Ancient viral DNA may help unlock what makes us human today

Buried in our DNA lies ancient viral code once dismissed as junk, and now it might be pulling the genetic strings.

McGill University and Kyoto University scientists have uncovered overlooked viral sequences in the human genome that could play a key role in regulating gene activity.

Using a new method to trace their evolutionary history, the team found that these ancient viral fragments aren’t just passive leftovers from infections past; they may actively help switch genes on and off.

Viruses that engineered us

“If we can clearly map what parts of our genome are specific to humans or primates, and what parts came from viruses, we’re one step closer to understanding what makes us human and how our DNA influences health and disease,” said Guillaume Bourque, one of the study’s lead authors and a professor in McGill’s Department of Human Genetics.

Roughly eight percent of our genome is made up of viral DNA, remnants from viruses that infected our ancestors millions of years ago.

While much of it has been considered genetic clutter, researchers now believe some of these sequences have been repurposed by evolution to influence critical biological functions.

The study zeroes in on a viral DNA family called MER11, revealing a previously unknown subgroup—MER11_G4—that is especially active in human stem cells and found only in humans and chimpanzees.

“The current annotation of viral DNA in the genome shouldn’t be treated as definitive. It’s time to revisit and refine it,” said Bourque.

This specific group contains a unique DNA motif that researchers say could be linked to how genes are regulated.

When the human genome was first sequenced 25 years ago, viral DNA was noted but largely ignored, in part because scientists lacked the tools to make sense of it. But that’s changing now.

Using modern computational approaches, the team reanalyzed the genome and found that many earlier annotations were either outdated or incomplete. Their new method doesn’t just compare sequences. It groups them based on how they evolved over time, revealing patterns that traditional techniques missed.

The code still works

This evolutionary lens allowed the researchers to identify cryptic subfamilies of endogenous retroviruses, specifically within the MER11 group.

Previously, only three MER11 subtypes had been documented. The new study identifies a fourth, MER11_G4, which appears to have regulatory potential. Notably, this group is highly active in human stem cells and may play a role in developmental processes by toggling certain genes on or off.

The discovery suggests that these viral elements might not be evolutionary debris after all. Instead, they could be part of the very system that controls gene expression—one that shapes how cells develop, respond to stress, or even contribute to diseases like cancer.

A clearer view of these viral elements could help researchers trace the origins of certain genetic disorders or explain why some gene mutations turn dangerous. It also opens new paths for studying how evolutionary relics in our DNA might still be influencing us today.

The findings have been published on July 18 in Science Advances.

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