Leprosy spread throughout America centuries before the arrival of Europeans

In 2017, biologist Nicolás Rascovan discovered something that made no sense. He was analyzing DNA extracted from the remains of people who had died thousands of years ago. In one of the samples taken in Canada, he found leprosy — one of the oldest and most stigmatizing diseases in history. But this was impossible, since all textbooks say that this disease was brought to America by the Spanish and Portuguese conquistadors.

Since then, Rascovan, a 41-year-old Argentine working at the Pasteur Institute in Paris, has been gathering DNA samples from many countries across the Americas to try to solve the mystery. On Thursday, after analyzing more than 400 samples from living people and almost as many from ancient remains, he presented the conclusion of his research: by the time Europeans arrived in America, leprosy had already been circulating for centuries among the Indigenous populations of the continent. The study, signed by 40 scientists from America and Europe, was published in Science, a benchmark of the world’s leading science.

The key to the discovery is that there are not one, but two major lineages of pathogenic bacteria that cause leprosy — a disease that, despite having a cure, still affects about 200,000 people every year in 120 countries.

Leprosy is caused by a bacterium that attacks the skin and nerves. If left untreated, it causes horrible wounds that disfigure the face or hands. For centuries, leprosy patients were treated as outcasts, marginalized and isolated in leper colonies that no one wanted to go near.

The new study is the most comprehensive to date on this pathogen, having examined ancient bone remains from various regions and clinical samples from Mexico, the United States, Brazil, Paraguay, and French Guiana. Most positive cases were detected in Mexico and the United States, which likely reflects a greater presence of the pathogen in those regions.

The strain analyzed in the new study is called Mycobacterium lepromatosis. The research shows that this pathogen was already affecting people in America more than 1,000 years ago and produced symptoms very similar to the better-known variant of the disease, associated with the bacterium M. leprae.

The study details that this American strain of leprosy spread rapidly across the continent, as they have found affected individuals from Canada to Argentina — over 600 miles apart — dating from a relatively recent period. It remains a mystery whether this spread occurred through animals acting as hosts or through human-to-human transmission, which would imply a dense network of communication and contact in pre-Columbian America.

The role of the conquistadors

The truth is that when the first Europeans arrived in America, they brought with them the better-known variant of leprosy, which then spread like many other imported diseases, causing significant damage to the local population. Today, this variant remains predominant in the American countries where leprosy still exists, including the United States. However, a few cases of infection with the native variant have also been detected.

“Until now, we barely knew what [diseases] people were getting before contact with Europeans,” Rascovan explains. “Now we’ve discovered that there’s the entire diversity of the leprosy bacteria on the continent, hidden somewhere, which has the potential to infect humans. We need to go out and monitor and understand where it’s hiding, in which animals or which humans, and what strategy it uses to keep evolving on the continent for 10,000 years.”

The leprosy bacterium does not grow in laboratories, which has traditionally complicated its scientific study. Researchers have had to sequence — i.e. read — the entire DNA of each sample and isolate the genetic fragments of the bacterium. Their results show that the two major branches of leprosy diverged between two million and 700,000 years ago. The study provides the first reference genome of this leprosy variant. One of the biggest questions is whether it arrived in America from Asia with the continent’s first inhabitants, or if it came earlier through animals and later started affecting people. This is the theory favored by Rascovan.

The study revealed a deeply divergent variant of M. lepromatosis that still infects people in the United States. This lineage differs from all other known strains by a significantly greater number of mutations and is estimated to have separated from the rest more than 9,000 years ago.

The research also uncovers another mystery about this variant of leprosy. One of the few places outside America where this new variant has been found is the United Kingdom and Ireland. It was not found in human remains or living people but in red squirrels. Researchers also analyzed the genome of these strains and believe the bacterium arrived in the British Isles in the 19th century. Again, how it got there is unknown: it could have been through the introduction of American squirrels or infected humans.

The study’s authors emphasize that this project was carried out in collaboration with Indigenous communities from North and South America, who actively participated in some cases. The genetic data generated was made available to descendant communities through ethical data-sharing platforms.

Íñigo Olalde, a geneticist at the University of the Basque Country in Spain, who did not participate in the study, highlights the value of the new work. “It’s a good scientific study that should make us think about all the unproven assumptions we have about diseases in the Americas before and after the arrival of Europeans,” he says. The study is also interesting because it provides the first reference genome of this new variant, which Olalde adds, “is key to understanding it.”

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