Quantification of Total HIV DNA as a Marker to Measure Viral Reservoir: Methods and Potential Implications for Clinical Practice

Abstract

The focus of this review is to examine the importance of quantifying total HIV DNA to target the HIV reservoir and the clinical implications and challenges involved in its future application in clinical practice. Despite intrinsic limitations, the quantification of total HIV DNA is currently the most widely used marker for exploring the HIV reservoir. As it allows estimating all forms of HIV DNA in the infected cells, total HIV DNA load is the biomarker of the HIV reservoir that provides most of the insights into HIV pathogenesis. The clinical role of total HIV-DNA in both untreated and treated patients is extensively supported by important lines of evidence. Thus, predictive models that include total HIV DNA load together with other variables could constitute a prognostic tool for use in clinical practice. To date, however, this marker has been primarily used in experimental evaluations. The main challenge is technical. Although the implementation of droplet digital PCR could improve analytical performance over real-time PCR, the lack of standardization has made cross-comparisons of the data difficult. An effort by investigators to compare protocols is needed. Furthermore, the main effort now should be to involve the biomedical industry in the development of certified assays for in vitro diagnostics use.

Real-world efficacy and safety of dolutegravir plus lamivudine versus tenofovir plus lamivudine and efavirenz in ART-naïve HIV-1-infected adults

“…To date total HIV DNA is the most widely used and studied marker for HIV reservoir, notwithstanding it includes integrated and nonintegrated viral genomes without differentiating the defective forms from the latent ones that can produce infectious viruses. [ 12 ] In this real-world study, we observed positive correlation between HIV-1 DNA and HIV-1 RNA at baseline, and both of them decreased during ART with DTG + 3TC. HIV-1 DNA decayed to a non-significantly lower level since week 8 in DTG + 3TC subgroups, suggesting the potent inhibiting ability on total HIV-1 DNA of DTG + 3TC regimen in individuals with high baseline HIV-1 RNA.…”

“…The quantification of total HIV DNA is currently the most widely used marker for exploring the HIV reservoir. [ 11 , 12 ] It was reported in previous studies that HIV-DNA decreases rapidly during the first year after ART initiation of some regimens not containing DTG, but afterwards the decay rate become slow and the HIV-DNA level remains almost stable for a long-time in virally suppressed patients. [ 13 , 14 ] Considering that DTG has been proved for its effectiveness of inhibiting HIV RNA, DTG + 3TC could possibly be a potent ART regimen for HIV DNA suppression.…”

Risk of Cardiovascular Diseases or Mortality in People With Higher Values of HIV-1 DNA

“…Compared with the quantitative viral outgrowth assay that is currently considered the gold standard for measuring latent HIV-1 burden, total HIV-1 DNA is both easier to perform and more costeffective, although it can lead to an overestimation of viral reservoir. [3][4][5] Recent studies have demonstrated the relevance of quantifying total HIV-1 DNA load during HIV infection as a predictive marker of disease progression in people living with HIV (PLWH). 6,7 The aim of our study was to evaluate if total HIV-1 DNA may be associated with clinical outcomes, specifically the occurrence of cardiovascular (CV) events or mortality.…”

“…Compared with the quantitative viral outgrowth assay that is currently considered the gold standard for measuring latent HIV-1 burden, total HIV-1 DNA is both easier to perform and more cost-effective, although it can lead to an overestimation of viral reservoir. 3–5…”

Immune activation and exhaustion marker expression on T-cell subsets in ART-treated adolescents and young adults with perinatal HIV-1 infection as correlates of viral persistence

“…Multiple assays are used to measure HIV-1 reservoir size in children and adults living with HIV-1 ( 15 , 16 ). Total HIV-1 DNA in peripheral blood mononuclear cells (PBMCs) is the most studied ( 17 ), with the caveat that total HIV-1 DNA substantially overestimates HIV-1 reservoir size as >90% of the proviruses persisting on ART are defective and therefore non-infectious ( 18 ). The newly developed multiplex HIV-1 DNA assay, the Intact Proviral DNA assay (IPDA), allows discrimination between defective and intact proviruses, providing a molecular assay to measure HIV-1 reservoir size ( 19 , 20 ).…”