid class (C), serum cytokines (D), circulating T-cell subsets (naïve and effector/effector-memory [TEEM]) (E), and circulating B-cell subsets (F) present at different concentrations (C, D) or frequencies (E, F) pre-inoculation (−7 or 0 dpi). Grey represents older and green represents younger rhesus macaques. P-values were calculated using the Mann–Whiney U test.