Subclinical CMV and EBV Shedding is associated with increasing HIV DNA Molecular Diversity in Peripheral Blood during Suppressive Antiretroviral Therapy.

Cytomegalovirus (CMV) almost universally infects persons with HIV (PWH), and it is a driver of persistent inflammation and HIV persistence. The mechanisms underlying the association between CMV (and possibly other herpes viruses) and HIV persistence are unclear. Serially collected blood samples were obtained from men who have sex with men (MSM) who started ART within 1 year of their estimated date of HIV infection (EDI). Total CMV and EBV DNA were quantified in peripheral blood mononuclear cells by droplet digital PCR. Deep sequencing of HIV DNA partial env gene was performed and the dynamics of viral diversity over time was analyzed in relation to CMV and EBV shedding status. In total, 37 MSM PWH were included and followed for a median of 23 months (IQR: 22-28). Participants started ART within a median of 3.1 months (IQR: 1.5-6.5) after EDI and remained virally suppressed thereafter. Eighteen participants (48.6%) were classified as high EBV shedders, while 19 (51.4%) were classified as CMV shedders. In multivariate analyses, normalized molecular diversity levels tended to increase over time among participants with detectable CMV and high EBV DNA (0.03±0.02, p=0.08), while they significantly declined among participants with no/low viral shedding (-0.04±0.02, p=0.047, Interaction p<0.01). Subclinical CMV and EBV shedding could contribute to the dynamics of the HIV DNA reservoir during suppressive ART. Whether persistent viral replication could be targeted as a strategy to reduce the size of the latent HIV reservoir is an avenue that should be explored.IMPORTANCE As part of this study we evaluated the molecular characteristics of the HIV DNA reservoir over time during antiretroviral treatment (ART) in relation to other chronic viral infections (i.e. Cytomegalovirus [CMV] and Epstein-Barr Virus [EBV]). We demonstrated that presence of CMV and high-level EBV DNA in peripheral blood cells was associated with changes in HIV DNA molecular diversity. Specifically, HIV DNA molecular diversity increased over time among participants with detectable CMV and high-level EBV DNA, while it significantly declined among participants with no/low viral shedding. Although the current study design does not allow causality to be inferred, it does support the theory that persistent CMV and EBV shedding could contribute to the dynamics of the HIV DNA reservoir during suppressive ART even when ART is initiated during the earliest phases of HIV infection.