DNA of the Black Death at East Smithfield, London

It seems as though every couple of months a new paper is published reporting Yersinia pestis DNA from ancient remains. This week brought the latest installment from London’s East Smithfield Black Death cemetery. This cemetery holds a special place in the scientific investigations of the Black Death because it is so well documented as being specifically for the first wave of plague in 1348-1350 and the  recovery of so many well-preserved skeletons. This cemetery has been the subject of several bioaracheological studies, primarily by former plague skeptic Sharon DeWitte, making this one of the best characterized set of Black Death victims yet to be discovered. DeWitte is also one of the co-authors of this study.

Using a new method of ‘targeted enrichment’  and high through-put sequencing an international group led by Hendrik Poinar was able to clone and sequence relatively long stretches of Yersinia pestis DNA from recovered remains. They were given access to 100 samples (53 bones and 47 teeth) from which they found 20 positive results for Y. pestis. Unfortunately they don’t indicate how many individuals these samples represent. Although the bone yielded more aDNA, the teeth had far more positive results; 37% of teeth to only 5.7% of bones. Poinar’s group believes this is consistent with a blood-borne pathogen because the tooth pulp is more vascular than bone.

Poinar’s group has reconstructed more of the ancient genome than any group to date. They had the advantage of knowing that this burial pit was open for only a short time and specifically for plague victims. They worked under the assumption that all victims of the plague died from the same strain and were therefore able to construct a composite organism. They could not have made this assumption in a churchyard cemetery that could be open for centuries. They were able to reconstruct 99% of the pPCP1 plasmid (95% with five fold coverage) and showed that its sequence matches 11 of 14 known strains today. They were also able to reconstruct a portion of the pMT1 plasmid that contains genes for the F1 antigen and a small portion of the bacterial chromosome. The Black Death strain seems to be a variant of the Medievalis biovar, but its exact placement is unclear. This has led to premature claims that the Black Death strain is extinct. Given that they haven’t shown a single mutation/polymorphism that makes a functional change, there is no evidence yet that the medieval strain was intrinsically more virulent than modern strains.

They took great pains to close all of the possible technical questions. They obtained human remains from the cemetery of St Nicholas Shambles also in London that dates from about a century earlier to serve as negative controls. These 10 specimens remained negative throughout. They analyzed the types of DNA damage found in human mtDNA from both East Smithfield and St Nicholas Shambles, and compared the level and types of damage to the Y. pestis aDNA to prove the Y. pestis DNA was original to the remains. They followed all of the isolation and contamination prevention procedures recommended for aDNA and sent their clones to two independent high-throughput sequencing facilities to confirm the sequence. By comparing the sequences of the two facilities they were able to resolve DNA damage from true polymorphisms/point mutations.

Why is this study important? First and foremost, it confirms that a well-known Black Death burial pit was due to Yersinia pestis. They developed a method to reconstruct more of the ancient genome than has been done before that should improve our phylogenetic analysis of Y. pestis. They answered all of the technical questions  that should finally bring consensus on the cause of the plague. This does not mean that other pathogens didn’t co-circulate or that every epidemic labeled as the plague really was. Now its time to dig into the epidemiology and get to the really important questions!


Schuenemann, V., Bos, K., DeWitte, S., Schmedes, S., Jamieson, J., Mittnik, A., Forrest, S., Coombes, B., Wood, J., Earn, D., White, W., Krause, J., & Poinar, H. (2011). PNAS Plus: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1105107108

DNA Detective Work Identifies Black Death Culprit, NPR: Science Friday, September 2, 2011. Ira Flatow interviews Hendrik Poinar and Michael McCormick. (podcast)