Pathology

Sociology

Archaeology

Genomics

Yersinia pestis

Disease

Population

Coronavirus disease 2019 (COVID-19)

Infectious disease (medical specialty)

Escherichia coli

Evolutionary biology

Biology

Pandemic

Phylogenetics

Gene

Comparative genomics

Outbreak

Demography

Genome

Virology

Geography

Lineage (genetic)

Yersiniosis

Plague (disease)

Enterobacteriaceae

Clade

Phylogeography

Genetics

Virulence

Medicine

Genetic diversity

Nature Communications

The second plague pandemic, caused by Yersinia pestis , devastated Europe and the nearby regions between the 14 th and 18 th 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.

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes