Plague ancestor found in 5,000-year-old human remains

The study shows the relationship between humans and the plague goes back further than was realized.

  • By Deborah Netburn Los Angeles Times (TNS)
  • Thursday, December 6, 2018 4:32pm
  • Nation-World

By Deborah Netburn / Los Angeles Times

In an ancient grave in Sweden, scientists have unearthed the oldest known strain of a deadly bacteria that has killed millions of people over thousands of years.

They call it Yersinia pestis. You may know it as the plague.

The new discovery suggests that the microscopic bacteria has been wiping out great swaths of the human population for more than 5,000 years — destroying empires, spurring political uprisings and leaving a permanent mark on regional gene pools.

“What we found in the Swedish grave site is not only the oldest sample of the Y. pestis genome but also the oldest version of the genome,” said Simon Rasmussen, a metagenomics researcher at the Technical University of Denmark, who led the work. “Think of it as the root of the tree.”

The oldest recorded plague pandemic, known as Justinian’s Plague, dates to 541 AD. Over the course of 200 years, it killed more than 25 million people across the Byzantine Empire, hitting the capital city of Constantinople especially hard.

The next major plague pandemic, known as the Black Death or the Great Plague, started in China in 1334 and spread along trade routes to Constantinople before reaching Europe in the 1340s. It also claimed the lives of an estimated 25 million people, including about half the population of Europe, according to researchers at the Centers for Disease Control and Prevention. Some towns weren’t left with enough survivors to bury the dead.

The third major outbreak, known as the Modern Plague, took root in China in the 1860s. It popped up again in Hong Kong in 1894 and spread to port cities around the world over the next 20 years, carried by stowaway rats on steamships. It was during this pandemic that scientists discovered the bacterial source of the disease, and that it is spread by fleas that pick it up from rats and pass it on to humans. Even with that knowledge, however, plague still managed to cause 10 million deaths.

Rat-associated plague can still be found in populations of ground squirrels and other small mammals in the Americas, Africa and Asia. It is now under control in most urban areas across the globe, and if it’s caught early enough, it can be treated with antibiotics. From 2010 to 2015, there were 3,248 human cases of plague reported worldwide and 584 deaths from the disease, according to the World Health Organization.

The new study, published Thursday in the journal Cell, reveals that the relationship between humans and plague goes back even further than scientists had realized. The bacteria identified by Rasmussen and his colleagues may represent a previously unknown outbreak of plague that struck Europe as much as 5,700 years ago.

The researchers already knew that the population of Europe plummeted 5,000 to 6,000 years ago, after it had grown for thousands of years. This sudden plunge is known as the Neolithic decline, and its cause is still up for debate.

Rasmussen and his colleagues wondered whether a plague pandemic could have been responsible.

“We were thinking, ‘Where have we seen this drop before?’ and that got us thinking about the Black Plague,” he said.

The disease was known to have existed across Eurasia at the dawn of the Bronze Age, which started around 4,500 years ago, but there was no evidence of its existence earlier than that.

To see if the plague was in Europe at the end of the Neolithic period, the group turned to databases of DNA extracted from ancient human remains — specifically, ancient teeth.

Because blood circulates through the center of our teeth, Rasmussen said, it is possible to detect the DNA of pathogens that were present in a person’s bloodstream at their time of death by examining a tooth sample.

“If you die from it and it’s in your blood,” he said, “then we can find it.”

After scanning for genetic sequences resembling modern-day Y. pestis, the group eventually found a match. It was in DNA extracted from the tooth of a 20-year-old woman who died in western Sweden between 5,040 and 4,867 years ago.

“This really surprised us,” Rasmussen said. “It was the oldest plague sample ever found.”

Next, the authors compared the newly discovered Y. pestis genome to 150 other plague samples that spanned thousand of years, going back all the way to the Bronze Age. This analysis revealed that the strain from the Swedish woman was closer to the origin of Y. pestis than any other, and therefore could inform scientists about the first plague ancestor from which all subsequent strains evolved, Rasmussen said.

How could this be? The Swedish woman lived in a small farming community, far from the center of the Neolithic world. Plague thrives in environments where large groups of people live in close quarters, share space with animals and stored food, and contend with poor sanitary conditions.

None of that explains how this woman contracted the disease.

So the researchers looked beyond genetics and considered the archaeological histories of human populations from the time period.

Although the young Swedish woman did not live in prime plague territory, there were other places in Europe where the disease could have flourished in the Neolithic era, Rasmussen said. These were the mega-settlements of the Trypillia Culture, built between 6,100 and 5,400 years ago and located in present-day Ukraine, Romania and Moldova. The largest of these settlements was home to as many as 20,000 people.

