scRNA-seq data from two macaques in AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T-cells infected in vivo
Persistent HIV-1 reservoirs of infected CD4 T-cells are a major barrier to HIV-1 cure, though the mechanisms by which they are established and maintained in vivo remain poorly characterized. To study host properties that govern productive cellular infection, we analyzed viral mRNA+ (vRNA) CD4 T-cells of untreated SIV-infected macaques by single-cell RNAseq. Transcriptionally active infected cells, defined by spliced vRNA, were highly enriched for vRNA: 10.3% and 7.5% of all mRNA in two animals. These cells expressed diminished FOS, a component of the Activator protein 1 (AP-1) transcription factor, relative to vRNA-low and -negative cells. Overall design: Plate-based single cell expression profiles from sorted CD4 memory cells of two macaques during acute SIV infection