Uncovering Genetic Traces to Discover How Humans Adapted to Historical Coronavirus Outbreaks

Coronavirus graphic. Credit: Gerd Altmann

An international team of researchers led by the University of Adelaide and the University of Arizona has analyzed the genomes of more than 2,500 modern humans from 26 populations around the world to better understand how humans have adapted to historic coronavirus outbreaks.

In a paper published in Current Biology, the researchers used advanced computational methods to discover genetic traces of adaptation to coronaviruses, the family of viruses responsible for three major outbreaks in the past 20 years, including the ongoing pandemic.

“Modern human genomes contain evolutionary information dating back hundreds of thousands of years, but it is only in recent decades that geneticists have learned how to decode the vast information captured in our genomes,” said lead author Dr. Yassine Souilmi of the University of Adelaide’s School of Biological Sciences.

“This includes physiological and immunological ‘adaptations’ that have enabled humans to survive emerging threats, including viruses.

“Viruses are very simple creatures whose sole purpose is to make more copies of themselves. Due to their simple biological structure, they are unable to reproduce on their own, so they must invade the cells of other organisms and hijack their molecular machinery in order to exist.”

Lead author Dr. Yassine Souilmi Australian Center for Ancient DNA, School of Biological Sciences, The University of Adelaide. Credit: The University of Adelaide

Viral invasions involve the attachment of and interaction with specific proteins produced by the host cell, known as viral interacting proteins (VIPs).

In the study, researchers found signs of adaptation in 42 different human genes that code for VIPs.

“We found VIP signals in five populations from East Asia and suggest that the ancestors of modern East Asians were first exposed to coronaviruses more than 20,000 years ago,” said Dr. Souilmi.

“We found that the 42 VIPs are mainly active in the lungs – the tissue most affected by coronaviruses – and confirmed that they interact directly with the virus underlying the current pandemic.”

dr. Ray Tobler, Australian Center for Ancient DNA, within the School of Biological Sciences at the University of Adelaide. Credit: The University of Adelaide

Other independent studies have shown that mutations in VIP genes can mediate susceptibility to coronavirus and also the severity of COVID-19 symptoms. And several VIPs are currently being used in drugs for COVID-19 treatments or are part of clinical trials for further drug development.

“Our past interactions with viruses have left telltale genetic signals that we can use to identify genes that influence infection and disease in modern populations, and may provide information about drug repurposing and the development of new treatments,” said co-author Dr. . Ray Tobler, of the University of Adelaide’s School of Biological Sciences.

“By uncovering the genes previously affected by historical viral outbreaks, our study points to the promise of evolutionary genetic analysis as a new tool in combating the outbreaks of the future,” said Dr. Souilmi.

The researchers also note that their results do not in any way replace existing public health policies and protections such as wearing masks, social distancing and vaccinations.

Reference: “An ancient viral epidemic involving genes interacting host coronavirus more than 20,000 years ago in East Asia” by Yassine Souilmi, M. Elise Lauterbur, Ray Tobler, Christian D. Huber, Angad S. Johar, Shayli Varasteh Moradi, Wayne A. Johnston, Nevan J. Krogan, Kirill Alexandrov, and David Enard, June 24, 2021, Current Biology.
DOI: 10.116/j.cub.2021.05.067

The team involved in this study also included researchers from the Australian National University and the Queensland University of Technology.