Archaeologists have shown that these settlements were abandoned and burned about once every 150 years. Usually, subsequent generations rebuilt right on the ashes of the previously destroyed buildings. Why the original structures were burned has never been explained.

Using the new findings as a guide, the researchers propose that the plague first evolved in these mega-settlements, morphing from a relatively benign stomach bug to a deadly microscopic killer around 5,700 years ago, around the time when the Swedish strain diverged from all others then in existence. This could explain the periodic burning of the buildings — perhaps they were set aflame to eradicate the disease.

The authors also suggest that the plague made its way from these settlements to the small Swedish farming village thanks to a vast trade network that was made possible by the recent expansion of animal-pulled wagons. As the disease spread along trade routes throughout the continent, it could have caused the Neolithic decline.

(EDITORS: STORY CAN END HERE)

It’s a good story, but not everyone is buying it.

“The report of the new strain is really interesting, but a connection to the Trypillia Culture is, from my perspective, not a given,” said Ben Krause-Kyora, a biochemist and archaeologist at Kiel University in Germany.

He noted that there was currently no evidence of Y. pestis from grave sites in the mega-settlements, nor have archaeologists encountered a sudden uptick in burials of the young and the elderly in those communities, as one might expect to see during a pandemic.

In addition, the increased use of the wheel would not necessarily have helped spread plague to the extent that the authors suggest, he said. The DNA sequence of the Y. pestis that was found in Sweden suggests it was not yet capable of being easily transmitted by fleas living on infected rats that might stow away on a cart. The strain present in the Neolithic Era would have spread from person to person at a much slower rate, so it wouldn’t have impacted great swaths of the population at once.

Johannes Krause, a biochemist and director of the Max Planck Institute for the Science of Human History in Germany agreed that there was not enough evidence to suggest the ancient strain evolved in the mega-settlements.

“This is wild speculation,” Krause said.

The authors concede they still have a lot more work to do to fortify their argument that they may have discovered the first plague pandemic.

“This is just what we have now based on the data,” Rasmussen said. “Of course there are many more things we would like to know.”

(EDITORS: STORY CAN END HERE)

For instance, turning up evidence of Y. pestis in one of the mega-settlements would strengthen their hypothesis, he said. It would also help to find the bacterium in other Neolithic communities across Europe, so they could create a more detailed picture of how the disease spread, and the extent of its impact on the population at the time.

In the meantime, the authors are already thinking about what to analyze next.

“There are a lot of ancient genomes coming out every month,” Rasmussen said. “And we could search for other pathogens as well. It’s just about looking.”

Talk to us

> Give us your news tips.

> Send us a letter to the editor.

> More Herald contact information.

More in Nation-World

FILE - Britain's Queen Elizabeth II looks on during a visit to officially open the new building at Thames Hospice, Maidenhead, England July 15, 2022. Buckingham Palace says Queen Elizabeth II is under medical supervision as doctors are “concerned for Her Majesty’s health.” The announcement comes a day after the 96-year-old monarch canceled a meeting of her Privy Council and was told to rest. (Kirsty O'Connor/Pool Photo via AP, File)
Queen Elizabeth II dead at 96 after 70 years on the throne

Britain’s longest-reigning monarch and a rock of stability across much of a turbulent century died Thursday.

A woman reacts as she prepares to leave an area for relatives of the passengers aboard China Eastern's flight MU5735 at the Guangzhou Baiyun International Airport, Tuesday, March 22, 2022, in Guangzhou. No survivors have been found as rescuers on Tuesday searched the scattered wreckage of a China Eastern plane carrying 132 people that crashed a day earlier on a wooded mountainside in China's worst air disaster in more than a decade. (AP Photo/Ng Han Guan)
No survivors found in crash of Boeing 737 in China

What caused the plane to drop out of the sky shortly before it was to being its descent remained a mystery.

In this photo taken by mobile phone released by Xinhua News Agency, a piece of wreckage of the China Eastern's flight MU5735 are seen after it crashed on the mountain in Tengxian County, south China's Guangxi Zhuang Autonomous Region on Monday, March 21, 2022. A China Eastern Boeing 737-800 with 132 people on board crashed in a remote mountainous area of southern China on Monday, officials said, setting off a forest fire visible from space in the country's worst air disaster in nearly a decade. (Xinhua via AP)
Boeing 737 crashes in southern China with 132 aboard

More than 15 hours after communication was lost with the plane, there was still no word of survivors.

