The novel coronavirus that has spawned the pandemic popped out of a lineage that has circulated unnoticed in bats for 40 to 70 years, scientists said on Tuesday after analysing the pathogen’s family evolutionary history.

Their study also suggests that the coronavirus’s ability to infect human cells emerged within bats, and challenges earlier suggestions that the virus used pangolins as an intermediate host before slipping into humans.

The origin of SARS-CoV-2, the virus that causes Covid-19, has remained a mystery. But Chinese researchers had in early February shown that it is most closely related to a virus called RaTG13, isolated from a horseshoe bat in Yunnan province in 2013.

During March and April, other research groups that had studied coronaviruses in pangolins suggested these scaly anteaters may have been the intermediate hosts where Sars-CoV-2 acquired its ability to infect human cells.

Now, Maciej Boni, an associate professor of biology at the Pennsylvania State University in the US, and his collaborators from four countries have analysed the evolutionary history of SARS-CoV-2 using available genomic data on sarbecoviruses, a specific group of coronaviruses.

Their analysis relied on three approaches to reconstruct the evolutionary history. It suggests that the two viruses, RaTG13 and SARS-CoV-2, share a single ancestral lineage and that SARS-CoV-2 is likely to have genetically diverged from related bat sarbecoviruses in 1948, 1969 or 1982.

“The lineage giving rise to SARS-CoV-2 has been circulating in bats unnoticed for decades,” Boni and his collaborators in Belgium, China, the UK and the US said in their study, published on Tuesday in the journal Nature Microbiology.
While SARS-CoV-2 and pangolin viruses share a common ancestor, the study’s findings also indicate that pangolins are unlikely to have been an intermediate host for the virus.

“This is an elegant analysis. It examines genomic data to provide insights into the origin of SARS-CoV-2,” said Uma Ramakrishnan, a scientist at the National Centre for Biological Sciences, Bangalore, who was not associated with the international study but is herself studying the evolutionary dynamics of viruses in bats.

“The study has also used data to challenge the assumption about pangolins. The capacity of the virus to infect human cells emerged in the bats themselves, not in pangolins.”

Scientists say the discovery that the lineage has circulated in bats for decades raises the possibility that there might still be unsampled virus lineages with a similar ability to infect human cells.

“Viruses can circulate under the radar and continue to evolve in their hosts until they reach a tipping point. When or how that point will come remains unknown,” Shahid Jameel, a senior virologist and head of the Wellcome Trust DBT-India Alliance, a UK-India research partnership, told The Telegraph.

This study, Jameel said, emphasises the need for surveillance.

“It also underscores the need to reduce contacts between wild animals and humans through a reduction of the destruction of animal habitats and (by) mitigating climate change.”

The international research team has suggested that it might be useful to conduct surveillance for more viruses closely related to SARS-CoV-2 along the region from Yunnan to Hubei.