When Undetectable Is Unachievable: Study Offers Insights into HIV Persistence

Cross-posted from NIAID Now

Effective antiretroviral therapy (ART) for HIV maintains individual health and prevents transmission of the virus to others. For most people living with HIV, ART reduces viral load—the amount of HIV genetic material, or RNA, in blood plasma—to a level so low that it cannot be detected with standard tests.

Rarely, people living with HIV are unable to maintain an undetectable viral load despite strict adherence to daily ART. New NIAID-funded research suggests that this sometimes can occur when a single cell from the HIV reservoir—the population of long-lived HIV-infected cells that ART cannot eradicate—multiplies to create many identical cells that produce enough virus to be detected by standard viral load tests.

The new findings, presented at the Conference on Retroviruses and Opportunistic InfectionsExit Disclaimer (CROI 2019), improve understanding of how HIV reservoirs persist for many years during ART, information that is critical to help advance HIV cure research. The work was led by John Mellors, M.D., of the University of Pittsburgh and colleagues.

Most people who receive treatment for HIV are able to achieve and maintain an undetectable viral load. A “detectable” viral load most commonly occurs when people are unable to take their antiretroviral drugs every day as prescribed. A wide variety of factors, ranging from limited access to medications to challenges with drug side effects, can influence a person’s ART adherence. ART also becomes less effective if HIV develops resistance to the medications that the person is taking. In these cases, adherence counseling or switching to a different ART regimen may help reduce viral load to an undetectable level.

The new study focused on individuals who had persistent, low-level viral loads despite receiving adherence counseling, and in some cases, a switch in ART regimen. Researchers evaluated blood samples from 10 such individuals who had been taking ART for an average of 10 years. They used sensitive experimental techniques to analyze HIV genetic material in blood plasma and within HIV-infected cells.

During its life cycle, HIV integrates its genetic material into the DNA of the infected cell—typically a CD4+ T cellExit Disclaimer. Most HIV-infected cells die rapidly, but a subset survive during ART. These cells contain HIV DNA—also called a provirus—but the majority of these proviruses are so defective that they cannot generate new HIV particles. However, a very small number of cells contain a so-called “intact provirus” capable of giving rise to new, infectious HIV particles. These cells comprise the HIV reservoir and are responsible for viral reboundExit Disclaimer if ART is discontinued.

CD4+ T cells, as well as other types of immune cells, can undergo a process known as clonal expansion in which a single cell divides multiple times, making many copies of itself. This process occurs to help maintain immune cell populations in the body or in response to an antigen recognized by the T cell.

In 2016, a research team reported the caseExit Disclaimer of a person whose HIV was suppressed on ART, but whose viral load rose to detectable levels following a cancer diagnosis. They found that a cell containing an intact provirus clonally expanded, giving rise to millions of essentially identical cells carrying the same provirus. Some of these cells produced infectious HIV, which was reflected as an increase in the patient’s viral load. The researchers suspected that the same phenomenon was occurring in the individuals in the current study, albeit in the absence of a cancer diagnosis.

In blood plasma from nine of the individuals, researchers detected genetically identical populations of HIV that showed no signs of antiretroviral drug resistance. In most cases, the HIV RNA sequences from plasma matched proviral sequences identified in HIV-infected cells. The scientists next conducted an experiment in which cells were stimulated in the laboratory to produce new HIV particles. They found that genetic sequences of the HIV particles produced in this experiment matched the provirus sequences and the plasma HIV RNA sequences. In addition, the investigators identified the specific sites in the human genome that the intact proviruses had integrated, confirming that the virus being produced was from these cell clones. Taken together, these findings show that clonally expanded cells with an intact provirus can produce new HIV particles, resulting in a low-level, detectable viral load that is not the result of drug-resistance or incomplete medication adherence.

While clonal expansion is part of T cell biology, it is not yet clear how frequently expansion occurs of a cell harboring an intact provirus and what the long-term effects may be for individuals. Notably, the viral loads of the individuals in this study were low, ranging from 40 to 356 copies per milliliter (cps/mL). By comparison, people with untreated HIV have viral load levels in the hundreds of thousands or even millions. Clinics in the United States generally consider a person’s viral load to be undetectable if it falls below 50 cps/mL, although different viral load tests have different cut-offs. Recent HIV treatment as prevention studies supporting the Undetectable = Untransmittable (U=U) concept considered anyone with a viral load under 200 cps/mL to be undetectable. The landmark HPTN 052 study used a cut-off of 400 cps/mL, suggesting that even the individuals with the highest viral loads in this study will not transmit HIV as long as they remain on ART.

The researchers suggest that clinicians should consider the possibility of clonal expansion when treating patients who have difficulty maintaining an undetectable viral load despite excellent ART adherence. Conceivably, by genetic sequencing of the virus in these patients, clinicians could readily identify cases of clonal expansion and avoid unnecessary ART regimen changes and stigma to patients who cannot achieve an undetectable viral load. They also note that more work is needed to clarify the mechanisms involved in growth and persistence of infected cell clones carrying intact proviruses to better inform the development of strategies to eradicate or control HIV reservoirs without ART.