Elevated HIV trans-infection of CD4 T cells in MRKAd5 vaccine recipients due to CD8 T cells targeting of adapted epitopes

We report the application of single-cell-based RNA sequencing technology for high-throughput profiling of antigen specific CD8 T cells induced by MRKAd5 vaccine (HVTN502 trial). Based on the transcriptomic data, we identified 68 differentially expressed genes comparing adapted versus non-adapted epitope specific CD8 T cells. Interestingly, CLOCK and HNF1B, which are critical for circadian rhythm, were found to be upregulated in both recipients with the non-adapted epitope specific CD8 T cell responses. The mRNA profiles of MRKAd5 vaccine-encoded non-adapted and adapted epitope specific CD8 T cell after in vitro expansion using autologous peptide pulsed monocytes were examined.