We’ve always assumed smallpox was a relentless killer — the virus that felled empires, the biological weapon that wiped out Native American populations. But a new discovery from 500-year-old mummies in Chile suggests that narrative might be too simple. The virus those people carried was different. And it’s prompting researchers to ask: Was smallpox always a global scourge, or did it evolve into one?
I remember reading about smallpox blankets in school and thinking, ‘That virus is pure evil.’ But maybe it wasn’t always that way. Look, the pathogen we know as Variola major killed about 30% of those it infected. But the version found in these ancient remains looks like a milder cousin — one that might have been more like today’s monkeypox than the medieval plague we imagine.
This is the kind of science that makes you sit up straighter. It’s not just about understanding the past; it’s about how viruses evolve, and what that means for the next pandemic. So let’s dig into what the team found, why it’s ‘very strange,’ and how it changes the story of one of humanity’s oldest enemies.
A Surprising Find in the Atacama Desert
The Atacama Desert in Chile is one of the driest places on Earth. That aridity, ironically, is a gift to paleo-geneticists. It preserves organic material — including the DNA of ancient viruses — for centuries. In 2020, a team led by scientists from the University of Copenhagen and the University of Chile began analyzing mummified remains from a 16th-century cemetery. They were looking for signs of disease. What they found, published in the journal Science in late 2024, was DNA from the smallpox virus, Variola.
But not the Variola we know. The ancient strain was missing key genetic segments that, in modern strains, are linked to virulence — the ability to cause severe disease. ‘This is very strange,’ the researchers wrote in their paper. ‘The ancient virus appears to be a sister lineage to the one that became the global killer.’
Think of it like a family tree. You share a common ancestor with your cousin, but you’re not the same. The ancient Chilean smallpox is that cousin — genetically related, but far less dangerous. The team estimates the lineage split from the ancestor of modern smallpox around 1,500 years ago. That means for centuries, a milder form of the virus circulated in South America, possibly causing symptoms more like chickenpox than the disfiguring, often fatal disease that later ravaged the continent.
What the Ancient DNA Tells Us
The viral DNA was fragmented, but the team was able to reconstruct about 80% of the genome using advanced sequencing techniques. They compared it to 56 modern smallpox strains and found that the ancient virus lacked several genes known to suppress the human immune response. ‘It’s like the virus was playing with a weaker hand,’ said one of the study co-authors in a press release. ‘It couldn’t shut down the host’s defenses as effectively.’
That’s a huge clue. The modern smallpox virus has a suite of genes that interfere with interferons — proteins our bodies use to signal a viral invasion. Without those genes, the ancient virus would have been more easily cleared by the immune system. The result: lower mortality, milder symptoms, and a very different epidemiological profile.
So what changed? The researchers hypothesize that the virus evolved increased virulence after it spread to Europe and Asia, where dense populations created more opportunities for transmission. A more deadly virus could still spread because it had a larger pool of hosts. But in the sparsely populated Americas, a killer that struck too fast might have burned itself out. Evolution, as always, is a matter of context.
Why This Matters for Modern Science
This isn’t just a history lesson. Understanding how smallpox became deadly helps us predict how other viruses might evolve. Consider the physics of wildfire smoke turning the sun red — it’s a different field, but the same principle of using evidence to reconstruct past events applies. Here, the evidence is ancient DNA, and it’s telling us that virulence can be a late-stage adaptation.
The implications for vaccine development are real. If we know which genes make a virus dangerous, we can target them. The modern smallpox vaccine uses a related virus, Vaccinia, to trigger immunity. But the ancient strain — with its missing genes — might have been a safer candidate for a live-attenuated vaccine. ‘We can’t bring it back,’ the researchers note, ‘but studying its genome tells us what a ‘good’ virus looks like — one that is less likely to cause severe disease.’
There’s also a darker side. If smallpox evolved to become more deadly, what about other pathogens? Monkeypox, for example, has been gaining virulence in recent outbreaks. The same evolutionary pressures that shaped smallpox could be at work today. This study gives us a template for monitoring those changes.
The ‘Very Strange’ Part – and What It Means
Here’s where it gets really weird. The ancient DNA was found in mummies dated to around 1500 CE — after the arrival of Europeans in the Americas. But the viral strain is so different from the European smallpox that arrived with conquistadors that it couldn’t have been brought by them. ‘This is a native American smallpox,’ the researchers write. ‘It was already here, and it was already infecting people.’
That contradicts the long-held belief that smallpox was introduced to the Americas by Europeans. The team suggests that the virus might have traveled with early Asian migrants across the Bering Strait thousands of years ago, then evolved independently in the Americas. And it stayed mild — until the European strain arrived in the 16th century, possibly mixing with the local one and creating a more virulent hybrid.
But wait — if the local strain was mild, why did smallpox kill so many Native Americans? The answer is likely that what decimated them was the European strain, not the native one. The native strain might have been endemic and relatively harmless, but when the European version arrived, it hit a population with no immunity. That’s a classic story of virgin soil epidemics. But the new finding suggests that the native strain itself might have been less deadly, challenging the idea that smallpox was universally horrible from the start.
So what does this mean for you? Next time you hear about a virus ‘escaping’ from a lab or evolving in the wild, remember: evolution is not a straight line. Viruses can be mild for centuries, then turn deadly. The key is to watch the genetic signals — the same ones the scientists found in those 500-year-old mummies. It’s a reminder that the past is never dead, as Faulkner said. It’s not even past. It’s written in the DNA of the dead, and it’s warning us to pay attention.
This article was originally published on QuasarPost. Follow Dr. Olivia Grant on Twitter for more science deep dives.
Frequently Asked Questions
How did they find ancient smallpox DNA in mummies?
Researchers extracted DNA from the teeth and bones of mummies found in a cemetery in the Atacama Desert, Chile. The dry conditions preserved the DNA for centuries. Using advanced sequencing techniques, they identified fragments of the Variola virus genome and reconstructed most of it.
Does this mean smallpox was never deadly?
No — the modern smallpox virus was devastating. But this study suggests that a milder form of the virus existed in the Americas before European contact. The deadly strain likely evolved later in densely populated regions of Eurasia. The discovery shows that virulence can change over time.
What are the implications for vaccine development?
Understanding which genes make a virus more dangerous helps scientists design better vaccines. The ancient strain’s missing virulence genes provide a blueprint for creating safer live-attenuated vaccines. It also helps researchers monitor modern viruses like monkeypox for signs of increased deadliness.
