In laboratories thousands of miles apart, scientists are poring over centuries-old DNA. Using the latest technology, they are searching for answers to a mystery that has haunted historians for hundreds of years. In the 16th century a deadly epidemic swept through Guatemala and Mexico – killing millions of Aztecs in the last days of their empire. And now, researchers are edging closer to finding out exactly what caused it.
Since its discovery in the 1860s, DNA has proved an invaluable tool to scientists across countless disciplines. However, its usefulness has been limited for those who work with human remains. In fact, up until recently, it has been almost impossible for researchers to extract DNA from skeletons.
But now, thanks to advanced methods of detection, researchers are now able to track traces of DNA in humans who have been dead for hundreds of years. And in the case of the Aztec Empire, this breakthrough may help to solve the mystery at last. By studying the teeth of people who lived in Mexico during the 16th century, scientists believe that they may have identified the culprit behind the deadly epidemic.
We’ll examine just what the scientists discovered about the fall of the Aztecs a little later, but let’s first learn a bit more about the people themselves. From its origins in the Valley of Mexico, the Aztec Empire grew to encompass much of what is now central Mexico. Stretching as far as modern-day Guatemala, the civilization was home to some six million people at its peak. And a population of over 140,000 thrived in its capital Tenochtitlán alone.
However, the glory days of the Aztec Empire were not to last. And in 1519 the Spanish conquistador Hernán Cortés landed on the shores of Yucatán. For the next two years, the Europeans waged a campaign of war and violence against the region’s indigenous inhabitants – before eventually emerging victorious in 1521.
According to historians, however, it wasn’t just their superior weapons that allowed the Spanish to conquer the Aztec Empire. Gruesomely, they were aided in their efforts by a smallpox epidemic which is widely believed to have killed up to eight million people. And with their populations decimated, the cities soon succumbed to the European invasion.
Although it had not been intentional, the Spanish had carried a deadly weapon with them to the Americas. With no natural immunity, the indigenous people of Mexico were particularly vulnerable to the European disease. And sadly, it would not be the last time that an epidemic would kill large numbers of the Aztec population.
As the Aztecs adjusted to life under Spanish rule, they were dealt another tragic blow. Just two decades after smallpox killed millions, another deadly epidemic swept through the remaining population. Dubbed cocoliztli – which means pestilence in Nahuatl – it spread across Central America at an alarming rate.
For the five years from 1545 it’s estimated that as many as 15 million people died after contracting the disease. To put that number in context, that amounted to around 80 percent of the Aztec population at the time. And although most of the victims were in the regions now known as Mexico and Guatemala, some experts believe that the affliction reached as far as Peru.
With such a high death toll, this tragic event ranks among the deadliest epidemics ever encountered in human history. In fact, the disease killed over half as many as the Black Death – which famously wiped out much of western Europe two centuries before. But despite its significance, the former contagion remained a mystery to modern science.
According to reports, the symptoms of the disease were alarming. Unfortunate victims would begin bleeding from multiple orifices, such as the nose, mouth and eyes. And those with the condition would then die within days of exhibiting these warning signs.
In 1576 Fray Juan de Torquemada, a Spanish missionary active in Mexico, penned a vivid description of the mysterious condition. He wrote, “The fevers were contagious, burning, and continuous, all of them pestilential – in most part lethal.”
“The tongue was dry and black,” Torquemada continued in his description of those with the bug. He added, “[They had an] enormous thirst, urine of the colors sea-green, vegetal-green, and black – sometimes passing from the greenish color to the pale. Pulse was frequent, fast, small, and weak – sometimes even null. The eyes and the whole body were yellow.”
According to Torquemada, once the initial stage of the condition had passed, victims often succumbed to “delirium and seizures.” Then, more symptoms would later develop. He continued, “Hard and painful nodules appeared behind one or both ears along with heartache, chest pain, abdominal pain, tremor, great anxiety and dysentery.”
Other sources, meanwhile, reported that people with the mystery bug experienced vomiting and developed reddish spots on their skin. But while contemporary physicians would have been aware of disorders such as malaria and measles, they believed that this was something new. And for hundreds of years, researchers have remained baffled by the identity of the strange affliction.
As time passed, the stricken Aztec people came no closer to understanding the illness that tore through their population. Instead, all they could do was dispose of the dead and wait for the carnage to end. Eventually, five years after it had began, the epidemic slowed down – but it did not completely disappear.
Tragically, some 25 years after the end of the first epidemic, the bug returned. And over the course of the next two years, it wiped out around 50 percent of the remaining Aztec population. At the time, Torquemada described the effect that this second disaster had on the land now occupied by the Spanish Empire.
“In the year 1576 a great mortality and pestilence that lasted more than a year overcame the Indians,” Torquemada wrote. “It was so big that it ruined and destroyed almost the entire land. The place we know as New Spain was left almost empty.” And elsewhere, the missionary also described how the local inhabitants attempted to deal with the disease.
“In the cities and large towns, big ditches were dug, and from morning to sunset the priests did nothing else but carry the dead bodies and throw them into the ditches,” Torquemada wrote. But despite the mounting death toll, physicians grew no closer to understanding the mysterious disease. Eventually, it simply petered out – although smaller outbreaks occurred in 1736 and 1813.
Over the years, scientists and historians have proposed a number of explanations for the deadly cocoliztli outbreaks of the 16th century. Some believe, for example, that the epidemic was caused by one of the diseases already known to have been brought over by the Spanish. However, neither smallpox, typhus or measles seem likely contenders.
