Treatment of human immunodeficiency virus (HIV) infection with antiretroviral therapy (ART) has significantly improved prognosis. Unfortunately, interruption of ART almost invariably results in viral rebound, attributed to a pool of long-lived, latently infected cells. Based on their longevity and proliferative potential, CD4⁺ T memory stem cells (T_SCM) have been proposed as an important site of HIV persistence. In a previous study, we found that in simian immunodeficiency virus (SIV)-infected rhesus macaques (RM), CD4⁺ T_SCM are preserved in number but show (i) a decrease in the frequency of CCR5⁺ cells, (ii) an expansion of the fraction of proliferating Ki-67⁺ cells, and (iii) high levels of SIV DNA. To understand the impact of ART on both CD4⁺ T_SCM homeostasis and virus persistence, we conducted a longitudinal analysis of these cells in the blood and lymph nodes of 25 SIV-infected RM. We found that ART induced a significant restoration of CD4⁺ CCR5⁺ T_SCM both in blood and in lymph nodes and a reduction in the fraction of proliferating CD4⁺ Ki-67⁺ T_SCM in blood (but not lymph nodes). Importantly, we found that the level of SIV DNA in CD4⁺ transitional memory (T_TM) and effector memory (T_EM) T cells declined ∼100-fold after ART in both blood and lymph nodes, while the level of SIV DNA in CD4⁺ T_SCM and central memory T cells (T_CM-) did not significantly change. These data suggest that ART is effective at partially restoring CD4⁺ T_SCM homeostasis, and the observed stable level of virus in T_SCM supports the hypothesis that these cells are a critical contributor to SIV persistence.

IMPORTANCE Understanding the roles of various CD4⁺ T cell memory subsets in immune homeostasis and HIV/SIV persistence during antiretroviral therapy (ART) is critical to effectively treat and cure HIV infection. T memory stem cells (T_SCM) are a unique memory T cell subset with enhanced self-renewal capacity and the ability to differentiate into other memory T cell subsets, such as central and transitional memory T cells (T_CM and T_TM, respectively). CD4⁺ T_SCM are disrupted but not depleted during pathogenic SIV infection. We find that ART is partially effective at restoring CD4⁺ T_SCM homeostasis and that SIV DNA harbored within this subset contracts more slowly than virus harbored in shorter-lived subsets, such as T_TM and effector memory (T_EM). Because of their ability to persist long-term in an individual, understanding the dynamics of virally infected CD4⁺ T_SCM during suppressive ART is important for future therapeutic interventions aimed at modulating immune activation and purging the HIV reservoir.