The biggest mystery: what it will take to trace the coronavirus source

Since the pandemic began, the question of where the coronavirus came from has been one of the biggest puzzles. It almost certainly originated in bats, and a new study out this week — the most comprehensive analysis of coronaviruses in China — adds further weight to that theory.

But the lack of clarity around how the virus passed to people has meant that unsubstantiated theories — promoted by US President Donald Trump — that it escaped from a laboratory in China persist.

By contrast, most researchers say the more likely explanation, given what is known so far about this virus and others like it, is that bats passed it to an intermediate animal, which then spread it to people.

In mid-May, the World Health Assembly, the World Health Organization’s key decision-making body, passed a resolution that calls on the agency to work with other international organizations to identify the animal source.

But scientists say that the nature of the evidence required means it’s going to be hard to track down the animal source — and also difficult to completely rule out the facility in question, the Wuhan Institute of Virology (WIV), as the source.

That the WIV, a laboratory highly regarded for its work on bat coronaviruses, is located in the city where the outbreak first emerged is probably just a coincidence. But the leading work its researchers are doing to unravel the original of the pandemic, as well as the unsubstantiated speculation about its possible role in the outbreak, has thrust it into the spotlight: several of the authors of the latest bat study work there.

An independent investigation at the facility is probably the only way to convincingly rule out the lab as a possible source of the outbreak, but scientists think such a probe is unlikely, given the delicate geopolitics that surround the issue.

Animal origin

In the latest study, researchers analysed partial sequences for some 1240 coronaviruses found in bats in China. They report that the virus fuelling the pandemic, SARS-CoV-2, is most closely related to a group of viruses found in horseshoe bats (Rhinolophus).

Their finding adds to an earlier report that a coronavirus called RATG13, which some of the authors found in intermediate horseshoe bats (Rhinolophus affinis) in Yunnan province, shares 96% of its genetic sequence with SARS-CoV-2¹.

The authors of the latest analysis note that the viral group to which both viruses belong seems to have originated in Yunnan province. But as the team only collected viruses from sites in China, they cannot rule out that a SARS-CoV-2 ancestor might have come from neighbouring Myanmar and Lao, where horseshoe bats also live.

A co-author of the study, posted on bioRxiv, is Shi Zheng-Li, the WIV virologist whose extensive work surveying coronaviruses in China has drawn particular attention during the pandemic. Shi has refuted suggestions that the lab has ever had a virus similar to SARS-CoV-2, and has previously cautioned about the risks of another SARS-like disease emerging from animals. “She had actually warned us that there are bat viruses in nature that can spill over to humans,” says Volker Thiel, a virologist at the University of Bern.

No bat viruses found so far are similar enough to SARS-CoV-2 to be a direct ancestor. So while the new virus could have been spread to people directly from bats, researchers think it’s more likely that it passed through an intermediate animal. Evidence suggests that the related coronavirus that causes severe acute respiratory syndrome (SARS) passed to people from bats by way of civets, and that camels were the intermediate source of another related virus that causes Middle East respiratory syndrome (MERS). Those species were found to host versions of the viruses almost identical to those seen in humans^2,3.

Finding a virus nearly identical to SARS-CoV-2 in an animal would provide the most persuasive evidence for how it passed to people. It would require extensive sampling of coronaviruses in wildlife and livestock in China, says Rob Grenfell, the director of the Commonwealth Scientific and Industrial Research Organisation’s Health and Biosecurity unit in Melbourne, Australia. China has reportedly started such investigations, but little information on their status has been released.

Similar investigations happened after the original SARS outbreak. The first cases emerged in November 2002, but the cause wasn’t identified as a coronavirus until April 2003. By then, authorities already suspected that animals were involved, because more than 30% of the early cases in Guangdong province, China, where the outbreak started, were in workers at a live animal market. A month later, researchers found the virus in civets at live animal markets. Researchers later linked civets to cases of SARS in people — a waitress and customer at a restaurant serving palm civets (Paradoxurus hermaphroditus) tested positive for the virus, along with six of the animals⁴.

But it took nearly 15 years and extensive animal sampling to find a closely related virus in bats. It was Shi Zheng-Li who led the team that sampled thousands of bats in remote caves in China. And even though they found⁵ all the genetic components of the SARS virus, they did not find one virus with the same genetic make-up.

Scientists say that pinpointing the animal source of SARS-CoV-2 could take just as long. Groups around the world are already using computational models, cell biology and animal experiments to investigate species that are susceptible to the virus — and so possibly the source — but so far it remains elusive.

Lab speculation

The WIV hosts a maximum-security lab that is one of a few dozen biosafety-level-4 (BSL-4) labs around the world. Although there’s no evidence to support the suggestion that the virus escaped from there, scientists say that completely ruling it out will be tricky and time consuming.

The lab does hold coronaviruses related to SARS-CoV-2, so it is possible that one could have escaped, perhaps if a lab worker accidentally became infected from a virus sample or animal in the facility and then passed it on to someone outside the facility. It is also theoretically possible that scientists at the lab tweaked the virus’s genome for research purposes before it escaped, but, again, there is no evidence that they did. Shi declined to respond to Nature’s questions about her experiments, saying that she has been inundated with media requests.

