Figure 5

Epitope escapes in complete genome haplotypes. The escape mutations acquired in the seven epitopes identified by Henn et al. [11] are given per reconstructed haplotype for each time point. Haplotypes reconstructed from each temporal sample are given in a descending order of their frequencies. The dominant haplotype for each time point is depicted by the same colors as in Figure 3. Multiple escapes for the same epitope are depicted by different colors. Escape mutations for each epitope are denoted by a 3-letter code with the first letter as the original epitope amino acid, second letter as the position in the epitope and the third letter as the mutated amino acid. Mutations at anchor residues are highlighted.