Defective HIV RNA Linked to Persistent Viremia During Long-Term ART

Antiretroviral therapy (ART) has enabled most people living with HIV to live long and healthy lives. However, a small portion of people experience detectable traces of the virus, known as nonsuppressible viremia (NSV), despite strict adherence to long-term treatment regimens and the absence of symptoms. The results of a study headed by researchers at Johns Hopkins University School of Medicine now suggest that most cases of NSV are explained by defective and noninfectious copies of the virus.

The study, which involved more than 50 people, found that while traces of HIV-1 RNA can persist in blood after optimal therapy, cases of non-suppressible viremia are driven by HIV-1 RNA with defects in a piece of the RNA known as 5’-leader. The team developed a digital PCR (dPCR) assay, CLAWS (Capturing 5′ Leader Anomalies Without Sequencing), that distinguishes intact from defective 5′L RNA.

“From a clinical perspective, this is important because people with HIV are taught that the absolute goal of their medication is to achieve undetectable viral load, and they worry,” said Francesco R. Simonetti, MBChBD, PhD, an assistant professor of medicine in the Division of Infectious Diseases at Johns Hopkins University School of Medicine. The new findings, said Simonetti and his team, should provide relief to many people living with HIV who fear a viral rebound or who are concerned about transmitting the virus to partners despite taking effective treatment.

Simonetti is senior and corresponding author of the team’s report in Nature Communications (“5′ leader defects drive persistent HIV-1 viremia on long-term ART”), in which they stated, “These findings identify 5′L-defective genomes as the predominant driver of NSV and establish CLAWS as a practical tool for monitoring viremia in clinical and cure-related settings.”Modern antiretroviral therapies, which date back to 1996, prevent HIV from infecting new populations of immune system cells, but aren’t able to retroactively prevent previously infected cells from releasing HIV viral particles. Since those cells usually represent a small portion of infected cells after a person is on stable therapy, most people with HIV (PWH) who take antiretroviral therapies are able to bring their viral loads to clinically undetectable levels in their blood.

However, in some cases, which are estimated to occur less than 1% of the time, people may experience clinically detectable levels after taking long-term antiretroviral drug therapy. “Traces of HIV-1 RNA can persist in plasma despite long-term suppressive antiretroviral therapy (ART), the authors stated. This could happen years later, or, in less frequent cases, they may have never achieved undetectable levels. “The sources of NSV remain poorly defined, in part due to limited tools to characterize plasma HIV-1 RNA,” the team continued. “NSV raises concerns for virologic failure, transmission, and immune activation, complicates ART management, causing anxiety and ultimately affecting the quality of life of PWH.”

For the newly reported study, the investigators examined blood samples from 52 people living with HIV who had detectable loads of the virus despite taking long-term antiretroviral drug therapy. These samples, which were assessed from 32 people and compared to an additional 20 samples, were collected between 2021 and 2025. The majority of participants were white men, between ages 58 and 68, and received care in the United States, Canada, and Denmark. The researchers found that most detectable forms of the virus, around 95%, were due to defective copies, and most defects were due to mutations or deletions in the 5’-leader region of HIV-1 RNA. This region is known to orchestrate the production of copies of the virus, but in this case, the defects prevented the generation of infectious virus.

“In 31 participants from the original NSV cohort and an additional 20 participants from the validation cohort, RNA transcribed from defective proviruses accounted for a median of 95% of plasma HIV-1 RNA, firmly establishing their central role in persistent viremia,” the investigators wrote in summary.

The study offers evidence that clinicians can now study the virus in blood plasma and confirm if clinically detectable levels are due to defective copies released from one or a few T-cell clones, said Simonetti. If so, he added, this could eliminate the need for extra medications and could prevent related complications. It could also help people living with HIV have access to surgeries or other procedures, such as hip or knee replacements or organ transplants, and participate in clinical studies if they know they have HIV under control.

“We know that these defective proviruses cannot infect new cells, but they are still clinically relevant,” said Simonetti. “Think of how many extra visits, extra drugs, extra costs, and tests they’ve been causing. It’s also clear from the new study that, over time on treatment, intact proviruses that make virus are pruned away, while defective ones escape the immune system,” he said. “Now we want to understand these differences in immune recognition to uncover HIV’s vulnerabilities.”

Similar to using a liquid biopsy to detect cancer mutations in DNA, the CLAWS assay developed by the researchers uses advanced technology to identify detectable viral loads that are due to defective copies. The method is cost-effective and can be broadly used in HIV clinics and research settings.

In their paper, the authors wrote in conclusion, “In summary, our results establish 5’L-defective proviruses as the major source of NSV and introduce CLAWS as a practical tool for dissecting persistent viremia. Beyond clarifying mechanisms of HIV-1 persistence, CLAWS provides immediate translational utility for clinical monitoring and HIV-1 cure research.”

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