Pangolins may not have been the intermediate host of SARS-CoV-2 after all

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Understanding the origins of the virus behind COVID-19 is one of the main questions scientists are trying to resolve while trying to manage the pandemic. But in a rapidly evolving situation, we are required to point the finger at a few innocent suspects along the way.

The current hypothesis looks like this: SARS-CoV-2 passed through a mysterious animal host on its alleged evolutionary journey from bats to humans. Critically endangered pangolins have been a prime candidate for this intermediate host, but now a genomic analysis by geneticist Ping Liu of the Guangdong Academy of Science in China has provided evidence that it may not be. the case.

SARS-CoV-2 belongs to the Betacoronavirus genus of coronavirus; this group of coronaviruses mainly infects mammals, and the new study suggests that pangolins are indeed natural hosts for them.

The team has reconstructed almost a whole genome of the coronaviruses found in two sick Malaysian pangolins (Manis javanica). They called the coronavirus isolated from these critically endangered animals pangolin-CoV-2020. Its final sequence included 29,521 base pairs, just slightly shorter than the 30,000 odd base pairs making up SARS-CoV-2.

The resulting genome showed sequence similarity of 90.32% with SARS-CoV-2 and 90.24% with the Rhinolophus affinis bat coronavirus BatCoV-RaTG13, which remains the closest known to SARS-CoV-2, with a correspondence of 96.18 percent.

But the sequence similarities don’t reflect the whole story. The genetic instructions for the very important protein peak of the SARS-CoV-2 virus corresponded more between the bat and the human coronavirus than that of the pangolin.

However, the pangolin virus shares essentially the same ACE2 binding receptor as that used by the COVID-19 virus – the part of the tip that allows the virus to enter and infect human cells. This was also found in another study which is still under review and has led to the suggestion that the human coronavirus could be a type of hybrid (a chimera) between a bat and a pangolin virus.

Liu’s team also believes that these similarities may indicate that a recombination event occurred somewhere in the evolution of these different viruses – where viral genomes have exchanged pieces of their genetic material with each other. . However, their analysis of the evolutionary relationship between the three viruses did not support the idea that the human version evolved directly from that of the pangolin.

“At the genomic level, SARS-CoV-2 was also genetically closer to Bat-CoV-RaTG13 than to pangolin-CoV-2020,” they wrote in their article.

There are clearly still many unknowns. With more than 4 million confirmed cases worldwide and a rapidly increasing death toll, the need to better understand this virus is only increasing.

However, one thing that all of these genetic studies have firmly excluded is the idea that the virus was made in the laboratory.

As for the pangolins, they were rescued by the Guangdong Wildlife Rescue Center after being smuggled for trade on the black market, and unfortunately died from their illness. Liu’s team could not determine whether their death was related to the coronavirus they had found.

But maybe a little good can come of it all, at least for the most trafficked mammal in the world, the researchers concluded:

“It will be important to minimize human exposure to wildlife to reduce the risk of spreading coronaviruses from wild animals to humans. “

The new research was published in PLOS pathogens.

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