Persistent cell-associated HIV-1 RNA in virally suppressed individuals on INSTI-based ART

Abstract

Integrase strand transfer inhibitors (INSTIs) are the cornerstone of modern antiretroviral therapy (ART), achieving durable plasma HIV-1 suppression in most people living with HIV (PLWH). Previous comparisons of INSTI- and non-INSTI-based regimens have largely focused on HIV reservoir proviral assessments— typically total HIV DNA —without assessing reservoir activity. In this first functional comparison, we measured cell-associated (CA) short HIV-1 RNA transcripts, a marker of active transcription, alongside HIV-1 DNA in white blood cells from 92 virally suppressed individuals on INSTI-based (n = 73) or non-INSTI-based (n = 19) ART. CA short RNA transcripts were detected in all participants and HIV-1 DNA in 99 %, despite undetectable plasma viremia in >93 %. Individuals with prior “blips” — defined as a maximum of two episodes with 20–200 copies/mL plasma HIV-1 RNA over more than two years — had significantly higher CA RNA and HIV DNA than non-blip participants, confirming our previous findings. However, reservoir size and transcriptional activity did not differ significantly between INSTI and non-INSTI groups. These findings indicate that while INSTIs effectively block new integration events, they do not suppress ongoing transcription from the latent reservoir. Therapeutic strategies directly targeting HIV transcription should therefore be prioritized in cure-oriented research for PLWH on long-term suppressive ART.