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Details of first historically recorded plague pandemic revealed by ancient genomes

last modified Jun 05, 2019 07:48 AM
Analysis of 8 new plague genomes from the first plague pandemic reveals previously unknown levels of plague diversity, and provides the first genetic evidence of the Justinianic Plague in the British Isles.


         Double burial at Edix Hill of an adult woman and a child aged around 10 or 11 when they died of plague in the mid-6th century. Copyright: Cambridgeshire County Council.

An international team of researchers have analysed human remains from 21 archaeological sites to learn more about the impact and evolution of the plague-causing bacterium Yersinia pestis during the first plague pandemic (541-750 AD).

In a study published in PNAS, the researchers reconstructed 8 plague genomes from Britain, Germany, France and Spain and uncovered a previously unknown level of diversity in Y. pestis strains. Additionally, they found the first direct genetic evidence of the Justinianic Plague in the British Isles.

The Justinianic Plague began in 541 in the Eastern Roman Empire, ruled at the time by the Emperor Justinian I, and recurrent outbreaks ravaged Europe and the Mediterranean basin for approximately 200 years. Contemporaneous records describe the extent of the pandemic, estimated to have wiped out up to 25% of the population of the Roman world at the time.

Recent genetic studies revealed that the bacterium Yersinia pestis was the cause of the disease, but how it spread and how the strains that appeared over the course of the pandemic were related to each other was previously unknown.

In the current study, an international team of researchers led by the Max Planck Institute for the Science of Human History analysed human remains from 21 sites with multiple burials in Austria, Britain, Germany, France and Spain. They were able to reconstruct 8 new Y. pestis genomes, allowing them to compare these strains to previously published ancient and modern genomes.



Map and phylogenetic tree showing the newly published (yellow) and previously published (turquoise) genomes. Shaded areas and dots represent historically recorded outbreaks of the First Pandemic. Photo Credit: Marcel Keller

Additionally, the team, in collaboration with members of the Department of Archaeology, University of Cambridge, found the first genetic evidence of the plague in Britain, from the Anglo-Saxon site of Edix Hill. By using a combination of archaeological dating and the position of this strain of Y. pestis in its evolutionary tree, the researchers concluded that the genome is likely related to an ambiguously described pestilence in the British Isles in 544 AD.

Background to site of Edix Hill

The Edix Hill cemetery near Barrington in southern Cambridgeshire was excavated between 1989 and 1991 by Cambridgeshire County Council’s Archaeological Field Unit, revealing part of an inhumation cemetery with 149 individuals buried between c. 500 and 650AD.

According to Craig Cessford of the Department of Archaeology, University of Cambridge, “Although there are some relatively impressive burials, in most respects Edix Hill is broadly typical of inhumation cemeteries of the period from East Anglia. There are no documentary sources that definitely record that the Justinianic Plague of the 540s reached Anglo-Saxon England, so its identification at Edix Hill represents a major discovery.”

“At least four individuals tested positive for Y. pestis, meaning that they almost certainly died of the plague. The total is likely to have been much higher than this, as less than 15% of the skeletons have been tested so far. As the Edix Hill cemetery served a small community or communities of perhaps 50 to 65 people, this must have been a major traumatic event, comparable to the later Black Death. Despite the disastrous circumstances, these individuals were buried with care and respect and are archaeologically indistinguishable from individuals who died of other causes. Some of the plague victims were buried individually, while others were buried in pairs, perhaps when two members of a family succumbed to the plague. All were accompanied with a range of grave goods.”

“It is unlikely that Edix Hill is unusual in being affected by the Justinianic Plague, more probably most, if not all, of Anglo-Saxon England was ravaged by it. This discovery therefore represents a major historical event that previously could only be guessed at, meaning that the story of Early Anglo-Saxon England must be rewritten.”

Skeletons from the cemetery are now being re-studied at the University of Cambridge by researchers on the project ‘After the Plague: Health and History in Medieval Cambridge’, funded by the Wellcome Trust. 

High diversity of Y. pestis strains during the First Pandemic

The researchers found that there was a previously unknown diversity of strains of Y. pestis circulating in Europe between the 6th and 8th centuries AD. The 8 new genomes came from Britain, France, Germany and Spain. “The retrieval of genomes that span a wide geographic and temporal scope gives us the opportunity to assess Y. pestis’ microdiversity present in Europe during the First Pandemic,” explains co-author Marcel Keller, PhD student at the Max Planck Institute for the Science of Human History, now working at the University of Tartu. The newly discovered genomes revealed that there were multiple, closely related strains of Y. pestis circulating during the 200 years of the First Pandemic, some possibly at the same times and in the same regions.

Despite the greatly increased number of genomes now available, the researchers were not able to clarify the onset of the Justinianic Plague. “The lineage likely emerged in Central Asia several hundred years before the First Pandemic, but we interpret the current data as insufficient to resolve the origin of the Justinianic Plague as a human epidemic, before it was first reported in Egypt in 541 AD. However, the fact that all genomes belong to the same lineage is indicative of a persistence of plague in Europe or the Mediterranean basin over this time period, instead of multiple reintroductions.”

Possible evidence of convergent evolution in strains from two independent historical pandemics

Another interesting finding of the study was that plague genomes appearing towards the end of the First Pandemic showed a big deletion in their genetic code that included two virulence factors. Plague genomes from the late stages of the Second Pandemic some 800-1000 years later show a similar deletion covering the same region of the genomes.

“This is a possible example of convergent evolution, meaning that these Y. pestis strains independently evolved similar characteristics. Such changes may reflect an adaptation to a distinct ecological niche in Western Eurasia where the plague was circulating during both pandemics,” explains co-author Maria Spyrou of the Max Planck Institute for the Science of Human History.

The current study offers new insights into the first historically documented plague pandemic, and provides additional clues alongside historical, archaeological, and palaeoepidemiological evidence, helping to answer outstanding questions.

“This study shows the potential of palaeogenomic research for understanding historical and modern pandemics by comparing genomes across millennia,” explains senior author Johannes Krause of the Max Planck Institute for the Science of Human History.

“With more extensive sampling of possible plague burials, we hope to contribute to the understanding of Y. pestis’ microevolution and its impact on humans during the course of past and present pandemics.”


Title: Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

Authors: Marcel Keller, Maria Spyrou, Christiana Scheib, Gunnar Neumann, Andreas Kröpelin, Brigitte Haas-Gebhard, Bernd, Päffgen, Jochen Haberstroh, Albert Ribera i Lacomba, Claude Raynaud, Craig Cessford, Raphaël Durand, Peter Stadler, Kathrin Nägele, Jessica Bates, Bernd Trautmann, Sarah Inskip, Joris Peters, John Robb, Toomas Kivisild, Dominique Castex, Michael McCormick, Kirsten Bos, Michaela Harbeck, Alexander Herbig, Johannes Krause

Publication: PNAS, DOI: doi:10.1073/pnas.1820447116



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