Dynamic decay of viral reservoirs in systemic and lymphoid compartments of SIV-infected rhesus macaques on long-term combined antiretroviral therapy

Abstract

Abstract Material & Method By quantitative real-time/digital PCR, we here longitudinally examined dynamic decay of viral parameters (cell-associated unspliced and multiply spliced viral RNA, episomal 2-LTR circular viral DNA and integrated proviral DNA) in systemic and lymphoid tissues in SIV-infected rhesus macaques on long-term combined antiretroviral therapy (cART, up to 20 months), and evaluated reservoir size and timing of viral rebound after treatment interruption. SIV RNA or DNA copy numbers were normalized and expressed as per 106 cell equivalents. Frequencies and absolute numbers of peripheral CD4+ T cells were analyzed before and after suppressive antiretroviral therapy. Results Our results showed that suppressive ART significantly reduced levels of cell-associated unspliced and multiply spliced SIV RNA/2-LTR DNA to undetectable, yet levels of integrated proviral DNA alone were stably maintained in systemic and lymphoid compartments throughout cART, which correlated with levels of viral replication prior to initiating cART. Following ATI, rapid clonal expansion of cells with integrated provirus were detected, as indicated by undetectable spliced tat/rev RNA and 2-LTR but increased levels of total proviral DNA, which may have contributed to subsequent viral rebound. Cell-associated SIV RNA and DNA levels completely recovered to pre-treatment levels in blood, spleen, lymph node, tonsil and gut-associated lymphoid tissues by 3 months after ATI. Conclusions These findings suggest that discriminating integrated HIV proviral DNA from non-integrated or defective proviruses in tissues are useful biomarkers for monitoring HIV persistence and latency for treatment and cure strategies.