Series of studies point towards natural coronavirus spillover event, scientists suggest

Scientists say the world is “getting warmer” in terms of finding the natural origins of the coronavirus pandemic, after a host of studies suggested the coronavirus did not escape from a lab but jumped from animals to humans.

The papers, published in the last few weeks, have provided what experts described as “many smoking guns” for the theory that the Sars-CoV-2 virus spilled over from bats to humans via an as-yet-unidentified animal.

Researchers are also believed to be heading back to caves where similar viruses have been found previously, as well as combing through old viral samples, to find any connections with the virus that causes Covid-19.

The papers come after a flurry of interest in the  “lab leak” hypothesis, which suggests that Sars-CoV-2 escaped from a lab in Wuhan, China, where the virus was first identified. There is a general consensus that the possibility needs to be explored.

However Professor David Robertson, head of viral genomics at the Centre for Virus Research at the University of Glasgow, and an author of one of the papers, told The Telegraph: “If you follow the data, the smoking guns are there [to suggest natural origins].” 

The first study, published in Scientific Reports, paints a vivid picture of the flourishing illegal wildlife trade in Wuhan. Between May 2017 and November 2019, some 47,000 wild animals from 38 species were sold across four markets in the city, including the Huanan market linked to an early cluster of cases. 

The research, which initially intended to study the spread of a tick-borne disease in Wuhan, found several animals now known to be susceptible to Covid – such as civets, racoon dogs, badgers and mink – were consistently caged in cramped, unhygienic conditions before being sold and butchered. But pangolins and bats were not identified in market stalls.

“The data that we have in our paper offers an observation that animals capable of being involved in Covid transmission were present in Wuhan up until the point of the epidemic being declared,” Dr Chris Newman, an evolutionary ecologist at Oxford University and co-author of the report, told The Telegraph. “But we don't know if they had Covid.”

The joint World Health Organization-China investigation into the origins of Sars-CoV-2 concluded it was “very likely” the virus jumped from bats to humans via an as-yet-unknown intermediary animal. 

But until now, the most recent hard evidence that wild animals were being illegally traded in Wuhan’s markets came from 2014, when British virologist Prof Eddie Holmes visited the sites and took photos of caged wildlife. 

While this and other unverified reports were mentioned in the WHO-China study, a source close to the investigation team said Chinese researchers refuted the possibility that live mammals were sold at the market because the only verifiable evidence was from 2014.  

The source added there has been some frustration that the data in the paper was not disclosed sooner. Dr Newman said delays were caused by one journal rejecting the paper after months of toing and froing, plus the process of peer review at Scientific Review. 

Regardless, Prof Holmes said the striking data adds weight to the theory that the wildlife trade was key in the spread of Covid, as do two other papers – though there is not yet a “smoking bat”. 

One, from an international team led by Chinese researchers, identifies “the closest relative” of Sars-CoV-2 found yet across most of the viral genome, among samples taken from bats in Yunnan province, China, between May 2019 and November 2020. It was published in Cell. 

Among 411 samples from horseshoe bats, the researchers found four new coronaviruses. They singled in particularly on RpYN06, which is similar to another bat virus reported by this team, RmYN02, last year.

Both are more similar to Sars-CoV-2 across most of their genomes than the virus usually reported to be closest – RaTG13, which was also found in bats in Yunnan. 

RpYN06’s spike protein differs from that of Sars-CoV-2 as it is a recombinant – a virus formed when two viruses infect one host and recombine to make a new virus. The spike protein is one of the areas most susceptible to change either through recombination or mutation. 

King’s College London virologist Professor Stuart Neil said the research was a sign that the world is “getting warmer” in identifying where Sars-Cov-2 came from. 

“These [viruses] are still not close enough to be ancestral, but they point towards even closer relatives being out there undiscovered.”

A third pre-print, from a British team, tracks the evolutionary history of the virus and its viral family in bats across Asia. It concludes Sars-CoV-2 diverged from its closest viral relatives 40 years ago, and calls for urgent research into what happened in between then and now.  

“The natural spillover scenario was always the most plausible because of the association with the market,” said Prof Robertson, a co-author of the pre-print. “This is being supported by the finding of more related viruses in bats.”  

He said the evidence was mounting now simply because science is a “process”. 

“It’s not a court case where we investigated and we have all the evidence, things will keep unfolding and undoubtedly we will find closer viruses.

“People are looking at this in China, Vietnam, and southeast Asia. For all we know, they have already sampled caves in China and know exactly what happened, but they are not telling us because they don’t want to be blamed.

He added: “The smoking guns are the market, the Sars-like evolution, the predictions that this would happen, and the finding of new viruses that are closer than RaTG13. The smoking guns are all there – we just don’t have the actual shooter.” 

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