Teeth from 178 individuals in three different locations (two European, one Asian) were screened for Y. pestis infection using the plasminogen activator (pla) gene. Fifty-three DNA samples from 32 individuals were used for further analysis by creating next-gene sequencing libraries and screening for Y. pestis DNA with whole-genome array capture. Of these, only three individuals had sufficient captured Y. pestis DNA for genomic analysis. These samples included one tooth from an individual in a mass grave in Barcelona, Spain, two teeth from an individual buried in a mass grave in Ellwangen, Germany, and a tooth from an individual buried in a single grave in Bulgar City, Russia. The Spanish and German samples were radiocarbon dated to 1300–1420 AD and 1486–1627 AD, respectively, while the Russian sample was dated to 1298–1388 AD. In addition, the Russian individual was dated archeologically to the latter half of the 14th century based on coins found in the grave that were minted after 1362. Because the sequencing coverage for the individual from Ellwangen was low (less than fivefold), the Spanish Y. pestis sequence came from combining the libraries created from each of the two teeth.
What is the importance of these three DNA samples? Having two samples contemporary with the Black Death (Spain and Russia) will help elucidate any connection among the strains circulating in Europe during the second plague pandemic with the strains from Asia. The German Y. pestis sample, dated after the Black Death, can be compared to the genetic information from remains found in the documented Black Death burial site in London, England and another post-Black Death plague strain, and reveal how Y. pestis may or may not have differed over time. The second Y. pestis pandemic started with the late 14th century Black Death, but lasted into the 18th century. Finally, how do these lineages compare to those seen in more modern times based on phylogenetic analysis of Black Death-era strains and modern varieties?
To better understand where these three new sequences fall within the phylogeny of Y. pestis, 3,351 SNPs were compared to those of seven known Black Death strains as well as 141 modern Y. pestis sequences. Included in the SNP cohort were some recently acquired data of modern Y. pestis strains from the Former Soviet Union, adding more depth to the Asian data. The Spanish, German and Russian sequences fell in the portion of the Y. pestis phylogeny that matched with the Black Death strains. Spyrou et al. focused on the sequences from England (read more here) from earlier work published by some of the same authors of the Cell Host & Microbe article, showing the three new strains were similar to each other as well as the English strains. The Spanish strain matched three London strains, but the Russian strain had four sequence changes including two SNPs that matched a fourth London Black Death strain, one SNP unique to the Russian individual and one that is shared with modern strains. This is where the SNP data and phylogeny become interesting. The authors conclude that because the Russian strain shares identity with both a Black Death strain and modern strains that include the third Y. pestis pandemic, the individual from Volga anchors the hypothesis that the Black Death spread eastward and founded the strain that was spread into the modern era as part of the third pandemic.
Not every strain identified so far made this eastern journey based on 10 historical samples of Y. pestis that infected humans with the plague during the Black Death and later into the 18th century. The German strain ended up grouped together with five strains associated with the Great Plague of Marseille in 1720–1722, making it likely that the German strain was ancestral to the French plague strain based on radiocarbon dating. Interestingly, there seems to be no modern equivalent of the German/French strains, suggesting that this Y. pestis strain did not survive beyond the second pandemic.
With each new set of remains infected with Y. pestis, researchers are able to create a clearer picture of what happened in the last few centuries of plague infection. Spyrou et al. showed how much Y. pestis evolved over time and in different locations. While the genetic diversity was low enough to keep all strains within the same branch of the phylogenetic tree, the differences suggested some strains did linger in Europe and others spread from Europe back to Asia, sharing lineage with subsequent strains that have infected humans more recently. Although, researchers did not directly address the possibility of a local reservoir of the plague in Europe, they did suggest that a diversity of infectious strains that occurred during the second pandemic persisted in Europe and that there was a connection between the second and third plague pandemics. As ever, I eagerly await the next dispatch in the history of the plague pandemic.
Spyrou, M.A., Tukhbatova, R.I., Feldman, M., Drath, J., Kacki, S., Beltrán de Heredia, J., Arnold, S., Sitdikov, A.G., Castex, D., Wahl, J., Gazimzyanov, I.R., Nurgaliev, D.K., Herbig, A., Bos, K.I. and Krause, J. (2016) Historical Y. pestis genomes reveal the European Black Death as the source of ancient and modern plague pandemics. Cell Host Microbe 19, 874–81.