HIV-1 recombination can afford rapid escape from acute CD8+ T cell responses. The first 114 amino acid region of Nef spanning the two variable T cell epitopes in CH078 were analyzed. The recombination breakpoints between the epitopes are shown. The major and minor T/F consensus sequences are displayed above the individual sequences. Sequences derived from the major T/F are highlighted in blue and sequences from the minor T/F are highlighted in yellow, while the regions in which recombination probably occurred are indicated in grey. The patient ID and days post screening (dps) which corresponded to Fiebig I/II are followed by individual sequence identifiers. The 2 epitopes are outlined by red boxes. Graphical inserts beneath each epitope indicate the magnitude of T cell responses targeting the major and minor T/F variant of each epitope (data derived from Figures 4A and C). On the right, the percentage of the recombinant viruses at each timepoint is shown. Non-recombinant viruses are broken down in the % major or minor virus. Note, at day 35, two 3′ sequences (of 27) with large deletions were excluded from analysis.