AI interpretationAI-generated
Ancient plague DNA from 17th-century Latvia reveals a virulence gene loss at the pandemic's end.
Researchers extracted DNA from teeth of 16 people buried in Riga, Latvia, during 17th-century plague outbreaks. Four remains contained Yersinia pestis DNA, and two yielded enough for full genome reconstruction. The strains fit within known post-Black Death diversity but did not cluster together, suggesting multiple introductions. Notably, the plague bacterium carried two versions of the pPCP1 plasmid: one with the pla virulence gene and one without. This pattern appears in most later strains but not Black Death ones, hinting that loss of pla may have helped end the pandemic.
- Four of 16 individuals from Riga cemeteries tested positive for Yersinia pestis DNA, confirming plague victims.
- Two reconstructed Latvian strains did not cluster together, indicating multiple plague introductions to the region.
- The bacterium carried two pPCP1 plasmids, one with and one without the pla virulence gene, a pattern common in post-Black Death strains but absent in Black Death strains.
Sample interpretation
Of 16 teeth samples, 5 had resolvable Y-chromosome lineages: N-Y15922 (2), R-L23 (1), T-L446 (1), and R-L51 (1). Mitochondrial DNA was resolved for 8 samples, with U5a2a1 and U5b1b1f each appearing twice, plus H1b, R1b1, H5a1a, and H1g1. These lineages reflect typical European diversity of the time, but the small sample size limits broader population conclusions.
For genealogy enthusiasts
This study shows that ancient DNA can track plague evolution in understudied regions like the Baltics. For ancestry enthusiasts, it highlights how pathogen genetics, not just human DNA, can reveal past epidemics and their impact on European populations.
Abstract
Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of pla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.