But others have theorized that the epidemic could have been caused by a condition such as influenza or pneumonic plague. And some experts have suggested that a type of viral hemorrhagic fever could have been behind the millions of deaths. However, up until recently, no definitive conclusions had ever been reached.
Then in January 2018 a study appeared in the scientific journal Nature, Ecology and Evolution. In it, a team of researchers from various academic institutions revealed the results of a fascinating study. The team had used new technology to uncover some significant revelations about the cocoliztli epidemic.
In order to get to the bottom of the mystery, researchers studied two deposits of human remains. One set, consisting of 24 skeletons, was unearthed from a burial ground used during the cocoliztli outbreak. However, an additional five came from a cemetery that predated the Spanish conquest – allowing the team to compare and contrast the two.
Historically, it has been difficult for researchers to extract DNA from human remains such as these. But new advances in technology have opened up many possibilities. Using software known as the MEGAN Alignment Tool (MALT), the team could analyze molecules extracted from the teeth of the dead.
One of the authors of the study, Åshild Vågene, explained the process to The Independent in 2018. She said, “This is ground-breaking for our field of ancient DNA. It allows us to screen for all pathogens that we know today without having to specify a target organism. We can look for the unknown, which is wonderful.”
To begin with, researchers used MALT to generate a list of every bacteria that was present in the teeth. Then, one expert examined the data manually to determine if anything cropped up regularly. And eventually, they identified one particular strain that was present in ten cases – Salmonella enterica.
Vågene told The Independent, “Ancient DNA doesn’t always preserve very well. It breaks down over time. So to be able to find it in ten out of 24 is significant.” But what exactly does the presence of Salmonella enterica mean in terms of understanding cocoliztli?
According to experts, Salmonella enterica could have caused enteric fever – a condition characterized by vomiting, fever and a rash. Furthermore, while that particular strain is uncommon in the 21st century, it is similar to the Salmonella that still spreads through communities today.
The Salmonella bacteria typically infects humans through food and water that has been contaminated. And in the past, experts believed that it was spread in much the same way. For people living in overcrowded conditions, it can easily spell disaster – although it has never been known to cause an epidemic quite as serious as cocoliztli.
For her part, Vågene has highlighted that the location of the bacteria in the skeletons implies that the victims were badly infected. She told The Independent, “Salmonella is a disease that you would normally catch through contaminated food or water sources. It would start in the gut, so finding it in the teeth suggests it had got into the bloodstream. The [condition] had spread everywhere in their body.”
But how did this deadly strain of Salmonella arrive in Central America? According to the study, it’s entirely possible that the bug – just like measles and smallpox – was carried across the ocean by the Spanish. In fact, another paper published by the biology website bioRxiv in February 2017 revealed further evidence to support this hypothesis.
According to this study, researchers studying the remains of a Norwegian woman who died in 1200 also detected Salmonella enterica in her DNA. But does this prove that the strain crossed the Atlantic to wreak havoc among the Aztec population? Admittedly, it is possible that the bacteria also existed in Mexico before the arrival of the Spanish. But there is currently no evidence to support such a claim.
According to Anne Stone, a professor at the School of Evolution and Social Change at Arizona State University, it is difficult to be certain. In a 2018 interview with National Geographic, she explained, “It is hard to know for sure. But I think that it likely was of European origin because it was new to the population and it hit them so hard.”
Moreover, Vågene highlighted that the Spanish might not have even known they were carrying the deadly disease. She told The Independent, “Seemingly healthy individuals could have traveled from Europe to Mexico without knowing that they had it.” Once there, meanwhile, it would have been easy for them to pass the infection into the local water supply.
But it may not have just been a lack of immunity that contributed to the huge death toll of cocoliztli. In the aftermath of the Spanish conquest, the remaining Aztec population was redistributed across Central America. The colonialists also introduced new agricultural practices across the region, and these two policies greatly increased the spread of the disease.
Today, experts acknowledge that these changes may have created crowded conditions similar to those in which Salmonella still thrives today. Others have suggested that the Spanish brought infected livestock to Central America – where the disease soon spread among the population.
But not everyone is convinced that the culprit behind cocoliztli has finally been found. Epidemiologist Rodolfo Acuña-Soto from Mexico’s National Autonomous University has long suspected that a viral fever caused the epidemic – and his opinions have not changed. And even the authors of the study have themselves acknowledged that Salmonella enterica might not have been solely to blame.
Instead, the researchers have proposed that the bacteria detected in the teeth may have interacted with other pathogens around at the time. Meanwhile, others have pointed out that DNA study is not an exhaustive approach. In a 2018 interview with The Atlantic, microbiologist Nicolas Rascovan explained that RNA viruses, for example, could not have been detected by these techniques.
As it stands, the team would need to carry out more tests in order to prove their theory that Salmonella enterica was behind the cocoliztli outbreak. Using samples from other burial sites, they will be able to build up a clearer picture of the tragic events. Until that time, they will continue to use technology such as MALT to learn more about how diseases have shaped our past.
But according to Kirsten Bos, who worked on the study, the bacteria could well be the answer that historians have sought for many years. In a 2018 interview with The Guardian, she explained, “We cannot say with certainty that Salmonella enterica was the cause of the cocoliztli epidemic. [But] we do believe that it should be considered a strong candidate.”