New Tool Uncovers HIV-Infected Cell Secrets

Researchers develop novel method to profile rare HIV-infected cells in people on antiretroviral therapy

Published on Mar. 4, 2026

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Researchers at the Gladstone Institutes and San Francisco VA Medical Center have developed a new tool called HIV-seq that can profile the features of rare HIV-infected cells from people with HIV on antiretroviral therapy. The tool allows scientists to better understand how HIV-infected cells persist and continue producing viral fragments, even when the full virus is suppressed by treatment. The researchers found key differences in the activity and characteristics of HIV-infected cells before and after starting therapy, providing insights that could lead to new ways to eliminate the persistent HIV reservoir.

Why it matters

People living with HIV who are on antiretroviral therapy can still experience long-term inflammation and related medical conditions due to the persistence of HIV-infected cells that continue producing viral fragments, even when the full virus is suppressed. Understanding the activity and features of these "active" reservoir cells could point to new ways to treat HIV and eliminate the persistent viral reservoir.

The details

The researchers developed a novel tool called HIV-seq that is custom-designed to recognize and profile the rare HIV-infected cells that persist in people on antiretroviral therapy. Compared to standard single-cell RNA sequencing methods, HIV-seq was able to recover and analyze more HIV-infected cells and higher amounts of HIV RNA within those cells. This allowed the team to characterize key differences in the HIV-infected cells before versus after starting therapy.

  • The study was published in Nature Communications on March 4, 2026.

The players

Nadia Roan

A senior investigator at the Gladstone Institutes and senior author of the study.

Julie Frouard

A scientist in Roan's lab and one of the first authors of the study.

Steven Yukl

A physician-scientist at the San Francisco VA Medical Center and senior author of the study.

Sushama Telwatte

An investigator at the Doherty Institute, University of Melbourne, who contributed to the study.

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What they’re saying

“Even though antiretroviral therapy keeps full-fledged HIV virus from being made, some of the infected cells continue spitting out viral products.”

— Nadia Roan, Senior investigator, Gladstone Institutes (Nature Communications)

“Using our new tool, we've found key differences in people's HIV-infected cells before versus after starting antiretroviral therapy. We hope it will be helpful for understanding how HIV develops, and how the long-lived HIV reservoir can persist for decades in people with HIV.”

— Nadia Roan, Senior investigator, Gladstone Institutes (Nature Communications)

“Now, for the first time, we can actually characterize these cells in a meaningful manner for people whose HIV is suppressed by antiretroviral therapy.”

— Steven Yukl, Physician-scientist, San Francisco VA Medical Center (Nature Communications)

What’s next

The researchers are already building on their findings by testing in laboratory models whether they can stop HIV reservoir cells from multiplying by targeting the pro-survival pathways they identified.

The takeaway

This new tool, HIV-seq, allows scientists to better understand the activity and characteristics of the rare HIV-infected cells that persist in people on antiretroviral therapy, providing insights that could lead to new ways to eliminate the long-lived HIV reservoir and improve outcomes for people living with HIV.