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NIH-halted study unveils its massive analysis of bat coronaviruses - Science Magazine
Jun 01, 2020 2 mins, 52 secs
In a preprint posted yesterday on bioRxiv, the researchers examine partial genetic sequences of 781 coronaviruses found in bats in China, more than one-third of which have never been published.

Although the analysis cannot pinpoint the origin of SARS-CoV-2, the virus that causes COVID-19, it does single out one genus, Rhinolophus, also known as Chinese horseshoe bats, as crucial to the evolution of coronaviruses.

“It seems that by sheer phylogeographic, historical, evolutionary bad luck, Rhinolophus ends up being the major reservoir for SARS [severe acute respiratory syndrome]-related coronaviruses,” says study co-author Peter Daszak, president of EcoHealth Alliance, a nonprofit that last month saw its multimillion-dollar grant to study bat coronaviruses with colleagues in China cut by the U.S.

Between 2010 and 2015, Shi, Daszak, and their collaborators captured hundreds of bats in numerous Chinese provinces and took oral and rectal swabs from them.

The new study, although â€œvery useful,” doesn’t clarify this scenario, says Edward Holmes, an evolutionary biologist at the University of Sydney who has studied the genetics of bat coronaviruses and co-authored the paper that first revealed the sequence of SARS-CoV-2.

But the paper does demonstrate a “huge diversity” of bat coronaviruses in China that potentially can jump between species, Holmes says.

Looking for coronaviruses outside of bats may still be key to the origin mystery.

“While bats are clearly major hosts for coronaviruses, until we have a wider sampling of wildlife species we will not be able to fully resolve the evolutionary events involved in the genesis of SARS-CoV-2, particularly whether it jumped straight from bats to humans or went through an intermediate host,” Holmes says.

He points to evidence of closely related coronaviruses in pangolins.

(Eight coronavirus sequences from pangolins are included in the analysis.) â€œI think the pangolin story has a lesson for us: Don’t get stuck in a box thinking that this is all about bats” Daszak says, although he stresses that he does not think existing data make a compelling case for SARS-CoV-2 having entered humans via pangolins. Sampling, he says, also needs to extend to neighboring countries Laos, Vietnam, and Myanmar.

“Future work discovering and characterizing the biological properties of bat alpha-coronaviruses may therefore be of potential value for public and livestock health,” Daszak and his colleagues write.

Duke University’s Feng Gao, who led an analysis published on 29 May in Science about the evolution of SARS-CoV-2, says the new work by Daszak, Shi, and colleagues underscores that researchers have just sampled “the tip of the iceberg” of the coronaviruses circulating between bats that could jump into humans and other species.

The entire genome of bat coronaviruses consists of about 30,000 RNA bases, but obtaining full sequences is often difficult and expensive.

Gao says getting full viral sequences would have provided much more biological information on the different viruses found.

“We won’t be able to do that work without the funding, unfortunately.” And even the hundreds of viruses included in the current paper are only a fraction of what remains to be discovered, Daszak says. â€œWe are looking at maybe 10,000 to 15,000 bat coronaviruses that are out there.”.

In an earlier paper, Daszak and co-workers found SARS-related antibodies to coronaviruses in about 3% of people they sampled in China living near bat caves, suggesting they had been infected by some of these viruses.

Many more viruses that are closely related to SARS-CoV-2 are just waiting to be discovered in wildlife, Daszak says.

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