PMC

A. Phylogenetic relationships among BCG strains. A. Maximum likelihood phylogeny based on 144 variable common nucleotide positions across 12 Mycobacterium bovis BCG genome sequences. The tree is rooted with M. bovis Ravenel SRR022532. Node support after 1000 bootstrap replications is indicated in black. Prior dates used to calibrate the phylogeny for Bayesian coalescent analysis are indicated in grey. B. The stacked bars show the proportion of missing M tuberculosis T cell epitopes in the 3 BCG groups identified in panel A and delimited by the dashed lines. Group 1: BCG Russia and Japan. Group 2: BCG Australia, Connaught, Copenhagen, Denmark, Glaxo, Mexico, Phipps, Prague and Tice. Group 3: BCG Pasteur

Conservation of M. tuberculosis T cell epitopes in BCG strains. A. dN/dS in various gene classes of BCG strains. The calculation was done after comparing each of the 12 BCG genomes to the inferred most recent common ancestor of MTBC. This shows the dN/dS in 1) non-redundant epitope regions, 2) non-epitope regions of antigens, 3) M. tuberculosis essential genes, 4) M. tuberculosis non-essential genes. B. Comparison between the number of synonymous and non-synonymous SNPs found in M. tuberculosis non-overlapping T cell epitope regions in BCG and random sequences of same size selected from the rest of BCG genomes. The graph shows that T cell epitope regions in BCG are less affected by SNPs than expected by chance (95% confidence interval in the random replicates is indicated as error bars).