A naturally occurring Tat R52W variant in brain-derived HIV attenuates transcription and may contribute to reservoir persistence.

UNLABELLED: HIV-1 persistence under suppressive antiretroviral therapy (ART) remains a major barrier to eradication, yet the contribution of naturally occurring viral variation to transcriptional regulation is incompletely understood. Here, we identify an HIV-1 Tat variant (R52W) that attenuates viral transcription through the disruption of the Tat-TAR RNA interaction. Full-length HIV-1 genomes derived from the brain microglia of a "Last Gift" donor, together with peripheral viral sequences obtained during suppressive ART, revealed the presence of the R52W variant in vivo . The same R52W variant was found in another virally suppressed donor within the same cohort. Additional analysis of 3,440 clinical blood isolates from people with HIV identified R52W in 73 sequences (2.12%) of individuals, including three on ART and a therapy controller, and across diverse viral subtypes. Structural modeling demonstrated that R52W destabilizes Tat-TAR binding, while functional assays showed markedly reduced Tat-mediated transcriptional activity, which was restored upon tryptophan-to-arginine reversion (W52R) in Tat. These findings establish a direct molecular mechanism by which a naturally occurring HIV-1 variant modulates viral transcriptional output. Together, our results identify transcriptionally attenuated HIV-1 variants in treated individuals and suggest that modulation of Tat-dependent transcription may represent an underappreciated determinant of viral persistence under suppressive ART.

SIGNIFICANCE: We identify a naturally occurring HIV-1 Tat variant (R52W) that attenuates viral transcription by disrupting Tat-TAR RNA interaction. This variant is detected in brain-derived and peripheral viral genomes and recurs across 3,440 clinical isolates from people with HIV, including multiple ART-suppressed individuals and a therapy controller. Functional and structural analyses demonstrate a direct mechanism for reduced Tat-mediated transcription. These findings reveal functional viral diversity under suppressive antiretroviral therapy and suggest that naturally occurring transcriptionally attenuated variants may contribute to HIV persistence in treated individuals.