Phylogenetic Analysis of Yersinia pestis Strains of the Caucasian Subspecies from the Foci of the Caucasus and Transcaucasia according to the Whole Genome Sequencing Data

Abstract

We have investigated the population structure of Yersinia pestis spp. caucasica strains from natural plague foci located in the Caucasus and Transcaucasia. According to the data of a whole genome SNP analysis of 28 strains of the Caucasian subspecies, seven of which are sequenced by us, and taking into account 1625 identified core SNPs, the presence of several phylogenetic lines and populations of Yersinia pestis ssp. caucasica corresponding to the geographical distribution of the strains has been determined. Strains of Y. pestis Caucasian subspecies include three separate clusters, the first of which is represented by strains from the East Caucasian high-mountain plague focus. Their genome has revealed 80 unique SNPs, which indicates their greatest antiquity and the long-standing divergence of this branch from the common stem of the evolution of Caucasian strains. The genomes of strains of two other clusters also differ in a large number of individual SNPs, 32 and 36, respectively. One of them includes strains from the Pre-Sevan mountain, Zangezur-Karabakh mountain, and Pre-Araks low-mountain foci with the grouping within the cluster of three separate subclusters: Pre-Sevan (IIa), Zangezur-Karabakh (IIb), and Zangezur-Karabakh-Pre-Araks (IIc). Another one, the third cluster of the Caucasian subspecies, consists of strains from the northwestern part of the Caucasus highlands (Gyumri and Javakheti-Akhalkalaki foci). Using PCR with hybridization-fluorescent registration of results and whole genome sequencing, two clinical strains of Y. pestis were shown to belong to the Caucasian subtype, which confirms the ability of this subspecies to cause plague in humans.