New Relative of SARS-CoV-2, Rc-o319 Coronavirus, Found in Japan


This study tells us there’re other undiscovered bat coronaviruses, even outside of China.
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The Centers for Disease Control and Prevention (CDC) has released a study from Japan, titled “Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan,” in late December 2020. In this study, a new bat coronavirus called Rc-o319 is discovered, which belongs to the same evolutionary clade as SARS-CoV-2 and RaTG13, and this article will discuss the significance of this finding.

For some basics: SARS-CoV-2 is the coronavirus that causes Covid-19. RaTG13 is a bat coronavirus that is the closest known relative of SARS-CoV-2. SARS-CoV-2 and RaTG13 belong to the coronavirus's beta genus under the sarbecovirus clade — betacoronavirus, sarbecovirus. So, Rc-o319, RaTG13, and SARS-CoV-2 will be called sarbecoviruses from now.

The study’s rationale

Horseshoe bats of the Rhinolophus species are infamous for being reservoirs of betacoronaviruses. RaTG13 is one such bat sarbecovirus that is 96% identical to SARS-CoV-2 at the genetic level. Current evidence suggests that SARS-CoV-2 evolved from a common ancestor of RaTG13.

RaTG13 is first sampled from a bat cave in the Yunnan Province of China. In fact, most of the bat coronavirus studies are from China. But Rhinolophus species and other bats are also found in other parts of Asia, Europe, and Africa, and nothing much is known about the coronaviruses they harbor.

Thus, Shin Murakami, associate professor at the Department of Veterinary Medical Sciences of the University of Tokyo, led a study to characterize the complete genome of a bat sarbecovirus called Rc-o316 in Rhinolophus cornutus, a bat species endemic to Japan.
Image by Pixabay

What the study did and found

In 2013, the researchers captured four R. cornutus from a cave in the Iwate prefecture of Japan. They then extracted RNA genetic material from the bats’ feces to screen for any presence of betacoronaviruses. Once candidates were identified, they proceed to sequence the full genome in 2020.

Sequence analyses revealed that a new bat sarbecovirus called Rc-o319 is 81.47% genetically identical to SARS-CoV-2. While 18.5% of genetic differences are massive, the full genome and key genes (spike protein and ORF1ab) of Rc-o319 still qualify as a place in the same clade as SARS-CoV-2 and RaTG13.

The study also showed that Rc-o319 could not infect human cells expressing the human ACE2 receptor. Another distinction of Rc-o319, the study found, is that it does not require TMPSSR2 to complete cell infection. Thus, the bat’s ACE2 receptor alone is sufficient for Rc-o319, whereas human ACE2 and TMPSSR2 are required for human SARS-1 and SARS-CoV-2.

* Adapted from Murakami et al. (2020). Phylogenetic tree of full genomes of Rc-o319, SARS-CoV-2, RaTG13 (highlighted in yellow), and others. Phylogenetic trees of other genes (spike protein and ORF1ab) can be found in the main paper.

“Among R. cornutus bats in Japan, we detected sarbecovirus Rc-o319, which is phylogenetically positioned in the same clade as SARS-CoV-2. Sarbecoviruses belonging to this clade previously were detected from other Rhinolophus spp. bats and pangolins…in China and could have played a role in the emergence of SARS-CoV-2,” the authors concluded. “We provide a hypothesis that a bat sarbecovirus with zoonotic potential might exist even outside China, because Rhinolophus spp. bats inhabit Asia, Europe, and Africa.”

The study also admitted that Rc-o319 is unlikely to jump directly to humans as it cannot bind to the human ACE2 receptor, unlike RaTG13 that also uses the human ACE2 receptor. However, as R. cornutus live in caves or tunnels with other bat species, and interact with other wild animals during the daytime, Rc-o319 may transmit to coinhabitant animals.

A closer look at Rc-o319

First, the study did not suggest that Rc-o319 is involved in the origin of SARS-CoV-2. Rather, the study tells us that other undiscovered sarbecoviruses could still change the current phylogenetic tree — just like the Japanese study added a new member, Rc-o319, into the sarbecovirus clade.

Rc-o319 is only 81.47% genetically identical to SARS-CoV-2, compared to RaTG13 with 96% identity. Scientists have predicted that the 4% genetic differences between RaTG13 and SARS-CoV-2 represent about 50 years of evolutionary time gap. Indeed, a published study in Nature suggests that the most recent common ancestor of RaTG13 and SARS-CoV-2 arose around 1950–1980.

As follows, the most recent common ancestor of Rc-o319 and SARS-CoV-2, as well as other sarbecoviruses in between, would be dated back even further. With the current phylogenetic tree, at least five ancestors are standing in between Rc-o319 and SARS-CoV-2. So, while Rc-o319 is related to SARS-CoV-2, it’s very distantly related. The different biological functions between Rc-o319 and SARS-CoV-2 further supports this notion. To restate, compared to SARS-CoV-2, Rc-o319 uses a different form of ACE2 receptor and does not need the TMPSSR2 co-factor to complete cell infection.

Is it possible that the Covid-19 pandemic started somewhere outside of China? Perhaps so, if a very closely related sarbecovirus of SARS-CoV-2 is discovered outside of China, which is certainly not Rc-o319. At this point, the Yunnan Province of China, where RaTG13 is sampled, is still the leading candidate region where Covid-19 started.
* Adapted from Murakami et al. (2020). Cropped portion of the phylogenetic tree depicting the associated common ancestors

Short abstract

Japanese researchers discovered a new bat coronavirus called Rc-o319 that belong to the same evolutionary clade (betacoronavirus, sarbecovirus) as SARS-CoV-2 and its closest known relative, RaTG13. But Rc-o319 is only 81.47% genetically identical to SARS-CoV-2. By contrast, RaTG13 and SARS-CoV-2 are 96% identical, and these 4% differences entail about 50 years of evolution. Thus, while Rc-o319 is related to SARS-CoV-2, it’s very distantly related. Still, this study tells us that other uncharted coronaviruses — even outside of China — may possibly alter our current knowledge of the SARS-CoV-2 evolutionary tree.

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