Clonally expanded HIV-1 proviruses with 5′-leader defects can give rise to nonsuppressible residual viremia

Patients on antiretroviral therapy (ART) typically achieve undetectable viral loads. However, some individuals experience persistent, nonsuppressible viremia (NSV) despite optimal adherence and no drug resistance. This study investigates whether defective HIV-1 proviruses—which make up over 90% of the viral reservoir—can contribute to this clinical phenomenon.

The researchers analyzed four study participants with long-term ART and persistent NSV. They performed longitudinal single-genome sequencing of plasma HIV-1 RNA and integrated proviral DNA. To understand the mechanism behind the NSV, they investigated the impact of observed 5'-leader (5'-L) defects on viral RNA dimerization, nucleocapsid binding, gene expression, and infectivity. They also used integration-site specific assays to track the clonal expansion of these infected cells over time and across different CD4+ T cell subsets.

The study found that NSV in these patients was driven by clonally expanded CD4+ T cells harboring proviruses with small deletions or point mutations in the 5'-leader region, specifically involving the major splicing donor (MSD) site. Despite these defects, the proviruses were inducible and produced noninfectious virions. These virions contained viral RNA but lacked sufficient envelope protein (gp160/gp41) for infectivity. The researchers demonstrated that these 5'-L defects cause splicing abnormalities, which reduce the production of mRNAs encoding envelope proteins. These infected clones were found to be stable, compartmentalized in effector memory T cells, and capable of producing viremia at levels detectable by clinical assays, complicating clinical management.

These findings reveal that defective proviruses are not biologically inert and can significantly complicate the clinical management of HIV-1. Because these proviruses produce noninfectious virions, they do not cause viral rebound in the traditional sense, but they do cause persistent viremia that can lead to unnecessary treatment changes and patient anxiety. The study suggests that sequencing the 5'-leader region could help clinicians identify these cases and avoid futile regimen intensifications.