Phylogenetic Analysis
We first compared the data of the 24 loci MIRU-VNTR against that of
MIRU-VNTRplus(https://www.miru-vntrplus.org/MIRU/index.faces). The most
frequent pattern found for the Beijing A strain was MLVA type 1048-33,
while the less common patterns with SLVs (Table 1) were MLVA types
1048-32 and 342-33 (Table 2). We next searched for these three MLVA
types in a compiled 24-MIRU-VNTR global dataset of 4,987 Beijing
isolates (Merker et al., 2015) and found
that MLVA type 1048-33 was scarce, with only five entries, and
remarkably two of were from Panama; 1048-32 was more frequent, 158
isolates widely distributed in Asia and fewer entries from Latin
America; 342-3 was poorly represented (12 isolates) (Table 2).
WGS-analysis revealed that Beijing A cluster corresponds to the modern
Beijing sublineage, specifically its Asian African 3 (Bmyc13; L2.2.5)
sublineage (Figure 2). The entries showing relatedness with Beijing A
strains in our study matched Vietnamese isolates (Figure 2). We selected
the currently publicly available sequences of MTBC Beijing subgroup
L2.2.5/Asian African strains (~ 200 strains) to
construct a maximum likelihood phylogeny that grouped, again, Colon
Beijing A representatives with strains isolated in Vietnam (Ho Chi Minh
City), with a good bootstrap support (96%).
Finally, (Figure 3) we focused on a smaller subset corresponding to the
clade that included the Panama Beijing A isolates and related Vietnamese
isolates to determine their convergence at a time point between
2000-2012 by BEAST analysis. The resulting median substitution rate was
estimated to be 4.0 x 10^-7 [95% HPD 2.75 x 10^-7 - 5.11 x
10-7], which corresponds to 1.6 subs/genome/year (95% confidence
interval 1.1 - 2.0/year).