The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

The Black Death, a catastrophic event occurring between 1347 and 1353, initiated the Second Plague Pandemic. Following its initial decline, plague outbreaks resurfaced intermittently across Europe, commencing with the pestis secunda. Despite its importance, the epidemiology of Yersinia pestis during this period remains underexplored.

In a recent study, 23 new Y. pestis genomes were discovered from contexts related to the Second Plague Pandemic, spanning Scandinavia, the Netherlands, Iceland, and Armenia, over a period of approximately 270 years. By employing a rigorous mutation-filtering pipeline to evaluate genetic diversity, researchers were able to document both Black Death and post-Black Death lineages, as well as multiple waves of plague at specific cemetery sites.

The study identified four pestis secunda genomes, including three from Armenia, indicating the eastward spread of this lineage before its eventual disappearance from Europe. Additionally, the research resolved a previously poorly understood Branch 1A sub-lineage of Y. pestis and provided the first genomic evidence of plague in Iceland, resolving long-standing questions about its presence on the island.

By comparing sequences against a reconstructed ancestral reference, the researchers identified mutations that define specific clades, including nonsynonymous changes in metabolic and biofilm-related genes with predicted structural effects. These alterations may have played a role in shaping the epidemiological dynamics of the Second Plague Pandemic.