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Scientists have recently discovered a new coronavirus living in bats that appears to be a close cousin of SARS-CoV-2, the pathogen responsible for the Covid-19 pandemic. While the discovery won’t shut down all speculation about the virus's origin story, it does suggest that bats are the most likely natural hosts for SARS-CoV-2, and the pathogen was not artificially created in a lab.
Known as RmYN02, the newly identified virus was discovered in samples taken from bats living in the Yunnan Province of southern China during the latter half of 2019. As reported in the journal Current Biology, researchers in China have carried out a genetic analysis of the new virus and found it shares 93.3 percent of its genome with SARS-CoV-2.
The newly analyzed coronavirus also appears to contain unusual insertions of amino acids in two subunits, S1 and S2, of the virus's spike protein. Importantly, this feature can also be found in SARS-CoV-2 and is often pointed to as being a sign of artificial manipulation. However, since the S1/S2 insertion can be seen in RmYN02, it suggests the feature can naturally evolve in the wild and isn’t necessarily proof of fiddling in a lab.
"It has been proposed the S1/S2 insertion is highly unusual and perhaps indicative of laboratory manipulation. Our paper shows very clearly that these events occur naturally in wildlife. This provides strong evidence against SARS-CoV-2 being a laboratory escape," senior study author Weifeng Shi, professor at the Institute of Pathogen Biology at Shandong First Medical University in China, said in a statement.
This is still not the closest known relative of SARS-CoV-2. That honor goes to RaTG13, a coronavirus identified from a horseshoe bat sampled in Yunnan province in 2013, which shares 96.1 percent of its genome with SARS-CoV-2. However, the genome of the newly described RmYN02 does contain one long encoding section called 1ab which shares 97.2 percent of its RNA with SARS-CoV-2.
Gaps in the story still remain, however. RmYN02 does not contain the key receptor binding domain that SARS-CoV-2 uses to infect human cells, a bit like a lock and key, meaning this pathogen would unable to make the fateful leap from wild animals to humans, known as zoonosis. As if to muddy the waters further, the protein spikes found on other coronaviruses harbored in Malayan pangolin do have a very similar receptor binding domain to SARS-CoV-2.
Nevertheless, the new description of RmYN02 is another piece of the puzzle that hopes to be solved with further research into the viruses that lurk within wildlife.
“Neither RaTG13 nor RmYN02 is the direct ancestor of SARS-CoV-2, because there is still an evolutionary gap between these viruses," said Professor Shi. "But our study strongly suggests that sampling of more wildlife species will reveal viruses that are even more closely related to SARS-CoV-2 and perhaps even its direct ancestors, which will tell us a great deal about how this virus emerged in humans."
