Molecular-Genetic Characteristics of Yersinia pestis Strains from the Volga-Ural Sandy Plague Focus

The aim of the work was to establish the phylogenetic diversity of subpopulations of Yersinia pestis strains from the Volga-Ural sandy natural plague focus during the period of epizootic and epidemic activity between 1912 and 2002 and to determine their geographic distribution.
Material and methods. One hundred and three samples from Volga-Ural sandy focus (1912–2002) were studied. High-throughput sequencing was performed on the MGI platform (DNBSEQ-G50RS, China) using MGIEasy Fast FS Library Prep Set and MGIEasy UDB Primers Adapter Kit A. To process the data and carry out the assembly of obtained raw short reads, Unicycler v0.4.9, FastQC v0.11.9 software was used. The analysis of VNTR loci was conducted using the TandemReapeatFinder program; the agglomerative clustering method was applied for hierarchical clustering (AgglomerativeClustering, scikit-learn v1.7.0 library). The SNP-typing was performed via Snippy v4.6.0. To construct phylogenetic tree we used the method of Maximum Likelihood in PhyML 3.1 (500 bootstrap replicas).
Results and discussion. Whole-genome SNP-analysis and phylogenetic reconstruction of the population structure have identified the main subpopulations common in the Volga-Ural sandy focus; the SNP genotypes of Y. pestis strains have been established, and their marker SNPs determined. It has been suggested that the cause of plague outbreak in 1945 could be genotype Pricasp 2. VNTR-analysis has revealed 57 MLVA25-genotypes and the most variable VNTR-loci (ms46 и ms62). Results of conducted SNP- and VNTR-analysis indicate active changes in the zones of intra-focal circulation as well as the consistent evolution of the medieval biovar of Y. pestis strains, the phylogenetic branch 2.MED1 in Volga-Ural sandy focus.

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