Intact Proviral DNA Assays May Effectively Measure HIV-1 Persistence

Researchers conducted a study to determine whether intact proviral DNA effectively measures HIV-1 persistence among patients who have achieved long-term viral suppression via antiretroviral therapy.

Intact proviral DNA (IPD) was found to be significantly associated with other measures of HIV-1 persistence and may be an accessible biomarker for inducible replication-competent virus, cellular expression of HIV-1 RNA, and total numbers of infected cells among individuals with HIV infection who have achieved long-term viral suppression via antiretroviral therapy (ART), according to results of a study published in the Journal of Infectious Diseases.

In this study, Researchers used data sourced from participants with HIV infection included in the AIDS clinical trial group (ACTG) A5321 observational study and its substudy, A5341s. All participants (N=25) had well-documented long-term HIV-1 RNA suppression via ART. To measure HIV-1 persistence and the HIV-1 reservoir among the included participants, the researchers assessed concentrations of infectious units per million CD4+ T-cells (IUPM) and IPD. Participants’ IUPM and IPD concentrations were compared against other measures of HIV-1 persistence, including 2 assays of total HIV-1 DNA, cell-associated unspliced HIV-1 pol RNA, and residual plasma HIV-1 RNA.

Among all participants included in the analysis, 92% were men, 16% were Black, and the median duration of ART was 8.9 (range, 3.7-17.4) years. In addition, 76% of participants had initiated ART during chronic HIV infection, 16% had initiated ART within 45 days of acute infection, and 8% had initiated ART as an HIV-1 controller.

The median concentrations of IUPM and IPD were less than 0.14 and 40.1 copies/106 CD4+ T-cells, respectively. Using quantitative polymerase chain reaction (qPCR) testing and IPD assay methods, the researchers found that the median cell-associated HIV-1 DNA was 208 copies/106 CD4+ T-cells, and the median total concentration of HIV-1 DNA was 421 copies/106 CD4+ T-cells. There was a median 1.9-fold increase (95% CI, 1.2-2.3) in total HIV-1 DNA assessed via IPD assay when compared against cell-associated HIV-1 DNA measured via qPCR.

The majority of participants (68%) were found to have concentrations of HIV-1 plasma RNA of less than 0.3 copies/mL, with a maximum concentration of 3.6 copies/mL.

Compared with intact proviruses, the researchers noted an 11- and 5-fold increase in the sum of intact and defective proviruses and cell-associated HIV-1 DNA copies, respectively.

The researchers found that estimated concentrations of latent intact HIV-1 measured via IPD assay were positively correlated with concentrations assessed via IUPM (r, 0.59; P =.002). Of note, in 5 participants, IPD concentrations were greater than 50 copies per 106 CD4+ T-cells and IUPM concentrations were below the limit of quantification. Participants’ IPD concentrations were also found to be significantly associated with total HIV-1 DNA (r, 0.62-0.76; P £.001) and cell-associated HIV-1 RNA (r, 0.59; P =.002).

This study was limited by its small sample size and by the number of participants with plasma HIV-1 RNA concentrations below the assay limit of less than 0.3 copies/mL.

According to the researchers, “the advent of the IPD assay is a substantive advance to the cure field as a scalable assay to increase our understanding of HIV-1 persistence [among individuals] on ART and to evaluate the effects of interventions on the intact subset of proviruses.” Additional research is needed to confirm these findings such that clinically validated biomarkers may accelerate the development of therapeutics to achieve ART-free remission.

Disclosure: One author declared affiliations with industry. Please see the original reference for a full list of disclosures.


Bosch RJ, Gandhi RT, Mar H, et al. Associations between multiple measures of HIV-1 persistence on suppressive antiretroviral therapy. J Infect Dis. 2022;jiac030. doi:10.1093/infdis/jiac030