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[Série] “The missing genome”: pathogens from beyond the grave

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Ancient DNA reveals well-kept secrets on migrations, evolution and interbreeding of human populations, but also on the history of pathogens and animals. Second article in a series on the sparkling science that is paleogenomics.

The scene takes place at the beginning of the 13th centuryAnd century on the territory of the Byzantine Empire, more precisely in Troy, in present-day Turkey. A pregnant woman, around 30, gives birth to a child. This new mother, however, is ill; she suffers from a high fever. She does not survive the birth, just like her baby, who is also affected by the infection, who dies before he is even born.

Stories like this, humanity has known since the dawn of time. What disease took these two lives away? Thanks to science, this little Trojan tragedy is now the subject of unprecedented understanding. The example illustrates the power of paleogenomics to rewrite the history of pathogens. A story inextricably linked to ours.

“Ancient DNA opens a window on a completely unexplored past, for which we have no historical evidence. Otherwise, you can’t look at a bone and know that the person it belonged to died of a bone infection. E.colifor example, it’s simply impossible, ”says Hendrik Poinar, director of the Center for Ancient DNA at McMaster University in Hamilton, Ontario, in awe.

In 2017, Professor Poinar and his colleagues published an article detailing the sad fate of the Trojan mother, who until then had been a mere skeleton. They got there because the bones of the deceased had two small calcified nodules – abscesses, probably – rich in organic matter.

The analyzes revealed the presence of the woman’s DNA, her fetus, but also of two bacteria: one typical of pregnancy-related infections (Vaginal Gardnerella), the other most associated with urinary tract infections (Staphylococcus saprophyticus). The genome of the second bacterium differs greatly from the strain of S. saprophyticus that circulates in humans today, but comes close to that which affects livestock. Scientists thus deduced that one day this bacterium had “jumped” from cows to humans.

“All of these findings come from a very small sample of one cubic centimeter,” says Poinar. Without these methods, we would never have had this kind of information on women’s health at the time. I think it really is cold. Only a handful of laboratories in the world know how to conduct such experiments.

Pathogen bestiary

cholera, malaria, E.coli : numerous pathogens in recent years have revealed their secrets to geneticists who know how to decipher their DNA.

The latest example to date: a team based at the Max-Planck Institute for Evolutionary Anthropology, Leipzig, proposed in an article published in mid-June in Nature geographical and temporal origin of the bacterium Yersinia plagueresponsible for the Black Death, which carried half of the European population to the afterlife in the 14th centuryAnd century.

The research team analyzed DNA from teeth found in a cemetery in Kyrgyzstan. The tombs – dated 1338 and 1339, seven and eight years before the arrival of the Black Death in Europe – indicate in Syriac that the victims were carried away by the “plague”. The genetic material of Yersinia plague preserved between their teeth appears to be the basis of the different strains that emerged later. Logical conclusion: this is where the genesis of the terrible pandemic of the Middle Ages lies.

Diseases such as the Black Death have had a profound impact on human evolution. Hendrik Poinar is also participating in a major research project, the results of which are about to be published, showing which human genes have been favored or disadvantaged by Yersinia plague. The team compared the genomes of individuals who died before, during and after the terrible episode of the 14thAnd century.

A similar study, but concerning tuberculosis, was published in 2021 by the team of Franco-Spanish geneticist Lluis Quintana-Murci. These scientists showed that a genetic mutation that predisposes humans to tuberculosis had significantly decreased in frequency (from 10% to 2-4%) over two millennia in Europe. There is a strong pressure of natural selection, they say.

Smallpox and vaccinia

Marie-Hélène B.-Hardy, a Quebec doctoral student working in Professor Poinar’s laboratory, is studying smallpox outbreaks in North America in the 1800s.And and XIXAnd centuries. “We are looking at the interrelation between the evolution of this virus and the evolution of public health policies,” explains the man who joined this internationally renowned team four years ago.

To do this, it relies on two major collections of human remains from Montreal and Philadelphia. The skeletons were mainly recovered during the “rescue excavations”, organized for example on the sidelines of an excavation made necessary by a construction site.

In some cases, like when the coffins are painted red, archaeologists are pretty sure it was smallpox that killed. But most of the time, they have to cross their fingers to find the infamous virus that causes it. And if they can’t find it, that doesn’t mean it wasn’t there. “With ancient DNA, the absence of evidence is not evidence of absence,” says M.myself B.-Hardy.

For the time being, the PhD student hasn’t found any genetic traces of smallpox in her samples, but she remains confident. The characterization of some strains would allow him to understand how the disease landed in North American cities: by sea or by internal trade routes? He also analyzes the historical vaccinia strains (responsible for “cowpox”), which were used in the 18th centuryAnd and XIXAnd centuries to immunize populations.

From plague to small colds

Paleogenomics helps better understand diseases of historical importance, such as smallpox – which decimated Native American populations when Europeans arrived – and the Black Death, but Poinar also hopes the scientific community will benefit from this powerful. science to probe the history of harmless diseases.

“What interests me very much, he says, is the burden imposed by diseases for which we have no historical records. We already know how terrible the plague was. However, we know next to nothing about the common pathogens that have affected humans on a large scale; however these are probably responsible for most of the deaths in history. “

“I’m not arguing that ancient DNA is the only way to discover the past,” he continues, “but I think it’s a particularly powerful tool for finding out which insects made humanity sick and what their genome was.” We can also test the virulence and genome toxicity of these pathogens in the laboratory. Understanding their evolutionary trajectory helps us know what the future holds. “

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