Media playback is unsupported on your device Media caption First look at a Great Plague skeleton

DNA testing has for the first time confirmed the identity of the bacteria behind London's Great Plague.

The plague of 1665-1666 was the last major outbreak of bubonic plague in Britain, killing nearly a quarter of London's population.

It's taken a year to confirm initial findings from a suspected Great Plague burial pit during excavation work on the Crossrail site at Liverpool Street.

About 3,500 burials have been uncovered during excavation of the site.

Testing in Germany confirmed the presence of DNA from the Yersinia pestis bacterium - the agent that causes bubonic plague - rather than another pathogen.

Some authors have previously questioned the identity of microbes behind historical outbreaks attributed to plague.

Daniel Defoe's 18th century account of the catastrophic event in A Journal of the Plague Year described the gruesome fate of Londoners.

"The plague, as I suppose all distempers do, operated in a different manner on differing constitutions; some were immediately overwhelmed with it, and it came to violent fevers, vomitings, insufferable headaches, pains in the back, and so up to ravings and ragings with those pains," Defoe wrote.

Image copyright Hulton Archive Image caption The Great Plague killed about a quarter of the capital's population

"Others with swellings and tumours in the neck or groin, or armpits, which till they could be broke put them into insufferable agonies and torment; while others, as I have observed, were silently infected."

Evidence of the pathogen had eluded archaeologists but seemed tantalisingly close when a suspected mass grave was discovered last year during a Crossrail dig at the Bedlam burial ground, also known as the New Churchyard, in East London.

Alison Telfer from Museum of London Archaeology (Mola) showed me around the area planned for one of the downward escalators going into the future Broadgate ticket hall at Liverpool Street.

"We've found about three-and-a-half thousand burials on this site," she told the BBC's Today programme.

"We've been working here for the last five-and-half-years on and off and we're hoping we'll be able to get positive identification of the plague on a number of the individuals.

Image copyright Crossrail Image caption More than 3,500 burials have been uncovered at the site

"Because of the position of the skeletons, they'd obviously been laid in coffins & put in very respectfully, nobody was thrown in anywhere in presumably what must have been quite a traumatic event."

This revelation is somewhat at odds with Daniel Defoe's version of events: "Tis certain they died by heaps and were buried by heaps; that is to say, without account." Panic and disorder only came towards the end of The Great Plague.

Vanessa Harding, professor of London history at Birkbeck, University of London, describes the experience of Londoners at the time.

"Not many people who actually get it survive but some do. And it seems to be quite easily transferred from person to person even if we're not sure currently about the agency or way in which this actually happens," Prof Harding said.

Image copyright Hulton Archive Image caption Daniel Defoe wrote that plague victims "died by heaps and were buried by heaps"

"But there are also what we might consider public health measures which from their point of view include killing cats and dogs, getting rid of beggars in the streets, trying to cleanse the city in both moral and practical terms. The people who do best are those who get out of London."

The search for the bacteria Yersinia pestis, which causes plague, in a selection of skeletons from the dig continued last year in the osteology department at Mola where all the Liverpool Street finds were stored and examined by Michael Henderson.

"They're carefully boxed, individual elements, legs separately, arms separately, the skulls and the torsos," he explained.

"We excavated in the region of three and a half thousand skeletons, one of the largest archaeologically excavated to this date. A vast data set that can give us really meaningful information."

Image copyright Crossrail Image caption DNA from the London remains was analysed at the Max Planck Institute for the Science of Human History in Germany

The bones are laid out in anatomical order. Teeth are removed and sent for ancient DNA analysis at the Max Planck Institute for the Science of Human History in Jena, Germany. "The best thing to sample for DNA is the teeth; they're like an isolated time capsule," said Mr Henderson.

In Germany, molecular palaeopathologist Kirsten Bos drilled out the tooth pulp to painstakingly search for the 17th century bacteria, finally obtaining positive results from five of the 20 individuals tested from the burial pit.

"We could clearly find preserved DNA signatures in the DNA extract we made from the pulp chamber and from that we were able to determine that Yersinia pestis was circulating in that individual at the time of death," she said.

"We don't know why the Great Plague of London was the last major outbreak of plague in the UK and whether there were genetic differences in the past, those strains that were circulating in Europe to those circulating today; these are all things we're trying to address by assembling more genetic information from ancient organisms."

Image copyright Crossrail Image caption A nearby gravestone marks the passing of Mary Godfree, a plague victim

Bos and her team will now continue to sequence the full DNA genome to better understand the evolution and spread of the disease.

There was nothing to identify those found in the mass grave under the Crossrail development but located a short distance away a headstone was found inscribed with the name Mary Godfree who fell victim to the plague. Her interment is recorded in the burial register of St Giles, Cripplegate, on 2 September 1665.

