Coronavirus outbreak in East Asia 25,000 years ago, genetic study finds

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The genomes of several East Asian populations bear the signature of a viral epidemic that occurred around 900 generations ago, or 25,000 years (28 years per generation), according to a new study published in the journal Current biology.

Souilmi et al. apply evolutionary analyzes to human genomic datasets to recover selection events involving dozens of human genes that interact with coronaviruses, including SARS-CoV-2, which likely began over 20,000 years ago . Image credit: Souilmi et al., doi: 10.1016 / j.cub.2021.05.067.

Throughout the evolutionary history of Homo sapiens, positive natural selection has frequently targeted proteins that physically interact with viruses, for example those involved in immunity or used by viruses to hijack the host’s cellular machinery.

Over millions of years of human evolution, selection has led to the attachment of genetic variants encoding virus interacting proteins (VIPs) at a rate three times that observed for other classes of genes.

Strong selection on VIPs has continued in human populations over the past 50,000 years, as evidenced by enriched VIP genes for introgressed adaptive Neanderthal variants and also selective scan signals (i.e. say selection that results in a beneficial variant at substantial frequencies in a population), particularly around VIPs that interact with RNA viruses, a viral class that includes coronaviruses.

Accumulating evidence suggests that ancient outbreaks of RNA viruses have occurred frequently during human evolution. However, scientists are currently uncertain whether selection has made a substantial contribution to the evolution of human genes that interact more specifically with coronaviruses.

“The modern human genome contains evolutionary information dating back tens of thousands of years, as studying the rings of a tree gives us insight into the conditions it experienced as it grew,” said the Professor Kirill Alexandrov, CSIRO-QUT synthetic biology researcher. Alliance and the Center for Genomics and Personalized Health at Queensland University of Technology.

In the study, Professor Alexandrov and his colleagues used data from the 1000 Genomes project, which is the largest public catalog of common human genetic variation.

They examined whether selection signals are enriched within a set of 420 VIPs that interact with coronaviruses (such as SARS-CoV-2) in 26 human populations.

These coronavirus VIPs include 332 SARS-CoV-2 proteins identified by high throughput mass spectrometry and 88 additional proteins that were manually selected from the literature.

Their analysis revealed a strong enrichment of the scanning signals at the level of the coronavirus VIPs in several populations of East Asia, which is absent from the other populations.

This suggests that an ancient outbreak of coronavirus – or another virus using similar VIPs – resulted in an adaptive response in the ancestors of East Asians.

The researchers found that 42 coronavirus VIPs may have been selected around 900 generations (25,000 years) ago and exhibit a coordinated adaptive response.

“We applied evolutionary analysis to the human genomic dataset to uncover evidence that the ancestors of the peoples of East Asia experienced an outbreak of a coronavirus-induced disease similar to COVID-19,” said Professor Alexandrov.

“During the epidemic, selection favored pathogenetically linked human gene variants with adaptive changes presumably leading to less severe disease.”

“By developing a better understanding of ancient viral enemies, we understand how the genomes of different human populations have adapted to viruses that have recently been recognized as an important driver of human evolution.”

“Another important benefit of this research is the ability to identify viruses that caused an epidemic in the distant past and which may do so in the future. “

“This allows us, in principle, to compile a list of potentially dangerous viruses and then develop diagnostics, vaccines and drugs for the eventuality of their return.”

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Yassine Souilmi et al. A former viral epidemic involving genes interacting with the host coronavirus more than 20,000 years ago in East Asia. Current biology, published online June 24, 2021; doi: 10.1016 / j.cub.2021.05.067


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