Animal Which Passed the Coronavirus from Bats to Humans Probably Wasn't a Pangolin, Study Suggests

The coronavirus which has infected more than 5 million people likely didn't jump from bats to pangolins to humans, according to a study. The authors of the paper published in the journal PLOS Pathogens explained that evidence does suggest that SARS-CoV-2, the name of the coronavirus which causes COVID-19, came from bats.

As direct interactions between humans and bats are relatively rare, scientists around the world are trying to find a potential intermediary host for SARS-CoV-2. This is an animal which has been infected with different viruses which merge to create a virus better at infecting humans.

In what are known as recombination events, viruses of two different strains co-infect the same cell of a host to create a germ with some genes from both parents. In the five months since the COVID-19 pandemic started, pangolins—scaly mammals who look like anteaters—have emerged as a potential source.

SARS-CoV-2 is a member of the large family of coronavirus germs, which includes SARS-CoV, the cause of severe acute respiratory syndrome (SARS), MERS-CoV of Middle East Respiratory Syndrome (MERS), and others which trigger some common colds.

SARS-CoV—the virus behind the SARS outbreak of 2002 to 2004—is thought to have jumped from bats to civets to people, and MERS—which emerged in 2012—from bats to dromedary camels to humans.

This suggests coronaviruses, which are common in bats, have the ability to adapt to other, non-bat hosts, Andrew Preston, a researcher in microbial pathogenesis at the University of Bath, U.K., who was not involved in the PLOS Pathogens study, told Newsweek.

To investigate whether pangolins were the intermediary host of SARS-CoV-2, Jinping Chen of the Guangdong Institute of Applied Biological Resources and colleagues looked at the genome sequences, or genetic make-up, of a coronavirus named pangolin-CoV-2020 (CoV-2020).

The virus was found in two sets of three sick Malayan pangolins in March and July 2019, long before the COVID-19 pandemic is believed to have started. Pangolins are illegally traded for their scales, which are used in traditional medicines. The two sets of animals were intercepted by customs officials in China.

The team pooled the sequences from the samples to mock up a whole genome of CoV-2020. The virus was found to be very similar to SARS-CoV-2. They also noticed it had many of the characteristics of Bat-CoV-RaTG13 (RaTG13), a coronavirus found in bats which is thought to be the closest known relative of SARS-CoV-2.

The pangolin virus and SARS-CoV-2 have a similar genetic make-up as the bat virus: CoV-2020 and SARS-CoV-2 at 90.3 percent; 90.24 percent between CoV-2020 and RatG13; and 96.18 percent for SARS-CoV-2 and RaTG13. This suggests they have a shared lineage.

But after the team looked at the evolutionary family trees and the genetic sequence of the spike protein which coronaviruses use to infect hosts, they concluded SARS-CoV-2 didn't arise directly from CoV-2020.

The evidence suggests that SARS-CoV-2 "originated from multiple naturally occurring recombination events among viruses present in bats and other wildlife species," they wrote.

As with all studies, the findings had some limitations. Dr. Jurgen Haas, professor of viral genomics at the University of Edinburgh in Scotland who didn't work on the paper, told Newsweek the number of viruses isolated from animals was small, and the researchers were only able to pull the whole genome sequence of the pangolin CoV-2020 virus together by pooling the sequences from three viruses.

pangolin, ant eater, stock, getty
A stock image shows a pangolin, which scientists have investigated as a potential intermediate host of the coronavirus. Getty

What do we know about how SARS-CoV-2 ended up in humans?

Experts who were not involved in the study told Newsweek the work offers additional evidence to support the idea that SARS-CoV-2 naturally evolved from a coronavirus from bats, but leaves the question of the potential intermediary host unanswered.

Scientists were able to start exploring the potential source of SARS-CoV-2 when a team in China shared a genome sequence of the mysterious new coronavirus in January 2020. It was thought that the virus may be zoonotic, having passed from animals to humans, as many early cases were linked to a wet food market in the Chinese city of Wuhan, the original epicentre of the outbreak.

By studying the genome sequence of SARS-CoV-2 and comparing it to other coronaviruses, scientists in China found it was 96 percent identical to RaTG13, which infects horseshoe bats. Bats are reservoirs of coronaviruses that often recombine, and carry 61 viruses known to infect humans. But RaTG13's spike protein which it uses to invade a host's cells is different to that of SARS-CoV-2, meaning it likely didn't spread directly from bats to people.

One pre-print study (meaning it hasn't been peer reviewed) shared online on the website bioRxiv in March indicated that SARS-CoV-2 diverged from RaTG13 between 40 to 70 years ago. "The SARS-CoV-2 lineage is not a recent recombinant, at least not involving any of the bat or pangolin viruses sampled to date," the authors wrote.

Professor David Robertson, of the MRC-University of Glasgow Centre for Virus Research and co-author of the bioRxiv study, told Newsweek: "We've shown that although relatively close in sequence space this still represents several decades of time."

Back in January, snakes were initially billed as a potential host in a study since noted to be flawed. The possibility of pangolins spreading the virus to humans later emerged after similarities were found in the spike proteins of SARS-CoV-2 and pangolin viruses.

But other animals should also be considered, according to Yang Zhang, professor of computational medicine and bioinformatics at the University of Michigan and colleagues, who co-authored a study linking SARS-CoV-2 to pangolins, writing on The Conversation. They said that more than one animal can spread a virus to a human.

"For example, while civets are best known for transmitting SARS, other animals such as raccoon dogs and ferret badgers are also able to carry SARS. Similarly, cats and ferrets can also be infected by SARS-CoV-2; it is still unknown whether humans can get infected by the coronavirus residing within these animals," they wrote.

The only way to prove which animal the coronavirus came from is to find it in the wild, Arinjay Banerjee, a postdoctoral researcher McMaster University who studies coronaviruses told Nature. "Other approaches will only give you anecdotal evidence," he said.

But as the virus has infected so many people, finding it in an animal may not reveal much at this stage in the pandemic, as it may have been infected by people, Li Xingguang, who studies viral evolution at Wuhan University of Bioengineering told Nature, stating: "The situation is very complex now."

As it stands, Robertson explained, the consensus is that SARS-CoV-2 was naturally transmitted from a horseshoe bat into the human population, and the data from the pangolins sampled to date suggest they are not the intermediate host for SARS-CoV-2. The PLOS Pathogens study supports this idea, he said.

Preston said the PLOS Pathogens study highlights the on-going threat of viruses jumping into humans and to monitor environments where humans and wildlife come into close contact.

Jeremy Rossman, honorary senior lecturer in virology at the University of Kent, told Newsweek further studies will likely identify different coronavirus strains in bats, pangolins and other animals and it is possible one will find the exact precursor virus to SARS-CoV-2. "However, the exact origins of the virus and its jump into humans may never be conclusively proven."