Tissue Origins and Immune Correlates of Viral Rebound in SIV-Infected Rhesus Macaques Following ART Discontinuation

Abstract

The majority of persons living with HIV-1 who discontinue antiretroviral therapy (ART) demonstrate viral rebound, but the tissue-level events that lead to rebound viremia remain poorly understood. Here we report the origin, dynamics, and correlates of viral rebound in 16 rhesus macaques (RMs) infected with molecularly barcoded SIVmac239M, treated with ART for 70 weeks, and necropsied on day 12 after ART discontinuation. Barcode analysis of plasma during daily post-ART sampling identified 1 to 38 rebounding viral lineages per animal, with a mean of 2.4 lineages contributing to initial rebound viremia. Analysis of barcode viral RNA expression in tissues revealed presumptive anatomic origin sites for 56 of 175 rebounding viral lineages, with enrichment in the gastrointestinal (GI) tract and GI-associated lymph nodes by mixed-effects logistic regression. Daily transcriptomic and proteomic profiling in peripheral blood following ART discontinuation showed up-regulation of pathways related to T cell signaling, cytokine responses, and cellular metabolism prior to detectable rebound viremia. These data show that viral rebound is initiated by oligofocal tissue expansion of a limited number of clonal lineages, followed by systemic dissemination and serial emergence of additional lineages from multiple tissues. Longer time to viral rebound was associated with metabolic, epigenetic, and immunologic signatures that suppress proviral reactivation. These findings advance our understanding of the tissue origins and host correlates of viral rebound and provide a framework for future studies examining GI-associated reservoir compartments, peripheral blood biomarker development, and host-directed strategies to prolong ART-free viral remission.