RmYN02 Coronavirus: Closest Identified Relative of SARS-CoV-2 Supports Natural Origin
Wed, April 14, 2021

RmYN02 Coronavirus: Closest Identified Relative of SARS-CoV-2 Supports Natural Origin

 

The discovery of the origin of the COVID-19 virus remains critical in research as it can provide the evolutionary precursor. Recently, researchers identified a coronavirus strain in bats with very close similarities to the pathogen of this pandemic.

The identification of the close relative of SARS-CoV-2, the virus of COVID-19, was led by Chinese researchers. Through a series of tests, they isolated the RmYN02 coronavirus and found it highly similar to SARS-CoV-2. Although the isolated virus was not the direct parent of the novel coronavirus, its properties could help scientists better understand the unusual spike protein of SARS-CoV-2. They published their findings in the journal Current Biology.

Close Relative of SARS-CoV-2 Discovered

Right now, scientists across the globe are working round the clock to study various aspects of SARS-CoV-2. Some groups are focused on the pathophysiology of the virus, other groups are dedicated to the environmental survivability of the virus, and a few more groups are fixated on the pathogen's true origin. The origin of SARS-CoV-2 is something that cannot be ignored because it tells the evolutionary process, which explains how the virus jumped to humans. Even if genome sequencing can show genetic details, the discovery of the origin is still more significant. Did human activities cause the jump? Did the virus jump to several animals before hitting humans? Are bats the true carriers of the virus or are they simply a vector? These questions can only be answered if the origin is found.

In China, an interdisciplinary group of researchers sought the origin of SARS-CoV-2. Their research was designed to clarify if the virus is genuinely from bats. They also wanted to confirm if the virus is natural or genetically manipulated. Any evidence to prove the origin of the virus could ease the mind of the public, which currently suffers from the ongoing pandemic. In case the virus was not engineered, it would suggest that the origin could harbor potential viruses capable of harming humans.

"Since the discovery of SARS-CoV-2, there have been a number of unfounded suggestions that the virus has a laboratory origin. In particular, 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," said Weifeng Shi, the senior author of the study and Director of the Institute of Pathogen Biology at Shandong First Medical University, asc quoted by ScienceDaily, an American science news distributor.

In the study, researchers analyzed 227 bat samples collected in the province of Yunnan in China. These samples were collected from May to October 2019. Bats were the preferred animal source of the samples due to great interest, initiated by the discovery of the SARS-CoV-1 in 2005. The discovery was followed by later studies that confirmed bats as natural reservoirs of RNA viruses, which included coronaviruses in general.

 

 

The RNA samples from bats were sent for metagenomic next-generation sequencing. The sequencing was conducted in early January 2020, shortly after SARS-CoV-2 was identified but before COVID-19 became a pandemic. The first nominated close relative of SARS-CoV-2 was the RaTG13 identified in Yunnan Province as well. But the new virus in this study was determined to be closer to SARS-CoV-2 than RaTG13. The virus in question is RmYN02, which shared 97.2% of its RNA with SARS-CoV-2 in the longest encoding section of the 1ab genome.

The sequencing also revealed a key difference between SARS-CoV-2 and RmYN02. The latter lacked the resemblance in the binding domain found in the former, meaning RmYN02 lacked the binding keys to the human ACE2 receptor, which SARS-CoV-2 uses to infect and hijack human cells. In other words, RmYN02 is unlikely to infect human cells, at least, based on this research.

The additional key similarity between SARS-CoV-2 and RmYN02 is the amino acid insertions at the meeting point of two subunits of the spike protein. SARS-CoV-2 has a four-amino-acid insertion which, so far, is the same across all tested samples of COVID-19. That insertion is located at the meeting point of S1 and S2. On the other hand, the insertions in RmYN02 are located elsewhere and not present at the same point as SARS-CoV-2.

In spite of the varying locations of the insertions, both SARS-CoV-2 and RmYN02 have independent insertion events. This proposes that the insertion of SARS-CoV-2 is not exclusive, but distinct if compared to the insertion of its relatives. This also supports the insertion being natural in origin since another virus features the same thing. As far as this study is concerned, certain coronaviruses in bats have insertion events located in different subunit junction. The location of these insertion events can determine what the viruses infect.

Researchers concluded that neither RaTG13 nor RmYN02 is the direct ancestor of SARS-CoV-2. The ancestor may still be out there waiting to be discovered. They suggest further research, through more sampling, to find the closest relative of the deadly virus. If the direct ancestor is identified, the puzzle on the emergence of the virus in human communities will be easier to solve.

 

 

COVID-19 worldwide

According to the 112th Situation Report of the World Health Organization, a specialized agency of the United Nations, the total cases of COVID-19 worldwide reached 4,006,257 on May 11, 2020. The total deaths due to the disease peaked at 278,892. As of that date, Europe had the highest number of confirmed cases at 1,713,606, followed by the Americas at 1,702,451, the Eastern Mediterranean at 265,164, the Western Pacific at 160,910, Southeast Asia at 100,881, and Africa at 44,533. Within 24 hours, a total of 47,073 new cases were reported in the Americas, 23,660 new cases in Europe, 9,436 new cases in the Eastern Mediterranean, 5,567 new cases in Southeast Asia, 1,907 in Africa, and 1,248 new cases in the Western Pacific.

The agency reported as well the 127 emergency medical teams or EMTs being prepared for deployment. As of May 11, 2020, 20 EMTs were deployed to support 16 countries and another 37 EMTs for national operations associated with COVID-19 response. Over 3,600 beds were managed by EMTs to increase the capacity of countries while 340 training events were conducted to assist nearly 11,000 frontliners.