Phylogenetic Analysis of Yersinia pestis Strains of Medieval Biovar, Isolated in Precaspian North-Western Steppe Plague Focus in the XX Century

Abstract

Objective of the study – comparative phylogenetic analysis of Yersinia pestis strains, isolated in Precaspian North-Western steppe focus in 1924–1926, 1972, and 1986–1990 to understand the causes of focal reactivation during different time periods of the XX century.Materials and methods. The work included 30 strains of Yersinia pestis from Precaspian North-Western steppe natural focus and adjacent plague foci. Whole genome sequencing of eight Y. pestis strains from the former was carried out. Also whole-genome sequences of 16 strains from neighboring natural foci were used. Whole-genome sequencing of Y. pestis strains was conducted in Ion PGM system (Life technologies). SNPs search across the core genome was performed using software package Wombac 2.0. Tree diagram Maximum Likelihood, HKU85 model, was constructed to analyze phylogenetic relations.Results and discussion. It is established that in early XX century (1924–1926), strains of phylogenetic branches 2.MED4 and 2.MED1, belonging to medieval biovar, main subspecies, circulated on Ergenin Upland in the Precaspian North-Western steppe natural focus. Later on they became extinct in the territory. It is shown that the strains, isolated on Ergenin Upland in 1972, constituted a common subcluster on the dendrogram with the strains from low-mountain and piedmont plague foci of Caucasus and Transcaucasia, dated the same time period. It was inferred that epizootic manifestations on Ergenin upland in 1972, after a long recess since 1938, were caused by importation of Y. pestis strains from low-mountain natural plague foci of Caucasus and Transcaucasia. It was noted that expansion of Caucasian strains was of short-term character, and plague infected animals have not been found on Ergenin Upland since 1974 (including modern period). It is established that Y. pestis strains isolated in the eastern part of Precaspian North-Western steppe focus between 1986 and 1990, do not have close genetic relation to the strains that circulated on Ergenin Upland in 1924–1926 and 1972. It is determined that each epizootic period (1913–1938 and 1972–1973) in Precaspian North-Western steppe natural focus culminated in the elimination of the circulating Y. pestis strains and rehabilitation of the focal territory.

Five Draft Genome Sequences of Historical Yersinia pestis Strains of Phylogroups 2.MED4 and 2.MED1 of the Medieval Biovar

“…At the end of the 19th century and beginning of the 20th, numerous outbreaks of plague were registered in the Northern Caspian Sea region in Russia and Kazakhstan. Our studies prove that since 1912, outbreaks in the Northern Caspian Sea region have been caused by Y. pestis strains of the phylogenetic branches 2.MED1 and 2.MED4 of the medieval biovar ( 3 , 4 ). The study of the genomes of the etiological agents of plague outbreaks in the Northern Caspian Sea region at the beginning of the 20th century is important for elucidating the causes of the high mortality rates among the population, as well as for historical reconstruction of the evolution of the medieval biovar of the plague pathogen.…”

Evolution and circulation of Yersinia pestis in the Northern Caspian and Northern Aral Sea regions in the 20th-21st centuries

“…During the period from the beginning of the 20th century till present days, while performing epidemiological and epizootiological monitoring in the natural foci of plague in the Caspian Sea and Aral Sea regions, specialists of the Plague Control System of the Soviet Union, and then Russia have gathered a unique collection of Y. pestis strains, which chronologically reflects the history of the foci. According to microbiological and molecular genetic studies of a large number of strains, it was revealed that in the foci of the Caspian and Aral Sea regions Y. pestis of the medieval biovar circulates [1,3]. The strains of this biovar are highly virulent and epidemiologically significant.…”