Former Rep. Matt Gaetz, R-Fla., center, arrives at the U.S. Capitol in Washington D.C. with Sen. JD Vance, R-Ohio, right, the vice president-elect, on Wednesday morning. Gaetz withdrew from consideration Thursday, saying he was an unfair distraction to the transition. (Haiyun Jiang / The New York Times)
Matt Gaetz withdraws from consideration as attorney general

“It is clear that my confirmation was unfairly becoming a distraction,” Gaetz wrote Thursday on X.

Attendees react after Fox News called the presidential race for Former President Donald Trump, during an election night event at the Palm Beach County Convention Center in West Palm Beach, Fla., on Wednesday. Trump made gains in every corner of the country and with nearly every demographic group. (Haiyun Jiang / The New York Times)
Donald Trump returns to power, ushering in new era of uncertainty

Despite criminal convictions and fears of authoritarianism, Trump rode frustrations over the economy and immigration.

Voters cast their ballots at a polling place inside the Weisman Art Museum at the University of Minnesota in Minneapolis on Election Day, Tuesday, Nov. 5 2024. Voters headed into polling stations on Tuesday in the closing hours of a presidential contest that both major parties said would take the country in dramatically different directions, capping a contentious and exhausting 107-day sprint that began when President Joe Biden abandoned his bid for a second term.  (Caroline Yang/The New York Times)
Live updates: Georgia called for Trump

The Daily Herald will be providing live updates on national election developments throughout Tuesday.

Liam Payne performs during the Jingle Ball at Madison Square Garden in New York in 2017. Payne, who rose to fame as a singer and songwriter for the British group One Direction, one of the best-selling boy bands of all time, died after falling from the third floor of a hotel in Buenos Aires on Wednesday. He was 31. (Chad Batka / The New York Times)
Liam Payne, 31, former One Direction singer, dies in fall in Argentina

Payne rose to fame as a member of one of the bestselling boy bands of all time before embarking upon a solo career.

In this photo taken from video provided by the Ukrainian Presidential Press Office, Ukrainian President Volodymyr Zelenskyy speaks to the nation in Kyiv, Ukraine, Sunday, Feb. 27, 2022. Street fighting broke out in Ukraine's second-largest city Sunday and Russian troops put increasing pressure on strategic ports in the country's south following a wave of attacks on airfields and fuel facilities elsewhere that appeared to mark a new phase of Russia's invasion. (Ukrainian Presidential Press Office via AP)
Ukraine wants EU membership, but accession often takes years

President Volodymyr Zelenskyy’s request has enthusiastic support from several member states.

FILE - Ukrainian servicemen walk by fragments of a downed aircraft,  in in Kyiv, Ukraine, Friday, Feb. 25, 2022. The International Criminal Court's prosecutor has put combatants and their commanders on notice that he is monitoring Russia's invasion of Ukraine and has jurisdiction to prosecute war crimes and crimes against humanity. But, at the same time, Prosecutor Karim Khan acknowledges that he cannot investigate the crime of aggression. (AP Photo/Oleksandr Ratushniak, File)
ICC prosecutor to open probe into war crimes in Ukraine

U.N. human rights chief Michelle Bachelet confirmed that 102 civilians have been killed.

FILE - Refugees fleeing conflict from neighboring Ukraine arrive to Zahony, Hungary, Sunday, Feb. 27, 2022. As hundreds of thousands of Ukrainians seek refuge in neighboring countries, cradling children in one arm and clutching belongings in the other, leaders in Poland, Hungary, Bulgaria, Moldova and Romania are offering a hearty welcome. (AP Photo/Anna Szilagyi, File)
Europe welcomes Ukrainian refugees — others, less so

It is a stark difference from treatment given to migrants and refugees from the Middle East and Africa.

Afghan evacuees disembark the plane and board a bus after landing at Skopje International Airport, North Macedonia, on Wednesday, Sept. 15, 2021. North Macedonia has hosted another group of 44 Afghan evacuees on Wednesday where they will be sheltered temporarily till their transfer to final destinations. (AP Photo/Boris Grdanoski)
‘They are safe here.’ Snohomish County welcomes hundreds of Afghans

The county’s welcoming center has been a hub of services and assistance for migrants fleeing Afghanistan since October.

FILE - In this April 15, 2019, file photo, a vendor makes change for a marijuana customer at a cannabis marketplace in Los Angeles. An unwelcome trend is emerging in California, as the nation's most populous state enters its fifth year of broad legal marijuana sales. Industry experts say a growing number of license holders are secretly operating in the illegal market — working both sides of the economy to make ends meet. (AP Photo/Richard Vogel, File)
In California pot market, a hazy line between legal and not

Industry insiders say the practice of working simultaneously in the legal and illicit markets is a financial reality.

Support local journalism

If you value local news, make a gift now to support the trusted journalism you get in The Daily Herald. Donations processed in this system are not tax deductible.