Phylogenetic Analysis of Yersinia pestis Strains Belonging to Caucasian Subspeciesfrom the Foci of Caucasus and Trans-Caucasus Regionaccording to the Data from Whole-Genome Sequencing
We have studied the population structure of Yersinia pestis strains ssp. caucasica, from natural plague foci situated in Caucasus and Trans-Caucasus regions. According to the data obtained from whole-genome SNP analysis of 28 ssp. caucasica strains, 7 out of which were sequenced with our own efforts, and taking into account 1625 identified core SNPs, existence of several genetic lines and populations of Yersinia pestis ssp. caucasica has been established. These lines and populations coincide with geographical distribution of the strains. Yersinia pestis ssp. caucasica comprise three separate clusters, the first one of which is represented by strains from East-Caucasian high-mountain plague focus. Their genome contains 80 unique SNPs, which testify to the greatest antiquity and early divergence of this branch from a common stem of Caucasian strains' evolution. The genomes of strains from two other clusters also differ in a great number of individual SNPs, 32 and 36, respectively. One of them includes the strains from Prisevansky mountain, Zangezuro-Karabakhsky mountain, and Preraksinsky low-mountain foci with the allocation of three separate sub-clusters within the cluster: prisevansky (IIa), zangezuro-karabakhsky (IIb) and zangezuro-karabakhsko-preraksinsky (IIc). The last and the third cluster of the caucasian subspecies comprises strains from north-western part of Caucasian Plateau (Gyumriisky and Dzhavakhetsko-Akhalkalaksky foci). Using PCR with hybridization-fluorescent registration of results and whole genome sequencing, appurtenance of two clinical Y. pestis strains to ssp. caucasica has been proved, which confirms the ability of this subspecies to cause plague in humans.