Once upon a time in Wuhan: Will we ever know the origins of Covid-19? [Updated August 24]

The bitter debate over the origins of the virus has been a low point for both science and science journalism. We need to recover from these embarrassments if we want to prevent the next pandemic.

What don’t we know and when didn’t we know it?

This week, as early as tomorrow, U.S. intelligence agencies are expected to deliver their report on the origins of Covid-19 to President Joe Biden. On May 26 of this year, Biden gave the intel community 90 days to look into it, and the time is now up. In his public statement on the order, Biden provided some key context:

Back in early 2020, when COVID-19 emerged, I called for the CDC to get access to China to learn about the virus so we could fight it more effectively. The failure to get our inspectors on the ground in those early months will always hamper any investigation into the origin of COVID-19.

As for the assumptions the intelligence agencies were making going into the inquiry, Biden added:

…shortly after I became President, in March, I had my National Security Advisor task the Intelligence Community to prepare a report on their most up-to-date analysis of the origins of COVID-19, including whether it emerged from human contact with an infected animal or from a laboratory accident. I received that report earlier this month, and asked for additional follow-up. As of today, the U.S. Intelligence Community has “coalesced around two likely scenarios” but has not reached a definitive conclusion on this question. Here is their current position: “while two elements in the IC leans toward the former scenario and one leans more toward the latter – each with low or moderate confidence – the majority of elements do not believe there is sufficient information to assess one to be more likely than the other.”

Everyone interested in this question—and that should be literally everyone, given the importance of knowing how, when, and where this killer pandemic got started—is hoping that 90 days was enough to at least generate some conclusions, even if they are only tentative. But many, and I am among them, think that is unlikely to happen, for a number of reasons—including, as Biden intimated above, the continuing refusal by Chinese officials to allow the international scientific and public health community to conduct an independent investigation into the origins of the virus.

To many, that lack of cooperation means China is acting as if it is guilty of something, perhaps a lab accident in Wuhan. Donald Trump, after initially praising China and President Xi for their handling of the pandemic in the earliest days, quickly turned around and began to blame China and to whip up anti-Chinese sentiment in the most crudely racist way (“China virus,” “Wuhan virus,” and other epithets designed to deflect attention from Trump’s own failure to recognize the seriousness of the pandemic.)

The reaction was swift from many scientists and science journalists, especially as Trump’s racist campaign led to acts of anti-Asian violence in the United States. In early 2020, a group of influential researchers and public health officials branded any thoughts that the virus might have come from a lab as a “conspiracy theory,” at the same time creating the red herring that a lab origin automatically meant China was genetically engineering viruses to be deadly to humans—the specter of bioweapons research. At that time, the hypothesis that the virus might have been the result of an unintentional lab accident, rather than deliberate bioengineering, was hardly discussed, even though it was always a more likely scenario given the Wuhan Institute of Virology’s long years of research into coronaviruses.

Given the overt racism of Trump and his minions, it was understandable that anyone with anti-racist sentiments might jump to China’s defense in the face of accusations Chinese scientists were somehow responsible for the pandemic. And for a solid year, few dared to be accused of being “conspiracy theorists” by suggesting that a lab origin for Covid-19 was a possibility that had to be considered and investigated.

Understandable, yes, but ultimately unwise. There is nothing racist in asserting that China has a long history of human rights abuses (think Hong Kong and the Uighurs), that it had hidden data during the earlier SARS epidemic, or that it punished and silenced Chinese scientists who sounded an early alarm about the new virus.

But the road to hell is paved with good intentions, as the saying goes, and for a solid year those supposedly good intentions stifled debate, discussion, and even scientific research into Covid-19 origins. Even earlier this year, when journalists began to explore the lab-leak hypothesis again and bona fide scientists called for a serious investigation, some reacted with a venom that could hardly be called scientific or journalistically fair. Here is one fairly notorious example:

Angela Rasmussen, a virologist now at the University of Saskatchewan, has emerged as one of the most virulent, if you will, opponents of the lab-leak hypothesis, and I think the rhetoric she uses above speaks for itself. This is not a scientific approach as we normally think of it, whatever Rasmussen’s credentials might be (she is often quoted in media stories on the debate and on the pandemic, where she is on somewhat firmer ground, although Rasmussen was skeptical that the virus was a major worry in the earliest days.)

Amy Maxmen is a science journalist at Nature whose coverage of the pandemic has been very good outside of the origins debate, and whose writings and Tweets demonstrate a serious social conscience; nevertheless, she too has become a self-appointed cheerleader for the natural origins hypothesis, despite growing recognition among serious scientists that there is just not enough evidence yet to come to firm conclusions about either of the two leading hypotheses.

