What We Know and Don’t Know About the Origins of Covid

Scientists and spy agencies have tried to determine where the coronavirus originated, but conclusive evidence is hard to come by and the nation’s intelligence agencies are split.

The Energy Department’s conclusion, with “low confidence,” that an accidental laboratory leak in China most likely caused the coronavirus pandemic has renewed questions about what sparked the worst public health crisis in a century — and whether the virus at the heart of it was somehow connected to scientific research.

Scientists and spy agencies have tried assiduously to answer that question, but conclusive evidence is hard to come by. The nation’s intelligence agencies are split, and none of them changed their conclusions after seeing the Energy Department’s findings, officials said.

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 scientific phenomenon known as “zoonotic spillover” — at the Huanan Seafood Wholesale Market in Wuhan, China, the city in which the first cases of Covid-19 emerged in late 2019.

But other scientists say there is evidence, albeit circumstantial, that the virus came from a lab, possibly the Wuhan Institute of Virology, which had deep expertise in researching coronaviruses. Lab accidents do happen; in 2014, after accidents involving bird flu and anthrax, the Centers for Disease Control and Prevention tightened its biosafety practices.

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 lab leak hypothesis; some say they believe the explanation of natural causes, and others say there may never be enough intelligence to draw a conclusion.

The Energy Department’s findings have given a boost to House Republicans, who are investigating the pandemic’s origins. 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 understand how to 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, the police had shut down and disinfected the market because a number of people linked to it had become sick with what would later be recognized as Covid. No live market 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 same 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.

And separate 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 two separate occasions.

Other scientists have disputed that studies like those can indicate a market origin with much confidence. They have said, 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 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.

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.”

The 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 in its collections that could have become the virus causing Covid-19, 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, the virus that causes Covid-19, 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 its 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 project was never funded. But the report pointed to that proposal, noting that the virus that causes Covid-19 has traits similar to what the researchers were looking for. That has persuaded some scientists that a lab leak was possible. The Senate Republican report surmised that the virus may have escaped — perhaps by infecting a researcher who then 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-19. 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 new conclusion 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.

What is Congress doing to address the question?

House Republicans have been trying to investigate the origins of the pandemic and gather evidence that might shed light on what caused it — including whether China concealed facts about the initial outbreak and what research American tax dollars may have financed in Wuhan.

Now that Republicans are in charge of the House, that investigative work is escalating in several committees, including the Intelligence Committee, the Energy and Commerce Committee and the Select Subcommittee on the Coronavirus Pandemic. The subcommittee will hold its first hearing on the origins question on March 8, a spokeswoman said.