Origin and Correlates of Viral Rebound in SIV-Infected Rhesus Macaques Following ART Discontinuation
The earliest events of viral rebound following discontinuation of ART in persons living with HIV-1 (PLWH) remain largely unknown. Here we show that viral rebound in SIV-infected rhesus macaques following ART discontinuation involves serial clonal reactivation in gastrointestinal (GI) and lymph node (LN) tissues followed by rapid local and systemic spread. We investigated viral rebound dynamics in 18 SIV-infected rhesus macaques treated with antiretroviral therapy (ART) for 70 weeks and necropsied on day 12  after ART discontinuation. Using molecularly barcoded SIVmac239M, we tracked viral clonotypes following ATI in both peripheral blood and necropsy tissues. Viral rebound originated by reactivation of a single or a few clonotypes from a limited number of GI tissues and deep LNs, followed by replication of each clonotype and then serial reactivation of additional clonotypes from different anatomic sites, resulting in oligoclonal plasma viremia. Daily transcriptomic and proteomics profiling in peripheral blood identified early upregulation of pathways related to T cell signaling, cytokine responses, and cellular metabolism prior to detectable plasma viremia, presumably reflecting initial viral replication in tissues. Taken together, these data demonstrate the early clonal dynamics of viral rebound in SIV-infected macaques following ART discontinuation, which provides critical information for the development of next generation HIV-1 cure strategies. Overall design: 18 outbred, Indian-origin adult male and female rhesus macaques (Macaca mulatta) (n = 6/group) were intravenously infected with 5,000 infectious units (IUs) of molecularly barcoded SIVmac239M7 and initiated ART on Day 6, Day 9, or Day 12 following infection. The ART regimen consisted of daily subcutaneous injections of a pre-formulated cocktail of tenofovir disoproxil fumarate (TDF; 5.1 mg/mL), emtricitabine (FTC; 40 mg/mL), and dolutegravir (DTG; 2.5 mg/mL). Animals were treated with daily ART for 70 weeks, and plasma and cell-associated SIV DNA (CA-DNA) and RNA (CA-RNA) was monitored longitudinally.