The Role of the Caspian, Aral and Balkhash Lakes in the Spread and Preservation of Yersinia pestis in Eastern Europe and Central Asia in the 20th and 21st Centuries

Based on phylogenetic analysis of whole-genome sequencing of Yersinia pestis 2.MED1 strains of the medieval biovar, combined with epizootic, epidemiological, and climatic data over a 100-year period, we have reconstructed the spread of plague in Eastern Europe and Central Asia (EECA) in the 20th and 21st centuries. The data suggest the important role of three great lakes—the Caspian, Aral, and Balkhash—in the spread and preservation of Y. pestis 2.MED1 in EECA. Three waves of Y. pestis 2.MED1 spread have been identified: Caspian (Caspian Sea region foci, 1912-1945; Caucasus, 1953-1986), North Aral (Northern Aral Sea region foci, 1945-1959; Caspian Sea region foci, 1945-2015; Pre-Caucasus, 1999-2003; Karakum, 1949-1965) and Central Asian (Kyzylkum, 1924, 1983-2020; Balkhash foci, 1939-2020; Northern Aral Sea region foci, 1967-2020; Eastern Caspian Sea region foci, 1968-1985). Favorable climatic conditions in the Caspian Sea region, the Northern Aral Sea region, and the Balkhash region in the 20th and 21st centuries contributed to the rapid formation of stable natural plague foci and the long-term persistence of Y. pestis 2.MED1 strains of the medieval biovar, with their sporadic spread into other foci of EECA. Periodic introductions of the pathogen are one of the reasons for the plague re-emergence and activation of plague foci in the EECA region.