Figure 3: Viral Evolution and Disease Progression. (a) Sequencing was performed for all recognized CTL epitopes in the ELISPOT assay (3–5 clones per epitope and 2–3 epitopes per animal) for each animal (6 animals) at all time points that the animal was virus positive (2–5 per animal) ( 𝑛 = 24–72 clones per analysis). Accumulated mutations were noted and the percent of epitopes that showed mutations (regardless of the effect of the mutation on CTL responses) were compared between the NP/RP and SP/LTNP groups. (b) CD4 T cell absolute counts were measured at every time-point in which ELISPOT assays were performed and these counts were compared between animals carrying virus with wild-type epitopes or mutated epitopes. (c) Comparison of the number of accumulated mutations observed in CTL epitopes in viral proteins. Statistical analysis was performed using unpaired two-tail t-tests.