Fig. 5: Germinal center dynamics of immune cell subsets in neonatal and adult SHIV infection.

Flow cytometry phenotype of immune cell subsets in LNs at ~12 months post neonatal and adult SHIV infection of RMs. All samples were collected from 12 months post-SHIV infection, except one dam who had samples collected at month 10 post-SHIV infection (see methods). A CD20+ B cells were further classified based on differential levels of Ki-67 and Bcl-6; resting B cells (ki67−, Bcl-6−), germinal center (GC) B cells (Ki-67+, Bcl-6+), and plasmablasts (Ki-67+, Bcl-6−). Resting, GC and plasmablast B cell subsets were reported as a percentage (%) of total LN B cells. B Autologous HIV-1 Env SOSIP trimer was used as a B cell bait to determine the percent of Ag-reactive B cells within each B cell subset. Antigen-reactive (Ag+) resting, GC and plasmablast cells were reported as a percent of total Ag+ LN B cells. C Helper T cells (CD3+, CD4+) were further subdivided into naïve or memory subsets based on CD45RA levels (naïve, CD45RA+; memory, CD45RA−). These T cell subsets were reported as a percent of LN CD4+ T cells. D Frequency of FOXP3+ Tregs within the memory helper T cell subset. Tregs were reported as a percent of total lymphocytes. E Frequency of TFR among Tregs. TFR cells were defined as CXCR5+ and ICOS+ among the FOXP3+ Tregs. TFR cells were reported as a percent of Tregs. F TFH cells (PD-1hi, ICOS + ) among the memory helper T cells, and TFR cells, shown as a percent of total lymphocytes. G Ratio of percent TFR to percent TFH within total lymphocytes in the LN. H (Left) Graph of ratio of % TFR:TFH and plasma viral load (PVL) in neonates and adults following ~12 months of SHIV infection; and (right) animal IDs with corresponding values for ratio of % TFR:TFH and PVL shown on the left. A–G These data were generated from a single experiment comparing cell subsets in neonate (N = 5) and adult (N = 5) RMs, and all graphs were generated in GraphPad Prism (v9 or v10) and statistics performed using two-sided Mann–Whitney testing; only statistically significant differences are indicated (p-values < 0.05). Geometric mean (horizontal bars) used for all comparisons except Ag+ graphs where arithmetic mean was used to allow values of zero. A–F Gating hierarchy of immune cell subsets is provided in source data; Source data are provided as a Source Data file.