Selective Decay of Intact HIV Proviral DNA on ART

HIV-1 proviruses persist in people on antiretroviral therapy (ART), but most are defective and do not constitute a replication-competent reservoir. Researchers at the 2020 virtual IDWeek conference reported that cells containing intact, replication-competent proviruses are selectively lost during suppressive ART.

In this exclusive MedPage Today video, lead investigator Rajesh Gandhi, MD, of Massachusetts General Hospital in Boston, discusses the study’s objectives and clinical implications.

Following is a transcript of his remarks:

The title of our presentation from IDWeek this year is called Selective Decay of Intact HIV Proviral DNA on Antiretroviral Therapy. This is a study done by the AIDS Clinical Trials Group and the first slide shows the authors for this particular study.

The current ways of measuring the HIV reservoir, reservoir assays, have substantial limitations. HIV DNA in particular overestimates the size of the replication-competent reservoir and that’s the part of the reservoir that can lead to viral rebound when antiretroviral therapies stop.

Conversely, the virus outgrowth assay, which is the way that the latent reservoir was characterized, is quite laborious and it’s quite an expensive assay. Recently, a new assay called the intact proviral DNA assay has been developed. It’s also called IPDA.

This is a droplet digital PCR assay, and what’s important about it is that it can distinguish between and separately quantify intact proviruses, which are those proviruses that are able to replicate and are able to cause viral rebound, and it can distinguish them from defective proviruses — proviruses that really don’t have the ability to replicate.

The three objectives of this study were first, to assess whether intact proviral DNA levels correlate with other measures of HIV persistence, the measures that we’ve used for many years.

Second, to evaluate whether intact proviral DNA levels correlate with inflammation, T cell activation, and T cell exhaustion. There has been a theory out there that the virus persistence might be driving inflammation.

Then the third is to assess whether intact proviral DNA levels decline over time in people who are on antiretroviral therapy.

Just to give some background, this is part of what’s called the ACTG, AIDS Clinical Trial Group HIV Reservoirs Cohort, or AHRC, also known as ACTG 5321. Fifty individuals with chronic HIV who initiated antiretroviral therapy in ACTG trials and who had well-documented and sustained virologic suppression were included in this study. We measured HIV DNA, cell-associated HIV RNA, intact and defective HIV proviral DNA by this IPDA assay, and then we measured markers of inflammation and T cell activation.

The first time point for this study had 44 individuals in it. This was a median of 7 years or so after initiation of antiretroviral therapy, so people had been suppressed for a good number of years. That was time point #1. Time point #2 was about 4 years later, 3.7 years later, and then time point #3, the third time point that we measured, was about 2 years after the second time point.

What did we find? First, and interestingly, we found that that first time point, the one that was taken 7 years after ART was started, about 10% of total proviruses were intact. Remember that number, 10%, because we’ll come back to that. We found that lower pre-ART CD4 counts were associated with higher total proviral DNA levels and lower fraction of intact proviruses on antiretroviral therapy.

Then, finally, we found that intact proviruses were correlated with some of our older measures of HIV persistence. They were correlated with HIV DNA, cell-associated HIV RNA, and also single-copy assay plasma HIV RNA. One important negative finding is that the intact proviral DNA was not correlated with inflammation in people on antiretroviral therapy.

We then looked at whether intact proviral DNA declined over time in a different way than defective proviral DNA, and what we found is that intact proviral DNA declined, whereas defective proviral DNA did not. That was an important finding, and several other groups have seen similar kinds of findings.

The median half-life for intact proviral DNA was about 7 years, whereas for defective proviral DNA there was really no meaningful decline in defective proviral DNA.

Then finally we looked at what was the fraction of total proviruses that were intact. What we found is when we looked at time point #1, #2, and #3, there was a slow but steady decline in the fraction of proviruses that were intact. It started out at just under 10% and went down to just under 6%.

What are the conclusions from this study? First, in people on long-term antiretroviral therapy, intact proviral DNA levels decline, whereas defective proviral DNA levels do not, and the fraction of total proviruses that are intact decreases substantially over time.

This selective decay of intact HIV proviruses suggests that during antiretroviral therapy some infected cells are expressing HIV that may be getting eliminated by the immune system or by cytopathic effects, and — this is important for interventional trials — it suggests that enhancing HIV expression may accelerate clearance of intact proviruses.

Then our last conclusion is that the more dynamic nature of the intact proviral DNA landscape, compared with the total proviral DNA, supports using the intact proviral DNA assay when we are going to assess interventions that are targeting the HIV reservoir.

Let me conclude by thanking all the co-authors of this study shown here on this slide, as well as the co-chairs of this study, Dr. Debra McMahon, Dr. Joe Eron, and Dr. John Mellors, the entire AIDS Clinical Trials Group 5321 team, the ACTG, the National Institutes of Health, and all of you for your attention.