A 16-color full spectrum flow cytometric analysis for comprehensive evaluation of T-cell reconstitution in SIV-infected rhesus macaques

T-cell reconstitution is central in human immunodeficiency virus (HIV) infection/disease progression. Simian immunodeficiency virus (SIV)-infected rhesus macaques (Macaca mulatta) have been the most widely used an-imal model for HIV research so far. An effective flow cytometry panel is crucial for monitoring the T cell reconstitution in SIV infection progression. We developed this sixteen-color flow cytometry-based panel for a T cell subsets analysis by manual gating and, once successfully gated, to characterize T cells function in-depth in rhesus macaques. This panel included markers to characterize CD4+ T cells and CD8+ T cells, T regulatory cells (Tregs), and T cell differentiation status (CD45RA and CCR7). Additionally, we included antibodies that measure T cell activation and proliferation molecules (CD69, HLA-DR, CD38 and Ki67), antibodies that examine the expressions of key PD-1 pathway molecule (PD-1), SIV potential target (CD32) and the primary SIV co-receptor CCR5 (CD195). High-dimensional single cell analysis was also performed to identify CD3+ T cells immuno-phenotypes of SIV-infected rhesus macaques. We designed this panel to evaluate the responses of different T cell subsets to SIV in whole blood from SIV-infected rhesus macaques.