New Tool Reveals Hidden Activity in HIV-Infected Cells

For people living with HIV, antiretroviral therapy prevents the virus from making new copies of itself, keeping illness and transmission under control. Yet not all infected cells are completely inactive. Some cells remain active, continuing to release viral fragments despite treatment. These fragments can cause chronic inflammation and increase risks such as organ damage and heart disease. The number of such “active” reservoir cells also affects how quickly the virus rebounds if treatment stops.

To better understand these cells, Nadia Roan’s team from the Gladstone Institutes collaborated with the San Francisco Veterans Affairs Medical Center to create HIV-seq, a new tool for profiling rare HIV-infected cells. The method, described in Nature Communications, enables scientists to observe how reservoir cells differ before and after treatment. By uncovering these variations, researchers hope to find new ways to eliminate or suppress the cells that continue producing viral material.

Traditional single-cell RNA sequencing has offered valuable insights into gene activity but has struggled to detect active reservoir cells during therapy. Julie Frouard, a co-first author, notes that past methods found only one or two infected cells per patient—too few for meaningful data. Because HIV RNA fragments do not fit the same patterns as human RNA, standard sequencing techniques often miss them. HIV-seq overcomes this gap by targeting HIV-specific RNA fragments, allowing scientists to recover far more infected cells for analysis.

Senior author Steven Yukl explains that HIV-seq identified 25 reservoir cells from three treated individuals, compared with more than 1,000 from untreated patients—the highest number recorded so far. This greater visibility now allows researchers to compare active and suppressed states of infection in unprecedented detail.

The results suggest striking contrasts in cell behavior. Before therapy, infected cells displayed cytotoxic traits and produced inflammation-related proteins, while also showing lower expression of genes that typically suppress HIV. Roan described these cells as “fiery.” After therapy began, however, reservoir cells appeared calmer, with anti-inflammatory features and enhanced survival mechanisms. Yukl noted that these findings align with ongoing trials testing drugs that may target the same survival pathways.

Roan’s team is now exploring whether blocking these pathways could stop reservoir cells from multiplying. The researchers believe HIV-seq will continue to shed light on how these persistent cells survive for decades, offering clues for future strategies against HIV.