In the rapid progressor studied here, we have shown using ultra-deep sequencing that escape mutations were selected in early infection across several of the known HLA-B*27:05 and HLA-B*57:01 epitopes, from the earliest timepoint when the CD4+ T cell count was 950 cells/mm3 and viral load was 65 copies/ml, preceding loss of immune control. This evidence concerns the gene HLA-B and infection.