Virus-hunters identify closest relative yet to Sars-CoV-2 in Laos bat cave

Virus-hunters have narrowed in on effectively the closest relative yet to Sars-CoV-2, the pathogen behind the Covid-19 pandemic, in bat caves in Laos.

The research is the latest piece of evidence to point towards the pandemic having natural origins, rather than being caused by a laboratory leak, including a study last week which suggested tens of thousands of people may be infected by bat coronaviruses every year.

The new paper, published as a pre-print by the French Institute Pasteur and the University of Laos, studied coronaviruses found in bats in four different limestone caves in Laos between July 2020 and January 2021.

The team identified bats infected with a number of viruses with key features that are incredibly similar to Sars-CoV-2.

“Sequences very close to those of the early strains of Sars-CoV-2 responsible for the pandemic exist in nature, and are found in several Rhinolophus bat species,” the authors write.

“These viruses may have contributed to Sars-CoV-2’s origin and may intrinsically pose a future risk of direct transmission to humans.”

The viruses found in the Laotian bats still differ from Sars-CoV-2, but they are particularly similar at the key part of the virus that allows it to bind to and infect human cells, the spike protein's receptor binding domain (RBD).

Professor Stuart Neil, head of the department of infectious diseases at King’s College London – who was not involved in the study – told The Telegraph: “Two or three of these viruses have RBDs which is only two or three changes from that seen in Sars-CoV-2 – essentially, closer to the original than some of the variants of concern we see out there in some respects.”

While the new paper does not rule out a lab leak hypothesis, it does provide more evidence of similar viruses circulating in bats naturally, bolstering the so-called “natural origins” theory.

The RBDs of the three viruses sequenced from bats in Laos – named BANAL-52, BANAL-103, and BANAL-236 – are closer to Sars-CoV-2 than the much-discussed RaTG13 virus identified in bats in Yunnan province, previously seen as the closest match. They also seemed to be as well adapted to infecting humans as Sars-CoV-2, which is another argument that lab-leak proponents have put forward: that the virus has been engineered to be particularly dangerous among people.

Professor Neil said it was likely that evidence would come in piecemeal, rather than identifying one “smoking bat”, as it has been dubbed. For example, other bat viruses have also been discovered which are also closer than RaTG13 in a number of ways, including in Cambodia.

“I’m not confident we’ll ever find something the same, but what we are going to find is viruses with bits that are almost the same,” he said. “It’s an incredibly complex ecosystem and whether we luck out and find the right one, or whether just in bits, will be an open question.”

However, he said the fact that the new research had shown that some bats were infected with several different coronaviruses simultaneously provided the perfect conditions for recombination – or the bringing together of these “bits”, like genetic building blocks, to form a new virus, such as Sars-CoV-2.

Experts estimate that the previous close matches found diverged from Sars-Cov-2 around 40 years ago; they suggest that the Laotian viruses diverged around 12 years ago.

Professor Eddie Holmes, an evolutionary biologist and virologist at the University of Sydney, told The Telegraph: “This is a very significant study that adds compelling support to a natural zoonotic origin of SARS-CoV-2.”

He also said it meant the theory of the miners in Mojiang province being involved – the miners worked close to the cave where RaTG13 was found – could be “thrown in the bin”.

“This work also highlights how commonplace these SARS-CoV-2-like viruses are in nature, including those with the capacity to infect humans. Doubtless many more viruses will be found,” he said.

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