A bacterial strain that is now extinct has been identified as the cause of the devastating Black Death plague in the 14th century.
The Black Death is estimated to have killed 30 to 50 million Europeans or about a third of Europe’s population between 1347 to 1351, after spreading there from China and the Middle East, making it one of the worst pandemics in human history.

The type of DNA analysis traditionally used in archeology, forensics, and genetic screening is polymerase chain reaction or PCR, which amplifies short sequences of DNA, that are later pieced together. The problem is that DNA degrades over time, so that ancient DNA tends to be in very small fragments that are difficult to piece together.

"It’s like taking Wikipedia and chopping all the words into two-letter words and then trying to reassemble it,” said McMaster University researcher Hendrik Poinar.

More recently, researchers have developed a technique called targeted enrichment.

“It's like a fishing rod that has bait specific for a type of fish,” Poinar said.
A "rod" designed specifically to hunt for the bacterium Yersinia pestis will pull up many small, overlapping pieces from different parts of the genome of that bacterium. By adjusting the temperature, the researchers can control how precisely the rod targets it "prey." If the temperature is very high, only a perfect match to the DNA of one particular strain will stick. But if the temperature is lowered slightly, similar DNA strains will also get attached.

"It’s a balancing act," Poinar said. "You can’t make it so stringent that you don’t catch differences and you can’t make it too loosey goosey so you catch everything under the sun.”

Now, based on a DNA analysis study led by anthropologist Hendrik Poinar of McMaster University in Hamilton and archeologist Johannes Krause at the University of Tubingen in Germany has concluded the pandemic was caused by a now-extinct strain of Yersinia pestis, the bacterium that causes bubonic plague.
The results were published Monday in an article in the Proceedings of the National Academy of Sciences. The lead authors are Verena Schuenemann at the University of Tubingen in Germany and Kirsten Bos, a graduate student at McMaster University.

While some researchers have always thought Yersinia pestis could be responsible for the Black Death, others had argued it couldn't be.
"It’s been a big controversy in the literature for many, many years," said Poinar in an interview Tuesday. "The rate and speed and death, mortality that it caused just seemed contrary to what we know about modern bubonic plague.”
There are still 2,000 cases of bubonic plague worldwide each year, but it spreads slowly via flea bites. The quick spread of the Black Death suggested that disease was airborne.

To settle the question, the researchers analyzed DNA from 109 human skeletons at the East Smithfield mass grave site in London, England, where Black Death victims were known to be buried.

Co-authors Bos and Sharon DeWitte "were over there pulling teeth out of the jaws of these individuals, then drilling root pulp out of the teeth, and then replacing the teeth back into the jaws,” Poinar recalled.

The samples were initially taken back to McMaster University, where Bos painstakingly searched for Yersinia pestis DNA among the massive amount of other DNA in the sample from humans, plants, fungi and other bacteria. She consistently found it in the bones of teeth in some victims.
On other other hand, she did not find Yersinia pestis samples from a nearby mass grave site that did not contain Black Death victims, suggesting that it was in fact linked to the Black Death.

Rather than using polymerase chain reaction (PCR), the common genetic technique used for forensics and DNA testing, the researchers used very new techniques called targeted enrichment and high-throughput sequencing. Those allow researchers to reconstruct long sequences of ancient, damaged DNA that have degraded over time.

"The technology’s changed," Poinar said. "That’s the only reason we were able to do it.”
Using that technique, the researchers identified a strain of Yersinia pestis that contains the same loop of DNA called a plasmid, found outside the bacterium's main chromosome, that is responsible for virulence in the modern strain. Because of their similarities, the researchers don’t believe that that particular loop was responsible for the Black Death strain’s exceptional virulence.

However, a quick look at the bacterium's main chromosome showed the Black Death strain did contain several unusual genetic characteristics to the researchers' knowledge, “are not found in any previously reported modern or ancient sequence” for the bacterium.

Poinar acknowledged that the study doesn't rule out the possibility that the Black Death bacterium co-operated with another pathogen to create "the perfect storm."
It also doesn't indicate why the strain was so deadly compared to others. The researchers hope to figure that out in the next stage of research.

"If we sequence the entire bug, we can actually look very specifically at changes that have occurred on its lineage," Poinar said. "And that will hopefully help us understand, ‘Are there indeed added points of virulence that might explain why it was such a deadly outbreak?’”

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