Retrospective Molecular Investigation of Plague Outbreaks in the Northern Aral Sea Region in the Mid-20th Century

The aim of the work is a retrospective molecular examination of plague outbreaks that occurred on the northern coast of the Aral Sea in the middle of the past century, and a phylogenetic analysis of the Yersinia pestis strains that caused them. Materials and methods. Whole-genome sequences of 39 Y. pestis strains from foci of the Northern Aral Sea region, isolated in 1945–1974, were used. Whole-genome sequencing was performed in the Ion S5 XL System (Thermo Fischer Scientific, USA). Data processing and sequence assembly were carried out using the Ion Torrent Suite software package, v5.12, FastQC v0.12.0, unicycler v0.5.0. Phylogenetic reconstruction was carried out using the wholegenome SNP analysis method, the dendrogram was constructed using the Maximum Likelihood algorithm using the PhyML v3.1 program. Molecular typing of strains was performed using the MLVA25 method. Results and discussion. Y. pestis strains isolated in the Northern Aral Sea region between 1945 and 1974 belong to the phylogenetic branch 2.MED1 of the medieval biovar of the main subspecies. Plague outbreaks in the Northern Aral Sea region in 1945, 1955, 1966, and 1969 were caused by strains of the Caspian subbranch 2.MED1, and the outbreak of 1967 – by strains of the Central Asian subbranch, which successively reached this region from the Northern Caspian and Balkhash regions. It is shown that the sources of human infection were epizootics occurring on the northern coast of the Aral Sea. It is established that in the 1960s, Y. pestis strains of the Caspian and Central Asian subbranches 2.MED1 medieval biovar circulated simultaneously in the Northern Aral Sea region. A characteristic feature of the plague outbreak of 1945 was the presence of a large number of SNPs specific to each strain, possibly due to the process of rapid adaptation of the Caspian subbranche 2.MED1 strains to the conditions of the natural biocenosis of the Northern Aral Sea region. Subsequently, the rate of evolution of the emerging Northern Aral population 2.MED1 significantly decreased, which was accompanied by the formation of individual clusters of strains with a small number of individual SNPs.

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