London: The youngest common ancestor of Sarbecoviruses – the coronavirus family to which SARS-CoV belongs – existed more than 21,000 years ago, almost 30 times older than previous estimates, a study finds.
The study, published in the journal Current Biology, showed that humanity may have been living since the Paleolithic about 2.5 million years ago to 10,000 BC.
Despite a very rapid evolution rate over short periods of time, viruses must remain highly adapted to their host in order to survive – this severely limits their freedom to accumulate mutations without affecting their fitness.
This causes the apparent rate of evolution of viruses to slow down over time. For the first time, the new research successfully recreates the patterns of this observed rate of decline in viruses.
The researchers developed a new method that can restore the age of viruses over longer periods of time and correct a kind of “evolutionary relativity” in which the apparent rate of evolution depends on the timescale of the measurement.
“Our estimate, based on viral sequence data from more than 21,000 years ago, is in remarkable agreement with a recent analysis of the human genomic dataset that suggests an ancient coronavirus infection at the same time,” said Mahan Ghafari of Oxford University.
The study also shows that while existing evolutionary models have often failed to measure divergence between virus species over time periods – from a few hundred to a few thousand years – the evolutionary framework developed in this study allows for a reliable estimate of virus divergence over wide time scales, possibly over the entire course of animal and plant evolution.
In addition to SARS-CoV-2, the new model also enables the reconstruction of the evolutionary history of RNA and DNA viruses in periods further back in the past.
The model predictions for the hepatitis C virus – a leading global cause of liver disease – are consistent with the notion that it has been circulating for nearly half a million years. So HCV may have spread around the world around 150,000 years ago as an integral part of the “out-of-Africa” migration of modern humans.
The various genotypes of HCV native to human populations in South and Southeast Asia and Central Africa may have emerged over this extended period, and this revised timescale could solve the long-standing mystery of their global distribution.