Rasmussen and Maxmen are not alone in their ferocity and their bias, but they are probably among the worst in that regard. The results of this kind of fierce partisan fighting in the light of a serious lack of solid data is, in my opinion, great harm to science, science journalism, and the public understanding of science—the latter being a goal to which everyone involved in the debate supposedly subscribes.

Is there a better way? Two recent articles, one in a lay publication and one in a scientific journal, point the way to more even-handed approaches in the face of scientific uncertainty. Let’s have a look.

Scientific uncertainly, uncertain science.

Last May, right around the time that both journalists and scientists began arguing for at least a reconsideration of the lab-leak hypothesis, New York Times reporter Apoorva Mandavilli—a talented journalist I considered a friend and colleague (we worked together at the NYU science journalism program)—Tweeted that the lab-leak hypothesis had “racist roots.” She very quickly deleted the Tweet, saying that it was “badly phrased” and acknowledging the reporting her colleagues at the Times were doing on the origins debate.

As many said at the time, including myself, it was a big mistake, and I hope Apoorva now regrets it. Certainly it was considered an embarrassment by many science journalists, although out of respect for Apoorva’s reputation little was said about it at the time.

So I was particularly pleased to see a News Analysis in yesterday’s Times by Apoorva, entitled “The U.S. Is Getting a Crash Course in Scientific Uncertainty.” While this article steers clear of the virus origins debate, perhaps wisely, Apoorva does discuss in detail the way that scientific and public health thinking about the pandemic has changed over the past 18 months, and the need for the public to be trained in dealing with the realization that no one has all the answers, whether it be about vaccines, masks, remote learning, and the like. As she puts it:

Scientific understanding of the virus changes by the hour, it seems. The virus spreads only by close contact or on contaminated surfaces, then turns out to be airborne. The virus mutates slowly, but then emerges in a series of dangerous new forms. Americans don’t need to wear masks. Wait, they do.

As we know, frequently shifting advice by public health officials has exacerbated a dangerous situation where a large percentage of the U.S. population does not want to be vaccinated, wear masks, or even acknowledge that the virus is something that should affect their lives in any way. Clearly, scientists and science journalists need to be able to communicate uncertainty about what the data is saying—even if, at a given moment, they have opinions, even strong ones, about where the data leads.

In the case of the virus origins debate, as I have said above, these two closely related groups have often failed to show respect, in their own thinking and writing, to those very uncertainties, and to convey them to the public in a fair and honest way.

So I was even more happy to see, in the July/August 2021 issue of mBio—a journal published by the American Society for Microbiology—an excellent model for how scientists and journalists should communicate with the public. In an editorial entitled “Can Science Help Resolve the Controversy on the Origins of the SARS-CoV-2 Pandemic?” authored by the journal’s Editor in Chief Arturo Casadevall and two other senior microbiologists, the three scientists go over the evidence for the major hypotheses dispassionately (they actually consider four of them) and conclude that while the “tools of science” can provide important information, they are “unlikely to provide a definitive answer.” (While the authors say that current data favor the natural origins hypothesis, they point out that “science can provide only probabilities, not certainty.”)

On the say to that unsatisfying conclusion, however, Casadavell and his colleagues provide a textbook example—or what should be in the textbooks, in my view—of how to deal with the evidence when a lot of data are missing. I’m going to invoke the fair use provision of U.S. copyright laws, and (I hope) the indulgence of the journal and the authors, and reproduce their Figure 1 as an example of this approach:

With this clear guide for readers, the authors methodically go through each scenario, giving the arguments pro and con for each one in what I think is the most neutral manner possible. I highly recommend that you read it.

One section of the article I particularly appreciated is a discussion of the notorious “furin cleavage site,” which SARS-CoV-2 has, but is unusual in the viral subgenus that both SARS-CoV-2 and SARS-CoV-1 (the causative agent of the earlier SARS epidemic) belong to. The furin cleavage site, which helps the virus enter human cells, has been bandied about as evidence for both the lab-leak and natural origins hypotheses. The authors write:

