According to a new study, the most recent common ancestor of sarbecoviruses (the family of coronaviruses to which SARS-CoV belongs) existed more than 21,000 years ago, which is nearly 30 times older than previous estimates.
According to the study, which was published in the journal Current Biology, humanity may have been exposed to sarbecoviruses – which have the ability to jump from animals to humans – since the Paleolithic period, which lasted roughly 2.5 million years to 10,000 BC.
Despite having a very rapid rate of evolution over short timescales, viruses must remain highly adapted to their hosts in order to survive; this severely limits their ability to accumulate mutations without reducing their fitness.
As a result, the apparent rate of evolution of viruses slows over time. For the first time, the new study successfully recreates the patterns of observed rate decay in viruses.
The researchers devised a new method for determining the age of viruses over longer timescales and correcting for “evolutionary relativity,” in which the apparent rate of evolution depends on the timescale of measurement.
“Our estimate based on viral sequence data from more than 21,000 years ago is in remarkable agreement with a recent analysis on human genomic datasets that suggests infection with an ancient coronavirus around the same time,” said Oxford University’s Mahan Ghafari.
The study also shows that, while existing evolutionary models have frequently failed to measure virus divergence over timescales ranging from a few hundred to thousands of years, the evolutionary framework developed in this study will allow for the reliable estimation of virus divergence over vast timescales, potentially spanning the entire course of animal and plant evolution.
Aside from SARS-CoV-2, the new model allows for the reconstruction of the evolutionary history of RNA and DNA viruses in the distant past.
The model predictions for the hepatitis C virus, a leading global cause of liver disease, are consistent with the idea that it has been around for nearly 500,000 years. HCV may have spread globally as an integral part of modern humans’ “Out-of-Africa” migration around 150,000 years ago.
The various genotypes of HCV indigenous to human populations in South and South-East Asia, as well as Central Africa, may have evolved over this time period, and this revised timescale may help to solve the long-standing mystery of their global distributions.