Scientific analysis of excavated skeletons in London has uncovered a macabre clue to their agonising death – and marked another first in the history of the capital.

Buried deep within the bones of bodies uncovered as part of the Crossrail line works at Liverpool Street, scientists have discovered traces of DNA from the bubonic plague.

The bodies were buried between 1650 and 1670, during the height of the last major outbreak of the dreaded plague – and now historians have another vital clue to its spread, impact and cause.

So quickly do plague victims fatally succumb to the illness that it has little chance to change the bone structure, offering little help to palaeopathologists.

MoLA senior archaeologist Don Walker Henderson examines the skeletons

Yet in this discovery, 20 individuals were tested for traces of the plague pathogen Yersinia pestis, and five were found to have been exposed to it – and due to its fatal grip, the plague is likely to be the cause of their death.

Professor of London History, Birkbeck, University of London Vanessa Harding said: “This is a very exciting finding. 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.”

Scientists at Max Planck Institute identify 1665 Great Plague DNA

Modern scientific techniques have allowed scientists at the Max Planck Institute in Jena , Germany, to isolate this DNA from teeth extracted from the skeletons. The enamel on the teeth acted as protective capsules, preserving the DNA of bacteria that was in the person’s bloodstream at the time of death.

It is the first identification of plague DNA from 17th century Britain – although the bacteria itself perished with its victims and is no longer active.

The discovery comes following a year-long study of skeletons found in a mass grave within the New Churchyard, the burial ground excavated by Museum of London Archaeology (MOLA) during construction of the new Elizabeth line station at Liverpool Street last year.

Museum of London Archaeologists examine a plague victim

Burial records confirm there was a rise in burial rates in the New Churchyard when the epidemic peaked in the summer of 1665 and historic records show how the graveyard struggled to cope with the numbers of the dead.

The Great Plague of 1665 killed an estimated 100,000 people in London, almost a quarter of the population.

Molecular palaeopathologists are now attempting to sequence the pathogen’s full DNA genome. In doing so they hope to be able to compare the 1665 Great Plague to the 1348 Black Death epidemic as well as recent modern outbreaks. This will allow scientists to further understand the evolution and spread of the disease.

Crossrail lead archaeologist Jay Carver said: “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.”

Excavation of the Bedlam burial ground, July 2015

In total 42 individuals were excavated from the mass grave but archaeologists estimate that it may have contained as many as 100 people.

The predominantly coffined burials were tightly packed in orderly rows that, over the centuries, collapsed in on each other as the coffins decayed. Although contemporary Plague Orders dictated that burials sit a minimum of 6ft from the surface, the top of the mass burial was only about 2ft from the surface. This was perhaps a matter of practicality for the gravediggers but “noisome stenches” were reported, eventually leading to burial restrictions.