SIVmac239 escape mutations in loss of SIV elite control. A) SIVmac239 viral loads for animal r00032 post-infection. Dotted line indicates threshold for elite control. T.O.D. = Time of Death. Time of elite control and breakthrough are boxed. Stars indicate time of whole viral genome sequencing shown in Additional file 1: Figure S1. The limit of detection for viral load assay was 30 vRNA copies/ml plasma. B) The name, position, and sequence of SIVmac239 Mamu-B*008:01 epitopes exhibiting pre- and/or post-breakthrough variation are shown at 20 and 107 weeks post-infection (WPI) with mutations highlighted in grey. C) The name, position, and sequence of 4 regions in SIVmac239 Gag from animal r00032 exhibiting pre- and/or post-breakthrough variation are shown longitudinally with mutations highlighted in grey. Dashes indicate no change from wild type SIVmac239. Periods indicate no data. D) IFN-γ ELISpot measurements of immune responses against the four regions of SIVmac239 Gag shown in panel C; 13 weeks post-infection (top panel) and 110 weeks post-infection (bottom panel). White bars = PBMC effectors. Black bars = CD8+ T cell-depleted PBMC effectors. Dotted line represents limit of detection for the assay. N.D. = no data. Bars indicate the mean of duplicate wells with standard deviations shown.