To reassure anyone worried whether plague bacterium was released from the excavation work or scientific analysis, it doesn't survive in the ground.</s>It wiped out nearly a quarter of London's population and was one of the triggers for the scientific renaissance that swept England in the 17th Century.

Now the bacteria that caused the Great Plague of London between 1665 and 1666 has been definitively identified as the bug that causes bubonic plague - Yersinia pestis.

Archaeologists used DNA testing on skeletons found in a mass grave in a churchyard uncovered during the construction of the new Crossrail Elizabeth that will run through the city's Liverpool Street Station.

Around 42 bodies were discovered in the pit, where they had been stacked up to eight deep and once would have been in coffins and wrapped in shrouds.

It is thought the pit may have contained up to 100 individuals although some of the pit had been disturbed by building work during the 19th and 20th Century.

Scientists took samples from the teeth 20 of the skeletons to search for traces of the plague pathogen.

They found five appear to have been exposed to it before they died and the researchers believe this is most likely to be the cause of death.

Scientists now hope to sequence the whole genome of the plague bacteria in the hope of comparing it to those responsible for the Black Death epidemic in 1348.

The research could help provide new insights into the evolution of the disease as it spread around Europe over several centuries.

Professor Vanessa Harding, an expert in London history at Birkbeck, University of London, said: 'This is a very exciting finding, for the history of London, the history of disease, and the history of burial.

'It confirms that Yersinia pestis was present in early modern London plague epidemics, and links them epidemiologically with the 14th-Century Black Death and the 1720 Marseille plague.

'We still need, however, to understand why the disease manifested itself in so many different ways, and whether other pathogens made a significant contribution to these epidemics.'

While Yersinia pestis has long been suspected as the cause of the Great Plague in the 17th Century, the new findings are the first to confirm it definitively.

It was the last major bubonic plague epidemic to have hit Britain and killed around 100,000 people in London.

The total death toll is likely to have been far higher, however, as many town and cities around England were hit far worse than London.

An account by Thomas Vincent in God's Terrible Voice in the City by Plague and Fire, describes London in August 1665.

He said: 'Now the cloud is very black, and the storm comes down upon us very sharp.

'Now Death rides triumphantly upon his pale Horse through our streets, and breaks into every house almost, where any inhabitants are to be found.

'Now people fall as thick as leaves from the Trees in Autumn, when they are shaken by a mighty wind.

'Now there is a dismal solitude in London-streets…Now we could hardly go forth, but we should meet with many Coffins, and see many with sores, and limping in the streets.'

Burial registers show there was a dramatic increase in burials at the New Churchyard, also called the Bedlam burial ground, in Liverpool Street in 1665.

Last year archaeologists unearthed a 7.5 feet wide pit at the site filled with bodies.

Samples were taken from the teeth of some of those found there because the enamel of teeth helps to protect DNA after death.

This means they can serve as time capsules, preserving genetic information that was circulating in an individual's blood stream at the time of death.

The DNA was sent to experts at the Max Planck Institute for the Science of Human History in Jena, Germany.

In 2014 skeletons excavated during the construction of another part of the Elizabeth line at Farringdon were found to contain traces of DNA from Yersnia pestis.

These individuals are though to have died in Europe's first major plague epidemic in 1348.

Researchers hope that further analysis of the new DNA may be able to answer questions about the relationship between the 17th Century Great Plague and the 14th Century Black Death.

They say it could also help to reveal whether these plague outbreaks, and other smaller ones around the same time, were part of a single wave or several as a result of trade from Asia.

Previous work on victims in Germany, Spain and Russia has suggested the Black Death and the Great Plague was caused by a single strain of bacterium.

Professor Harding added: 'The excavation also underlines the strength of custom and order in time of crisis, showing that plague burial, even in mass graves, could be controlled and orderly, with bodies in coffins laid neatly on each other – not quite the shambolic 'plague pit' of popular discourse.'

Among the other items found at the site of the mass grave were a headstone, reused in a wall later, which belonged to a plague victim named Mary Godfrey, who died in 1665.

The mass grave is one of around 3,300 burials that have been uncovered during excavations at the New Churchyard.

Most of those who were found in the mass burial pit, however, were young people under the age of 17-years-old.

Don Walker, senior osteologist at the Museum of London Archaeology, which as been leading the excavations, said identifying the bacteria responsible for the deaths was a major step forward in understanding the disease.

He said: 'This discovery has the potential to greatly enhance scientist's understanding of the disease and coupled with detailed research of the skeletons reveal more about this devastating epidemic and the lives of its victims.'

Crossrail has conducted an extensive archaeology programme during the construction of the new line.

To date it has found more than 10,000 artefacts and fossils spanning 55 million years of London's past.

Jay Carver, Crossrail lead archaeologist, said: 'The Crossrail project has given archaeologists a rare opportunity to study previously inaccessible areas of London.

