HIV-seq reveals gene expression differences between HIV-transcribing cells from viremic and suppressed people with HIV

Abstract HIV-transcribing cells can perpetuate chronic inflammation in ART-suppressed people with HIV (PWH) and likely contribute to viral rebound after ART interruption. However, these cells are difficult to study using single-cell RNA-seq (scRNA-seq) due to their low frequency and low levels of HIV transcripts, which are usually not polyadenylated. By spiking in capture sequences targeting conserved regions of HIV during scRNA-seq – a new method we call “HIV-seq” - we detect double the mean number of HIV reads per cell from PWH. HIV RNA+ cells are enriched among T effector memory cells during both viremia and ART suppression but exhibit a cytotoxic signature during viremia only. In contrast, HIV-transcribing cells from ART-suppressed timepoints exhibit a distinct anti-inflammatory signature involving elevated TGF-β and diminished IFN signaling. These findings demonstrate that HIV-seq is a useful tool to better understand the mechanisms by which HIV-transcribing cells can persist during ART.