However, the significance of the furin cleavage site in SARS-CoV-2 may be overblown. Spike furin cleavage sites may provide optimal infectivity and/or pathogenesis for some coronaviruses but not all of them. A furin cleavage site is not necessary for the virulence of all coronaviruses, and SARS-CoV-1, a virus with approximately 10 times the mortality of SARS-CoV-2, has no such site. Interestingly, the furin site in SARS-CoV-2 is an inefficient proteolytic site relative to those found in other betacoronaviruses such as HKU1 and mouse hepatitis virus (MHV) (22). Furthermore, among MHV strains, while most have cleavage sites and encode efficiently cleaved spikes, the MHV2 strain encodes an uncleaved spike and is highly pathogenic (23) and cleavage at the S1/S2 site can be carried out by proteases other than furin (22). A better understanding of molecular motifs associated with certain feral species could provide additional clues, but that too could come about only from extensive reconnaissance of the natural reservoirs combined with experimental work on cell tropism and pathogenesis, knowledge that is currently unavailable. However, any virus adapted either to laboratory conditions or to an intermediate host could have accumulated sufficient sequence changes such that finding its ancestor in the wild may no longer be possible with certainty. Hence, short of more transparency from laboratory operations or human disclosure, deep sampling and genomic analysis alone are unlikely to provide definitive information to support the lab escape hypothesis.

I quote this at length because, while I have read pretty much every article in the mainstream and scientific media about the viral origins debate, I have rarely seen the furin cleavage site referred to other than as an argument for one side of the argument or the other. Moreover, while the authors themselves lean towards the natural origins hypothesis, they frankly admit that a lack of transparency (presumably by Chinese officials) is hampering our ability to figure out just what the genomic data are trying to tell us.

Throughout the Casadevall article, the authors explore the way that each piece of evidence we currently possess can be used as a point for both sides of the argument.

The authors conclude with a quote from Maggie Bender, a writer for the online publication Vice, that aptly summarizes the problem of scientific uncertainty and the responsibility of both scientists and science journalists to convey it adequately:

Science values possibility, but people value certainty. So far, science communication hasn’t been able to bridge the two successfully. And during the largest public health crisis of a generation, that disconnect has had disastrous consequences. This discomfort with probability and an overreliance on false assuredness are the issues at the heart of the debate over the origins of SARS-CoV-2.

I wish scientists and science journalists would follow the example of these authors when they write about Covid-19 origins or other controversial subjects. They would be doing both themselves and the public a big favor, even if it requires more effort in the writing and more commitment by readers trying to understand what is going on.

In other words, it is not helpful to call scientists and science journalists racists, trolls, assholes, China apologists, Fauci-lovers, or other epithets when we are looking for answers to the origins of a pandemic that has cost more than 4 million lives worldwide. We have real scientists, and we have real journalists; all they need to do is real science, and real journalism.

The morning after afterthoughts.

It often happens that after I post a commentary on this newsletter, I think of some things I wish I had said. That’s true for all writers, of course, and usually we have to just let it go or say it next time. But one of the advantages of online publishing, of course, is that you can add thoughts as they happen.

In looking at the role science journalists have played in the lab-leak debate, it seems that some have learned the lessons of the Trump era a little too well. I taught journalism at City College of New York during the Trump presidency, but even before he was elected, as a science journalism prof at both New York University, we told our stories to be aware of the pitfalls of “objectivity.” We cautioned that they no longer had to give “both sides” when covering climate change, since there was a solid scientific consensus that human activity was warming the planet; and we didn’t have to give “equal time” to creationists, since the scientific evidence solidly supported the theory of evolution. (In a much earlier era, journalists struggled with how much coverage they should give to a few scientists who denied AIDS was caused by HIV.)

During the Trump presidency, it took while to apply these standards to what the president was doing, even after it became clear that Trump was lying on an almost daily basis. I think at least three years went by before the New York Times finally began using the “L word” and say that Trump was lying; now that he and his cult followers are still pushing the “Big Lie” about who won the last election, the Times and other publications have been less hesitant.

So when Trump began pointing the finger at China and blaming the entire country (not just its leaders, mind you) for the Covid-19 pandemic, perhaps it was understandable that some journalists jumped to counter what they considered yet another racist lie. I have been a strong advocate of calling it like it is, both as a journalism teacher and a journalist. But avoiding “both-sides-ism” does not absolve journalists of seeking out the truth about any particular claims, nor does it void their responsibility to do the reporting and be transparent about what the facts say, or don’t say.

As many have pointed out, you don’t fight anti-Asian racism by making excuses for China’s lack of transparency during the pandemic, a serious lack of international cooperation that persists to the present day (and which the intel agencies reporting back to Biden this week will have had to deal with as a major obstacle to knowing what really happened.)

This is why I have been so hard on those journalists (and scientists) who have conflated the desirable goal of fighting racism with the outcome of what is a scientific question, how did the Covid-19 pandemic start. To be blunt, it is a matter of scientific and journalistic maturity, as well as professional competence and ethical responsibility, to keep these things separate even when they seem to be intermeshed.