The bacterium Yersinia pestis—the cause of pandemics commonly referred to as the plague or the Black Death—is responsible for the death of anywhere from 75–200 million people (in contrast the COVID-19 pandemic has killed roughly seven million people globally.) Y. pestis is spread through flea bites, causing either bubonic or septicemic plague, or through respiratory droplets—causing pneumonic plague.

There has been a lot of interest in the lineages of Y. pestis that have existed throughout history, which have been identified in several individuals from European and Asian areas between 5000 and 2500 years ago. One of these is termed the “LNBA lineage” (Late Neolithic and Bronze Age.)

Now, researchers at the Francis Crick Institute have identified three 4,000-year-old British cases of Y. pestis—the oldest evidence of the plague in Britain to date.

This work is reported in the paper, “Yersinia pestis genomes reveal plague in Britain 4000 years ago,” in Nature Communications.

The scientists took small skeletal samples from 34 individuals across two sites, a mass burial in Charterhouse Warren in Somerset and one in a ring cairn monument in Levens in Cumbria, screening for the presence of Y. pestis in teeth. This technique is performed in a specialist clean room facility where they drill into the tooth and extract dental pulp, which can trap DNA remnants of infectious diseases.

They then analyzed the DNA and identified three cases of Y. pestis in two children estimated to be aged between 10–12 years old when they died, and one woman aged between 35–45. Radiocarbon dating was used to show that it is likely the three people lived at roughly the same time.

“The ability to detect ancient pathogens from degraded samples, from thousands of years ago, is incredible,” noted Pooja Swali, a PhD student at the Crick. “These genomes can inform us of the spread and evolutionary changes of pathogens in the past, and hopefully help us understand which genes may be important in the spread of infectious diseases. We see that this Y. pestis lineage, including genomes from this study, loses genes over time, a pattern that has emerged with later epidemics caused by the same pathogen.”

Map showing the distribution of LNBA Yersinia pestis strains. New genomes sequenced in this study are in purple. [Pooja Swali et al. Nature Communications.]
The plague has previously been identified in several individuals from Eurasia between 5,000 and 2,500 years before present (BP), a period spanning the Late Neolithic and Bronze Age (LNBA), but hadn’t been seen before in Britain at this point in time. The wide geographic spread suggests that this strain of the plague may have been easily transmitted.

This strain of the plague—the LNBA lineage—was likely brought into Central and Western Europe around 4,800 BP by humans expanding into Eurasia, and now this research suggests that it extended to Britain.

Using genome sequencing, the researchers showed that this strain of Y. pestis looks very similar to the strain identified in Eurasia at the same time.

The individuals identified all lacked the yapC and ymt genes, which are seen in later strains of plague, the latter of which is known to play an important role in plague transmission via fleas. This information has previously suggested that this strain of the plague was not transmitted via fleas, unlike later plague strains such as the one that caused the Black Death.

“This research is a new piece of the puzzle in our understanding of the ancient genomic record of pathogens and humans, and how we co-evolved,” noted Pontus Skoglund, PhD, group leader of the Ancient Genomics Laboratory at the Crick. “We understand the huge impact of many historical plague outbreaks, such as the Black Death, on human societies and health, but ancient DNA can document infectious disease much further into the past. Future research will do more to understand how our genomes responded to such diseases in the past, and the evolutionary arms race with the pathogens themselves, which can help us to understand the impact of diseases in the present or in the future.”

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