Unveiling novel conserved HIV-1 open reading frames encoding T-cell antigens using ribosome profiling.
Alternative reading frames (ARFs) were described in several viral genomes using ribosome profiling such as HCMV, KSV, and SARS-CoV-2 but no demonstration has been made on HIV genome. Using ribosome profiling, we uncovered 98 conserved HIV ARFs distributed across the genome, with high conservation among HIV clade B and C isolates. Our analysis revealed that at least 42 ARFs encode viral polypeptides, as demonstrated by T-cell responses targeting 45 ARF-derived peptides in patients under treatment or naturally controlling the infection. At the same time, we identified a ligand of HLA-A*0201 derived from an identified ARF on primary infected cells. These responses were mediated by polyfunctional CD4+ T-cells secreting at least 3 cytokines simultaneously. Our discovery expands the list of conserved viral polypeptides that might be potential targets for vaccination strategies. Overall design: RiboSeq of supT1 cells infected by the virus HIV NL4-3 XCS. Cells are harvested 20h post-infection. Two independant infections have been done, which were sequenced in triplicate