Tracing East Asia’s Ancient Coronavirus Epidemic

Our DNA holds traces of an ancient battle between our cells and a coronavirus, suggesting that an epidemic similar to COVID-19 struck East Asia about 20,000 years ago.

AsianScientist (Jul. 5, 2021) – COVID-19 may be the most pressing health issue nowadays, but a closer look at our DNA has revealed that the battle between humans and coronaviruses is older than originally thought. Publishing their findings in Current Biology, an international team has reported genetic evidence of an ancient viral epidemic that spread across East Asia around 20,000 years ago.

Before the current pandemic, waves of coronavirus infections had already swept the globe in the form of SARS in 2003, followed by MERS in 2012. Meanwhile, four other human-infecting coronaviruses are known to cause mild respiratory symptoms, much like the common cold. By comparing genetic variations and factoring in the rate at which these viruses mutate, scientists previously estimated that the oldest of these coronaviruses emerged around 800 years ago.

However, the new discovery of an ancient coronavirus outbreak stretches this time scale to as far back as 20,000 to 25,000 years ago. Unlike the other coronaviruses identified from clinical specimens, researchers from the US and Australia uncovered clues to this past epidemic in human DNA archived in the 1000 Genomes Project.

“The modern human genome contains evolutionary information tracing back tens of thousands of years, like studying the rings of a tree gives us insight into the conditions it experienced as it grew,” said co-corresponding author Professor Kirill Alexandrov from the Queensland University of Technology.

As viruses rely on hijacking the genetic machinery of cells to reproduce, their acts of infiltration leave distinct markings in human DNA, particularly for a set of genes that code for virus-interacting proteins (VIPs). These proteins are typically involved in protective immunity or viral entry into host cells, opening the gateway for these pathogens to survive and spread.

By tracing genetic variations through several generations, the researchers found 42 coronavirus-specific VIP genes that appeared around the same time in evolutionary history and uniquely in ancestral East Asian populations—proving that a large coronavirus epidemic had indeed swept the region thousands of years earlier.

Their results also provided insight into how the genomes of ancient humans adapted to the viral threat. Over time, genetic variations that help protect against the virus would have been favored and passed on to succeeding generations, leading to less severe disease. Accordingly, the team found that these advantageous traits rose in frequency through the years, becoming the dominant form in the population at the height of the epidemic.

Moreover, the adaptive mutations occurred near DNA sequences in lung tissue that affect disease susceptibility by switching genes on and off. These genetic signatures further suggested that the ancient coronavirus infected and caused disease in a similar fashion to its modern descendants.

According to the researchers, the identified VIPs could serve as novel drug targets against COVID-19 and similar infections. By taking an evolutionary approach to these viral foes, the key to addressing present and future outbreaks might just be discovered by studying humanity’s past.

“Another important offshoot of this research is the ability to identify viruses that have caused epidemics in the distant past and may do so in the future,” said Alexandrov. “This, in principle, enables us to compile a list of potentially dangerous viruses and then develop diagnostics, vaccines and drugs for the event of their return.”

The article can be found at: Souilmi et al. (2021) An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.

Source: Queensland University of Technology; Photo: Shelly Liew/Asian Scientist Magazine.
Disclaimer: This article does not necessarily reflect the views of AsianScientist or its staff.

Asian Scientist Magazine is an award-winning science and technology magazine that highlights R&D news stories from Asia to a global audience. The magazine is published by Singapore-headquartered Wildtype Media Group.

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