The Origins of the Covid Pandemic: What We Know and Don’t Know

The New York Times, March 17, 2023 (with Sheryl Gay Stolberg and Benjamin Mueller)

WASHINGTON — Long after the Covid pandemic emerged from Wuhan, the origin of the coronavirus remains a subject of intense scientific scrutiny, and even more intense political debate.

A team of researchers has added fuel to the bonfire by presenting data at a World Health Organization meeting suggesting a wild animal known as a raccoon dog was sold at the same stall at the Huanan Seafood Wholesale Market in Wuhan, China, where investigators found traces of the coronavirus.

The scientists suggested that raccoon dogs could have served as a so-called intermediate host for the virus, allowing it to spread through the market.

That development arrives less than three weeks after reports that the Energy Departmenthad concluded — albeit with “low confidence” — that an accidental laboratory leak in Wuhan most likely caused the coronavirus pandemic.

Scientists who have studied the genetics of the virus, and the patterns by which it spread, say the most likely cause is that the virus jumped from live mammals to humans — a phenomenon known as “zoonotic spillover” — at the Huanan market, where the first cases of Covid-19 emerged in late 2019.

But other scientists say circumstantial evidence points to the virus having escaped from a lab, possibly the Wuhan Institute of Virology, which had deep expertise in researching coronaviruses. Lab mistakes do happen: In 2014, after accidents involving bird flu and anthrax, the Centers for Disease Control and Prevention tightened its biosafety practices.

Government agencies have been analyzing the origin of the pandemic since 2020, but they remain split about the most likely explanation. Most still favor a spillover. None of them changed their conclusions after seeing the Energy Department’s findings, officials said.

The debate is politically fraught. The lab leak theory gained currency among Republicans in the spring of 2020 after President Donald J. Trump, who used inflammatory terms to blame China for the pandemic, latched onto the idea.

Many Democrats have not been persuaded by the hypothesis. Some say they believe it was spillover, and others believe there may never be enough intelligence to draw a conclusion.

But apart from the politics, experts say that understanding what caused a public health crisis that has killed nearly seven million people could help researchers and governments prevent the next one.

Here’s what we know, and don’t know, about the origins of the coronavirus.

Why is it hard to know for certain how the pandemic started?

It is often difficult to find the origins of viruses, but China has compounded that problem by making it very difficult to gather evidence.

By the time Chinese researchers arrived to collect samples from the Huanan market, it had been closed down and disinfected because a number of people linked to it had become sick with what would later be recognized as Covid. No live animals were left.

Some scientists also believe that China has provided an incomplete picture of early Covid cases. And they worry that a directive to hospitals early in the outbreak to report illnesses specifically linked to the market may have led doctors to overlook other cases with no such ties, creating a biased snapshot of the spread.

What have scientists done to investigate?

Experts have tried to work around the holes in the data.

Scientists have examined cases of patients hospitalized before the call went out for doctors to look for ties to the market. They have also mapped the locations of early Covid cases in Wuhan — including both people who were initially linked to the market and those who were not — and found what they say are signs that the virus started spreading at the market.

Some of those scientists have studied maps of where investigators found the virus in the Huanan market, including walls, floors and other surfaces, and found that those samples clustered in an area of the market where live animals were sold. The raccoon dog DNA came from one of those stalls.

And genetic analyses from the very early stages of the pandemic, some scientists have said, suggest that the virus spilled over into people working or shopping at the market on at least two separate occasions.

Other scientists have disputed that studies like those can indicate a market origin with much confidence. They believe, for example, that the evidence for two separate spillovers at the market could also be evidence of the virus evolving as it spread from person to person.

Some researchers have also argued that for all the attention being paid to the Wuhan Institute of Virology, not enough has been paid to a different research site in the city, the Wuhan Center for Disease Control and Prevention. That center is much closer to the Huanan market.

What’s all this fuss about raccoon dogs?

On March 14, some of the scientists who had published studies pointing to the Huanan market offered more data. They said their new findings were consistent with the spillover hypothesis.

