Coronaviruses closely related to SARS-CoV-2 discovered outside China

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Coronaviruses closely related to the COVID-19 pandemic virus have been discovered in Japan and Cambodia, reports Nature. The viruses, both found in bats stored in laboratory freezers, are the first SARS-CoV-2 relatives to be found outside China.

Two lab freezers in Asia have yielded surprising discoveries,. Researchers told Nature that they have found a coronavirus that is closely related to SARS-CoV-2, the virus responsible for the pandemic, in horseshoe bats stored in a freezer in Cambodia.

Meanwhile, a team in Japan has reported the discovery of another closely related coronavirus – also found in frozen bat droppings – writes Smriti Mallapaty in the article published on 23 November 2020

The viruses are the first known relatives of SARS-CoV-2 to be found outside China, which supports the World Health Organization’s search across Asia for the pandemic’s animal origin. Strong evidence suggests that SARS-CoV-2 originated in horseshoe bats, but whether it passed directly from bats to people, or through an intermediate host, remains a mystery.

The virus in Cambodia was found in two Shamel’s horseshoe bats (Rhinolophus shameli) captured in the country’s north in 2010. The virus’s genome has not yet been fully sequenced – nor its discovery published – making its full significance to the pandemic hard to ascertain.

If the virus is very closely related to – or even an ancestor of – the pandemic virus, it could provide crucial information about how SARS-CoV-2 passed from bats to people, and inform the search for the pandemic’s origin, says Veasna Duong, a virologist at Institute Pasteur in Phnom Penh, who led the search of the old samples in Cambodia and alerted Nature to their discovery in early November.

To provide such insights, the virus would have to share more than 97% of its genome with SARS-CoV-2, which is more than its closest known relative, say researchers.

But the new virus might be more distantly related, in which case, studying it will help scientists to learn more about the diversity in this virus family, says Etienne Simon-Loriere, a virologist at the Pasteur Institute in Paris, who plans to sequence the virus, after which it will be shared publicly, writes Nature.

That is the case with the other virus, called Rc-o319, identified in a little Japanese horseshoe bat (Rhinolophus cornutus) captured in 2013.

That virus shares 81% of its genome with SARS-CoV-2, according to a paper published on 2 November – which makes it too distant to provide insights into the pandemic’s origin, says Edward Holmes, a virologist at the University of Sydney in Australia.

No matter what the Cambodian team find, both discoveries are exciting because they confirm that viruses closely related to SARS-CoV-2 are relatively common in Rhinolophus bats, and even in bats found outside of China, says Alice Latinne.

She is an evolutionary biologist at the Wildlife Conservation Society Vietnam in Hanoi, who has seen some of the Cambodian team’s analysis but was not involved in the investigation. Latinne says the discoveries confirm that Rhinolophus bats are the reservoir of these viruses.

“This is what we were looking for, and we found it,” Nature quotes Duong as saying. “It was exciting and surprising at the same time.”

Pandemic origins

The findings also suggest that other as yet undiscovered SARS-CoV-2 relatives could be stored in lab freezers, says Aaron Irving, an infectious diseases researcher at Zhejiang University in Hangzhou, China. He also plans to test stored samples of bats and other mammals for antibodies against SARS-CoV-2.

“I did not expect to find a relative of SARS-CoV-2,” says virologist Shin Murakami at the University of Tokyo, who was part of the team that decided to retest frozen animal samples for viruses in the wake of the pandemic, Nature writes.

Only a handful of known coronaviruses are closely related to SARS-CoV-2, including its closest known relative RaTG13. It was discovered in intermediate horseshoe bats (Rhinolophus affinis) in the Chinese province of Yunnan in 2013, and was published only earlier this year.

There are also several other coronaviruses, found in other Rhinolophus bats and pangolins captured between 2015 and 2019, which scientists now know to be closely related to SARS-CoV-2, says the Nature report.

Read the full report in Nature. See the link below.

 

Detection and Characterisation of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan

Emerging Infectious Diseases. Volume 26, Number 12 – December 2020 Dispatch.

Authors

Shin Murakami, Tomoya Kitamura, Jin Suzuki, Ryouta Sato, Toshiki Aoi, Marina Fujii, Hiromichi Matsugo, Haruhiko Kamiki, Hiroho Ishida, Akiko Takenaka-Uema, Masayuki Shimojima and Taisuke Horimoto

Author affiliations: The University of Tokyo, Yamaguchi University, Iwate University and the National Institute of Infectious Diseases, all in Japan.

Abstract

Epidemiology of bat Betacoronavirus, subgenus Sarbecovirus is largely unknown, especially outside China. We detected a sarbecovirus phylogenetically related to severe acute respiratory syndrome coronavirus 2 from Rhinolophus cornutus bats in Japan. The sarbecovirus’ spike protein specifically recognizes angiotensin-converting enzyme 2 of R. cornutus, but not humans, as an entry receptor.

During the past 20 years, coronaviruses belonging to the genus Betacoronavirus have caused multiple human epidemic or pandemic diseases, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease (COVID-19).

Two viruses of the subgenus Sarbecovirus are severe acute respiratory syndrome coronavirus (SARS-CoV), which causes SARS, and SARS-CoV-2, which causes COVID-19.

Although Rhinolophus spp. bats in Asia, Europe, and Africa are considered natural reservoirs of sarbecoviruses, the epidemiology and distribution of these viruses remain largely unknown, especially outside China.

Previously, partial RNA-dependent RNA polymerase (RdRp) genes of betacoronaviruses were detected in little Japanese horseshoe bats (Rhinolophus cornutus). However, limited sequence information left the genetic and virological properties unclear.

We detected and determined the entire genome sequence of a bat sarbecovirus belonging to a phylogenetic clade that includes SARS-CoV-2 from R. cornutus bats in Japan. Further, we used a pseudotyped virus system to characterize an entry step of this virus into cells.

 

The full Nature story – Coronaviruses closely related to the pandemic virus discovered in Japan and Cambodia

 

Emerging Infectious Diseases article – Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan

 


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