FIG 3 .

Maximum likelihood phylogenetic reconstruction from the concatenated alignment of 408 variable sites (SNVs and MNVs). Vaccine strains resequenced in this study are indicated in black, California isolates are indicated in blue, and Vermont isolates are indicated in red. Yellow circles denote pertactin-deficient strains, and black circles denote strains recovered from fatal cases. The scale bar indicates number of substitutions per site and has been corrected for ascertainment bias based on the nucleotide composition of invariant sites in E476. All epidemic genomes were included in this analysis.