Figure 3.

Matching of potential linear epitopes (9-amino-acid fragments) in natural sequences by selected vaccine candidates. Highly similar sequences were removed from an alignment of all available VEEV-clade, WEEV-clade, and EEEV-clade sequences in GenBank in November 2019. For each vaccine, the fraction of vaccine-matched 9-mers, “9-mer coverage”, was computed for each sequence; sequences were plotted in descending rank order of coverage. For example, for the E3 protein, vaccine pVXH-6 covers ~50% of WEEV isolates at a level of 82% of 9-mers or better (those to the left of the red dot), whereas 32% of isolates (those to the right of the gold dot, x-axis value 0.68 and above) are covered at a level of 41% or less. Colors identify candidate vaccines as in Figure 2.