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  • Numerous theories exist around the origins of the SARS-CoV-2 virus, which causes COVID-19, but none has yet been proven.
  • Parts of the genome of the SARS-CoV-2 virus are so unusual that it has given rise to theories that the virus must have been developed in a lab.
  • Researchers have now discovered that bats living in caves in Laos host strains of viruses so similar to SARS-CoV-2 that they could infect humans.
  • This discovery could prove the natural origins of the COVID-19 pandemic and that direct bat-to-human transmission of the virus is a possible cause of the pandemic.

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Since SARS-CoV-2, the virus that causes COVID-19, was first detected in Wuhan, China, in December 2019, there have been global efforts to determine its origins.

As the pandemic was thought to originate in Wuhan, many efforts have focused on China, with the assumption that, as the virus was first detected there, it probably started there.

Now, two papers under review by the journal Nature and published as preprints are casting some doubt on these assumptions and indicate that in order to discover the origins of the virus, researchers may have to look farther afield.

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One of the reasons SARS-CoV-2 is so infectious is a region on its spike protein that gives it its ability to bind to a receptor present on the surface of many human cells called ACE2.

In a paper submitted to Nature, researchers from the Pasteur Institute in Paris, France, and from Laos have now reported finding viruses with receptor binding domains very similar to those found on SARS-CoV-2 in cave bats in North Laos.

The researchers took blood, saliva, anal feces, and urine samples from 645 bats from 46 different species found in limestone caves in North Laos, which is close to the Southwest China border.

They discovered three separate virus strains in three different species of Rhinolophus bat, commonly known as horseshoe bat. RNA sequencing revealed that these viruses were over 95% identical to SARS-CoV-2, and one, the closest virus to SARS-CoV-2 found so far, was 96.8% similar.

Further experiments showed that the receptor binding domain of the viruses had a high affinity for human ACE2 receptors. This was comparable to the affinity of SARS-CoV-2 strains that scientists discovered at the beginning of the pandemic, suggesting these viruses could infect humans directly.

Last year, scientists detected a similar virus in Yunnan, in Southwest China. It was 96.1% similar to SARS-CoV-2, meaning the present paper describes the closest virus detected yet.

Prof. Edward Holmes from the University of Sydney, Australia, who has studied the emergence and spread of SARS-CoV-2 but was not involved in this research, told Medical News Today the paper was “really significant.”

“In my opinion, these viruses won’t just be found in bats and pangolins. Ecology isn’t like that. I suspect that they will also be found in other mammalian species but have not yet been sampled,” Prof. Holmes said.

“Some of these Laotian viruses are extremely close to SARS-CoV-2 in the key receptor binding domain (part of the spike protein) of the virus. This means that the functional core of the virus exists in nature, so there is no need to think that the virus was somehow created or adapted in a lab.”

– Prof. Edward Holmes

Further doubt was cast on the assumption that the virus responsible for the COVID-19 pandemic originated in Wuhan with another preprint submitted to Nature.

A study by a team from the Chinese Academy of Medical Sciences and Peking Union Medical College in Beijing has suggested that SARS-CoV-2-related viruses are “extremely rare” in bats in China, after taking nose and anal swabs from over 13,000 bats between 2016 and 2021 at 703 locations across the country.

The paper also showed that SARS-CoV-2 was undetectable in samples taken from Wuhan Huanan Market, 40 days after the closure of the market, which was due to fears that the initial infection event had occurred there.

Authors conclude that further research should be done south and southwest of China to determine whether the SARS-CoV-2 virus originated there.

One of the reasons it has been so hard to establish where the coronavirus originated is viral genomes that change through a process called recombination, rather than just through mutations. Viral recombination occurs when two different strains infect the same host cell.

As they replicate in the same cell, they can interact, and the virus progeny they generate can have some genes from both parents. This can make it hard to work out the lineage of that virus.

“Recombination seems to be important for how these viruses evolve overall,” Spyros Lytras, an evolutionary virologist from the University of Glasgow in the United Kingdom, told MNT.

“So, essentially we are saying these viruses switch bits of their genome all the time, and the new viruses from Laos really highlight that. Even though [these viruses] are found in the same place, the same cave essentially, they all have different bits of their genome that have different combinations of recombinant parts.”

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