Perusing a database in which genetic sequences of coronaviruses are shared, the researchers discovered that Chinese investigators had quietly uploaded data from their Jan. 1, 2020, search in the Huanan market — after a delay of more than three years.

The data included all the genetic sequences the investigators collected, not just those from coronaviruses. And it included DNA from a wild species called the raccoon dog, the researchers told the World Health Organization.

That finding is at odds with claims from Chinese authorities that wild animals were not sold at the Huanan market.

Raccoon dogs are vulnerable to coronavirus infections. Two decades ago, they may have served as the so-called intermediate host for another coronavirus: the one that caused the SARS epidemic.

The discovery of raccoon dog DNA at the market, if confirmed, would not be definitive proof that the animals were brought to the market harboring the coronavirus that started the pandemic. But the researchers found it striking that the raccoon dog DNA came from a stall that was also positive for SARS-CoV-2, the virus that causes Covid.

After the scientists discovered the raccoon dog DNA, the newly uploaded sequences were removed from the database. It is not clear why that happened. The scientists are preparing a report of their findings.

Why do some people suspect a laboratory leak?

In October, Republicans on the Senate health committee published an analysis of the origins of the pandemic that argued it was “most likely the result of a research-related incident,” while acknowledging that the conclusion was “not intended to be dispositive.”

Many of its assertions were echoed by House Republicans, who held a hearing in early March outlining the case for a the lab leak theory.

The Republicans’ report spotlighted what its authors described as holes in the natural origins theory, as well as “persistent biosafety problems” at the Wuhan Institute of Virology.

The report, though, relied largely on existing public evidence, rather than new or classified information, and did not produce evidence to show that the Wuhan institute stored any virus that could have become the coronavirus causing Covid, with or without scientific tinkering.

The lab leak hypothesis is bolstered, the report said, by the absence of any published evidence that SARS-CoV-2 was circulating in animals before the pandemic. Samples of virus collected on refrigerators, countertops and other surfaces at the Huanan market were genetically similar to human samples, suggesting the virus was shed by humans, not animals, it said.

But some experts said the inability to find an infected animal did not prove anything, because China shut down the market and killed all of the animals before they could be tested.

In 2018, before the pandemic, the Wuhan institute and its partners — including EcoHealth Alliance, a research group whose work has been financed by the United States — sought Defense Department funding to collect and experiment on coronaviruses with novel traits that would make them highly transmissible in humans.

The group’s project was never funded. But the Senate Republicans’ report noted that the coronavirus has traits similar to those the researchers were looking for. That has persuaded some scientists that a lab leak was possible. The report surmised that the virus may have escaped, perhaps by infecting a researcher who carried it outside the lab.

The National Institutes of Health paid for some of EcoHealth Alliance’s work in Wuhan, but N.I.H. officials have repeatedly said the viruses being studied with American taxpayer dollars bore no genetic resemblance to the one that causes Covid. But Dr. Lawrence A. Tabak, the N.I.H.’s acting director, acknowledged during a recent congressional hearing that he did not know what other work the Wuhan institute was doing.

What does the American intelligence community say?

In May 2021, several months after he took office, President Biden ordered the nation’s intelligence agencies to conduct a 90-day inquiry into the cause of the pandemic. The findings of that review were released in August 2021 and reaffirmed what the agencies had previously said: Both the natural origins theory and the lab leak theory were plausible.

In a statement at the time, Mr. Biden called on China to be more transparent about what had led to the emergence of the virus there in late 2019.

The Energy Department’s recent conclusion — that the pandemic was caused by a lab leak — is based on intelligence that is not publicly available, so it is difficult to know what accounted for the change. But the department’s use of the phrase “low confidence” indicates that its level of certainty is not high.

The F.B.I., however, has concluded with “moderate confidence” that the virus emerged accidentally from a lab.

Four other intelligence agencies and the National Intelligence Council have concluded, with low confidence, that the virus most likely emerged through natural transmission. The C.I.A., the nation’s pre-eminent spy agency, has not taken a position and remains undecided.