The entire genome of the Black Death, one of the most vicious epidemics in the history of humankind, has been sequenced by scientists from Canada, Germany, and the USA, according to an article published today in Nature. They are calling it the ancestor of all modern plagues, and add that it is the first time anybody has been able to draft a reconstructed genome of any early pathogen.

The authors say they will now be able to follow how the pathogen has evolved and whether and how its virulence changed over time. Their study has laid the foundations to a more profound understanding of infectious diseases today.

In a recently published study, the same team explain how they managed to pull out miniscule degraded DNA fragments of the agent that caused the Black Death, and demonstrated that a certain variant of the Yersinia pestis bacterium was what caused the plague that wiped out 50 million from Europe’s population between 1347 and 1351.

Yersinia pestis, a variant of this bacterium caused the Black Death that killed 50 million Europeans

Geneticist Hendrik Poinar, from McMaster University, Canada, explained that their next step was to try and “capture” and sequence the whole genome.

Poinar said:

“The genomic data show that this bacterial strain, or variant, is the ancestor of all modern plagues we have today worldwide. Every outbreak across the globe today stems from a descendant of the medieval plague. With a better understanding of the evolution of this deadly pathogen, we are entering a new era of research into infectious disease.”

Johannes Krause, of the University of Tubingen, Germany, said:

“Using the same methodology, it should now be possible to study the genomes of all sorts of historic pathogens,” said Krause, one of the lead authors of the study. “This will provide us with direct insights into the evolution of human pathogens and historical pandemics.”

Pathogens today, which kill approximately 2,000 people annually, are direct descendants of the same bubonic plague.

Bubonic plague is a zoonotic disease – it can be transmitted from animals to humans – that circulates mainly among small rodents and the fleas that infest them. It is one of three types of infections caused by Yersinia pestis. Bubonic plague kills about two out of every three infected people within four days if they do not receive treatment.


Poinar said:

“We found that in 660 years of evolution as a human pathogen, there have been relatively few changes in the genome of the ancient organism, but those changes, however small, may or may not account for the noted increased virulence of the bug that ravaged Europe. The next step is to determine why this was so deadly.”

Biogenetic technology today makes the prospect of DNA recovery and sequencing of ancient specimens much more feasible, the authors explained. By understand how ancient pathogens have evolved, we are better able to understand the characteristics and traits of emerging and re-emerging infections.

Sharon DeWitte, of the University of South Carolina, Kirsten Bos, of McMaster University, and Verena Schuenemann, of the University of Tubingen analyzed what was left of the skeletons of victims in the East Smithfield “plague pits” in London. Since being buried there, the Royal Mint was built on top. They selected promising specimens, which they knew still had traces of Y. pestis after thorough screening, from the dental pulp of five victims.

The scientists managed to extract, purify and enrich the specimens so they could identify the plague DNA as opposed to DNA from fungal, human and other non-plague DNA.

They were able to calculate the age of the Yersinia pestis’ ancestor that caused the Black Death by linking the 1349-1350 dates of the skeletal remains to the genomic data.

The date coalesced at around the 12th to 13th centuries, meaning that earlier plagues were probably caused by another ancestor pathogen. Experts had previously believed that, for example, the Justinian plague of the 6th Century was caused by the same pathogen as the medieval Black Death. The Justinian plague is believed to have caused the death of about 100 million people globally – it spread east across the Eastern Roman Empire and kept on spreading.

Written by Christian Nordqvist