Scientists discover coronavirus outbreak in human DNA 20,000 years ago

By studying human DNA, geneticists have discovered that there was already a coronavirus epidemic in our ancient past. It happened between 20,000 and 25,000 years ago.

Whoever said that history tends to repeat itself was quite right. Pandemics are not new to us; we have seen them before. But what is the likelihood that our ancient ancestors experienced something similar to what we are experiencing now with the Covid19 pandemic?

Apparently, it is quite possible!

A team of scientists from the University of Arizona and the Australian Center for Ancient DNA (ACAD) conducted a study that found an epidemic outbreak of coronavirus in the East Asian region that occurred ~20,000 years ago and left traces in the DNA of modern humans from that region.

“We found traces of humanity’s age-old arms race in the battle with coronaviruses written into our DNA,” Yassin Suilmi, one of the study’s co-authors, wrote in the paper.

But what does this mean for us modern humans?


Viruses are tiny, simple creatures that are not alive (no cells, no way of turning food into energy) and yet they are not dead. Their only purpose is to reproduce, and for that they need hosts. When they invade, they interact with specific proteins produced by host cells, which are called viral interacting proteins (VIB).

They are responsible for many of the pandemics we have seen throughout human history, and their numbers are no longer countable.

“In the 20th century alone, three varieties of influenza virus led to widespread outbreaks that killed millions of people: the ‘Spanish flu’ in 1918-20, the ‘Asian flu’ in 1957-58 and the ‘Hong Kong flu’ in 1968-69,” Suilmi writes.

Such major disease events usually result in significant population adaptations that can lead to resistance to infection or reduction of symptoms. Geneticists have now created tools that allow them to look for traces in our genes that are indicative of historical adaptation events.

“Our team was interested to see if historical encounters with ancient coronaviruses left any such trace in modern human populations,” Suilmi says in the paper.


To see if there was any major coronavirus outbreak in ancient history, the research team collected DNA samples from thousands of people from 26 populations and analyzed 420 genes encoding VIP functions that specifically interact with coronaviruses (CoV-VIPs) to try to find traces indicating adaptation. Forty-two of these genes showed strong adaptation signals, and all were found in East Asian populations.

“These independent lines of evidence support the presence of an ancient epidemic of coronavirus (or similarly interacting virus) that originated in the ancestors of modern East Asian populations,” the scientific paper says.

The 42 CoV-VIPs accumulated roughly the same number of mutations, meaning that they evolved rapidly simultaneously under the pressure of a large selective event. By determining the timing of these mutations, the researchers hypothesized that the coronavirus outbreak occurred in East Asia between about 20,000 and 25,000 years ago.

Suilmi also reported that “42 VIPs are expressed mainly in the lungs, which are the tissue most susceptible to COVID-19 symptoms,” and added that “these VIPs interact directly with the SARS-CoV-2 virus responsible for the current pandemic.”


This study shows that during the epidemic, some genes involved in viral interactions underwent positive selection, which may have led to increased resistance and reduced disease severity.

“Our results show that looking for genetic traces of historical viral outbreaks can help us treat future outbreaks,” Suilmi says.

But how?

“Analysis of evolutionary genomics has identified several new candidate genes that could become new drug targets,” the paper says. Suppose that certain mutations in the VIP genes are responsible for attenuating the effects of coronavirus infection. If so, they could become targets for drug research that could still be useful today, when we are still fighting this pandemic.”

“By uncovering the identity of our ancient pathogenic enemies, evolutionary genomic methods may ultimately improve our ability to predict and thus prevent future epidemics,” the authors conclude.

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