'The discovery of the ancient DNA, which has eluded scientists for so long, is yet another piece of the jigsaw that we are piecing together to learn more about the lives and deaths of 16th to 18th Century Londoners.'</s>(CNN) In 1665, the Great Plague of London killed more than 75,000 people in the space of a year, almost a quarter of the city's population back then. It caused 8,000 deaths per week during its peak in September 1665.

To date, scientists and archaeologists alike have been unable able to state assuredly that the disease behind the deaths was in fact the Bubonic Plague -- until now.

DNA sequenced from ancient skeletons dating back to the 17th century was found to match that of the bacteria responsible for the plague, known as Yersinia pestis. The bacteria typically live in fleas found on small animals and rodents, such as rats, which can jump onto humans and bite them to spread the bacteria. Infections typically cause flu-like symptoms, sudden fever and chills, body aches and vomiting, killing up to 60% of people if left untreated.

"For the first time, we understand what caused the 1665 plague," said Don Walker, senior human osteologist at the Museum of London Archaeology , who led the excavation. "No one really knew what caused it."

More than 3,300 burials were uncovered in 2015 at the site known as the Bedlam burial ground, near Liverpool Street station in London, within the New Churchyard archaeological site. They were discovered during the development of the new Elizabeth Line , part of the capital's Crossrail line, due to start running in 2018. Within the grounds, the teams soon found a mass grave containing 42 skeletons of people suspected to be victims of the Great Plague of London.

"We were hoping to find a plague pit, and we did," Walker said. "As we knew that the cemetery covered the period of outbreaks of the plague."

Fragments of pottery, glass and coffins found in the grave were used to date the grounds to between 1650 and 1670, confirming that this was in fact a " plague pit ," -- or at least, suspected to be until DNA proved otherwise. Though many historians assumed that the large-scale deaths were caused by the plague, this is the first time evidence has become available to prove it. "The only way you'd know is through DNA," said Walker.

"This is a very exciting finding, for the history of London, the history of disease, and the history of burials," added Vanessa Harding, professor of London history at Birkbeck University of London.

Finding and sequencing the DNA of these skeletons, which were more than 300 years old, is no easy task, namely because the availability of any DNA to work with is limited. Any Yersinia bacteria on the surface of the skeletons would have died long ago, meaning scientists had to extract DNA from teeth, where enamel helps protect and preserve DNA with less risk of contamination.

"You get much less DNA and need to amplify it," explained Walker.

Scientists from the Max Planck Institute in Jena, Germany, analyzed DNA extracted from 20 skeletons found in the mass burial pit, as well as 20 skeletons from other parts of the burial ground to compare. Traces of plague bacteria were found in five of the skeletons sampled from the mass burial pit, with the remaining 15 thought to have lost their traces. The quick fatality of the bacteria means there is less time for them to flourish, and then stay on human remains; DNA has an even lower survival rate when buried in the ground.

Zero traces were seen in those acting as a control group.

"The discovery of the ancient DNA, which has eluded scientists for so long, is yet another piece of the jigsaw that we are piecing together to learn more about the lives and deaths of 16th to 18th century Londoners," said Jay Carver, the lead archaeologist at Crossrail.

The team behind this research believes the DNA of these 300-year-old bacteria could help us understand more about plague infections past and future.

"[This finding] confirms that Yersinia pestis was present in early modern London plague epidemics, and links them epidemiologically with the 14th-century Black Death and the 1720 Marseille Plague," said Harding. "We still need, however, to understand why the disease manifested itself in so many ways, and whether other pathogens made a significant contribution to these epidemics."

Historically, the disease spread rapidly and had a high fatality rate, but today's infections appear to be contracted less easily and spread more slowly. This change in its epidemiology was why some experts questioned whether the Great Plague of London was caused by the same disease.

"Looking at the DNA ... could help tell us why the disease has changed in this way," said Walker. "It's important for historical research, but will hopefully also contribute to modern medical research."</s>INTERNATIONAL NEWS - DNA testing has for the first time confirmed the identity of the bacteria behind London's Great Plague.

The plague of 1665-1666 was the last major outbreak of bubonic plague in Britain, killing nearly a quarter of London's population.

It's taken a year to confirm initial findings from a suspected Great Plague burial pit during excavation work on the Crossrail site at Liverpool Street.

About 3,500 burials have been uncovered during excavation of the site.

Daniel Defoe's 18th century account of the catastrophic event in A Journal of the Plague Year described the gruesome fate of Londoners.

"The plague, as I suppose all distempers do, operated in a different manner on differing constitutions; some were immediately overwhelmed with it, and it came to violent fevers, vomitings, insufferable headaches, pains in the back, and so up to ravings and ragings with those pains," Defoe wrote.
German scientists confirm that the cause of the Great Plague of London from 1665–1666 was Yersinia pestis (cause of the Bubonic plague).