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Analysis of Ancient Plague DNA Suggests Long-Term Persistence of Yersinia Pestis in Europe

NEW YORK (GenomeWeb) – Genetic analysis of samples obtained from the skeletons of victims of the second plague pandemic indicates that the disease-causing Yersinia pestis bacterium persisted in Europe, even as it was continuously re-introduced from central Asia. 

The second plague pandemic raged from the 14th century to the 17th century, peaking between 1346 and 1353, a time period known as the Black Death, when it claimed the lives of about a third of the European population. Researchers only recently concluded that strains of Y. pestis were indeed behind both the second plague pandemic and the earlier Plague of Justinian.

In this new study, researchers led by Julia Riehm at the Central Institute of the Bundeswehr Medical Service in Munich analyzed ancient DNA collected from plague victims at different burial sites in Germany. All eight skeletons that were positive for Y. pestis DNA shared a bacterial genotype that is also highly similar to those previously uncovered in ancient plague victims from other European countries. As some of the plague victims lived about 300 years apart, this suggests that Y. pestis was continuously present in Europe for at least that time period, as the researchers reported today in PLOS One.

"[T]he results of the present study clearly indicate that at least one genotype, which was introduced to Europe at the beginning of the Black Death from Asia, persisted in Europe from the 14th century until the Thirty Years' War (1618–1648)," Riehm and her colleagues wrote in their paper. "We therefore suggest a model in which Y. pestis was introduced to Europe from Asia in several waves combined with a long-time persistence of the pathogen in not yet identified reservoirs. "

Of the 30 skeletons that were excavated from two sites in Germany, eight tested positive for the presence of the Y. pestis-specific pla gene through qPCR, and six of them had enough material for further analysis. One individual had such a high copy count of the pla gene that the researchers believe that person had a severe, generalized infection.

Five of these samples were from plague victims excavated from a church in Manching-Pichl in southern Germany, and radiocarbon dating estimated them to be from the 14th century. The other sample came from three male soldiers who were buried together in Brandenburg in northeastern Germany during the Thirty Years' War in the 17th century. This, the researchers noted, represents the easternmost plague sample yet analyzed.

The researchers genotyped these samples at 16 positions, and the findings were confirmed by sequencing PCR products. The SNPs for typing were selected from different parts of the Y. pestis phylogenetic tree, allowing the new samples to be placed on the tree.

Despite the gap in time and distance, all five plague samples harbored an identical genotype. This same SNP pattern, Riehm and her colleagues noted, was also present in three individuals from about 1348 to 1350 buried in the East Smithfield cemetery in London and in individuals from Hereford, UK, and Saint Laurent-de-la-Cabrerisse, France, suggesting that this genotype was widespread.

The genotype of the German plague victims, they noted, placed them on branch 1 of the Y. pestis phylogenetic tree and also indicates a large geographic distribution of this genotype in Europe.

Still, three deviant SNPs — s12, s1431, and s1195 — have been found in other studies, and indicates that other genotypes were also present.

Though previous studies have suggested that the plague was imported at least twice from Central Asia into Europe via trading routes, or that the bacterium was continuously imported into Europe, Riehm and her colleagues instead said it was likely that Y. pestis was introduced in several waves while also persisting locally in a reservoir.