The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541–750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.
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European Union (EU)
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Springer Science and Business Media LLC
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The Cambridge work is supported by the Wellcome Trust (Award no. 2000368/Z/15/Z) and St. John’s College, Cambridge (J.E.R., T.K., C.C., C.L.S.); the European Union through the European Regional Development Fund (Project No. 2014-2020.4.01.16-0030) (C.L.S.); and the Estonian Research Council personal research grant (PRG243) (C.L.S). M.A.S., M.K., K.I.B. and J.K. were supported by the Max Planck Society and the ERC starting grant APGREID (to J.K.). R.T., A.H. and K.I.B. were supported by the Max Planck Society.