In April, lab director Yuan Zhiming said the virus did not come from the lab. He told Chinese state broadcaster CGTN: “We know what virus research is being carried out, we know how viruses are managed, we know how samples are managed. The virus is definitely not coming from here.” No one at the Wuhan Institute of Virology responded to Nature’s multiple requests for comment on the suggestions that the lab might have involved in the outbreak.

In 2017, Nature visited the Wuhan BSL-4 lab and Yuan showed off its gleaming new equipment, high-security testing rooms and a ventilation system carefully designed to ensure that the pathogens were securely contained. He said that his team had worked with French biosafety scientists to build the most advanced biosafety research lab in the world, and that the group was taking every measure to prevent accidents. Yuan said he “wanted to let the world understand why we want to construct this lab, and to describe its role in safeguarding the world”.

There is also no record of accidents at the institute, but viruses, including SARS, have previously accidentally escaped from labs, including in China — although none has led to a significant outbreak. An accidental release of SARS was traced back to a lab in Beijing in 2004 when researchers there got sick. But there have been no reports of researchers at WIV becoming ill.

Determining whether the lab had anything to do with the virus will require a forensic investigation, say several scientists. Investigators would be looking for viruses that matched the genetic sequence of SARS-CoV-2 and, if they found one, any evidence that it could have escaped. To do that, authorities would need to take samples from the lab, interview staff, review lab books and records of safety incidents, and see what types of experiment researchers had been doing, says Richard Ebright, a structural biologist at Rutgers University in Piscataway, New Jersey.

In an interview with Chinese publication Caixin in February, Shi said she hoped there would be an investigation, because she was confident that no connection would be found between her institute and the new coronavirus. Chinese state media have also said an investigation is likely, although no details have been released.

But such an investigation might not yield anything conclusive either way, says Frank Hamill, who previously managed a BSL-4 lab in the United States. Hamill, who currently works for MRIGlobal, which advises laboratories on biosafety, in Gaithersburg, Maryland, says that it would be in the best interests of the lab to be more open about what research its staff are doing. But he adds that US biosecurity laboratories are far from fully transparent about their own research. “We are in a tough spot when we ask the Wuhan institute to open up its files and let people starting poking around. It’s a bit hypocritical,” says Hamill.

A product of nature

Some scientists outside China have studied the virus’s genome in detail and conclude that it emerged naturally rather than from a lab.

An analysis⁶ published in Nature Medicine on 17 March discusses several unusual features of the virus, and suggests how they likely arose from natural processes. For starters, when performing experiments that seek to genetically modify a virus, researchers have to use the RNA of an existing coronavirus as a backbone. If scientists had worked on the new coronavirus, it’s likely that they would have used a known backbone. But the study’s authors report that no known viruses recorded in the scientific literature could have served as a backbone to create SARS-CoV-2.

To enter cells, coronaviruses use a ‘receptor binding domain’ (RDB) to latch onto a receptor on the cell’s surface. SARS-CoV-2’s RBD has sections that are unlike those in any other coronavirus. Although experimental evidence — and the sheer size of the pandemic — shows that the virus binds very successfully to human cells, the authors note that computer analyses of its unique RBD parts predict that it shouldn’t bind well. The authors suggest that as a result, no one trying to engineer a virus would design the RBD in this way — which makes it more likely that the feature emerged as a result of natural selection.

The authors also point to another unusual feature of SARS-CoV-2, which is also part of the mechanism that helps the virus to work its way into human cells, known as the furin cleavage site. The authors argue that natural processes can explain how this feature emerged. Indeed, a similar site has been identified in a closely-related coronavirus, supporting the authors claim that the components of SARS-CoV-2 could all have emerged from natural processes.

The analyses show that it is highly unlikely that SARS-CoV-2 was made or manipulated in a lab, says Kristian Andersen, a virologist at Scripps Research in La Jolla, California, and the lead author of the paper. “We have a lot of data showing this is natural, but no data, or evidence, to show that there’s any connection to a lab,” he says.

But several scientists say that although they do not believe that the virus escaped from the lab, analyses are limited in what they can reveal about its origin.

There is unlikely to be a characteristic sign that a genome has been manipulated, says Jack Nunberg, a virologist at the University of Montana in Missoula, who does not believe the virus came from a lab. If, for instance, scientists had added instructions for a furin cleavage site into the virus’s genome, “there is no way to know whether humans or nature inserted the site”, he says.

In the end, it will be very difficult, or even impossible, to prove or disprove the theory that the virus escaped from a lab, says Milad Miladi, who studies RNA evolution at the University of Freiburg in Breisgau, Germany. And despite scientists such as Shi warning the world that a new infectious respiratory disease would emerge at some point, “unfortunately, little was done to prepare for that,” he says. Hopefully governments will learn and be better prepared for the next pandemic, he says.