Did gain-of-function research create covid-19? We asked Ralph Baric.


[Baric is referring to a 2015 collaboration with Zhengli Shi of the Wuhan Institute of Virology, or WIV, in China, which created a so-called chimera by combining the “spike” gene from a new bat virus with the backbone of a second virus. The spike gene determines how well a virus attaches to human cells. A detailed discussion of the research to test novel spike genes appears here.]

However, the sequence was repeatedly requested after the covid-19 pandemic emerged, and so after discussion with the NIH and the journal, it was provided to the community. Those who analyzed these sequences stated that it was very different from SARS-CoV-2.

How did that chimeric work on coronaviruses begin?

Around 2012 or 2013, I heard Dr. Shi present at a meeting. [Shi’s team had recently discovered two new coronaviruses in a bat cave, which they named SHC014 and WIV1.] We talked after the meeting. I asked her whether she’d be willing to make the sequences to either the SHC014 or the WIV1 spike available after she published.

And she was gracious enough to send us those sequences almost immediately—in fact, before she’d published. That was her major contribution to the paper. And when a colleague gives you sequences beforehand, coauthorship on the paper is appropriate.

That was the basis of that collaboration. We never provided the chimeric virus sequence, clones, or viruses to researchers at the WIV; and Dr. Shi, or members of her research team, never worked in our laboratory at UNC. No one from my group has worked in WIV laboratories.

And you had developed a reverse-genetics technique that allowed you to synthesize those viruses from the genetic sequence alone?

Yes, but at the time, DNA synthesis costs were expensive—around a dollar per base [one letter of DNA]. So synthesizing a coronavirus genome could cost $30,000. And we only had the spike sequence. Synthesizing just the 4,000-nucleotide spike gene cost $4,000. So we introduced the authentic SHC014 spike into a replication-competent backbone: a mouse-adapted strain of SARS. The virus was viable, and we discovered that it could replicate in human cells.

So is that gain-of-function research? Well, the SARS coronavirus parental strain could replicate quite efficiently in primary human cells. The chimera could also program infection of human cells, but not better than the parental virus. So we didn’t gain any function—rather, we retained function. Moreover, the chimera was attenuated in mice as compared to the parental mouse-adapted virus, so this would be considered a loss of function.

One of the knocks against gain-of-function research—including this research—is that the work has little practical value. Would you agree?

Well, by 2016, using chimeras and reverse genetics, we had identified enough high-risk SARS-like coronaviruses to be able to test and identify drugs that have broad-based activity against coronaviruses. We identified remdesivir as the first broad-based antiviral drug that worked against all known coronaviruses, and published on it in 2017. It immediately was entered into human trials and became the first FDA-approved drug for treating covid-19 infections globally. A second drug, called EIDD-2801, or molnupiravir, was also shown to be effective against all known coronaviruses prior to the 2020 pandemic, and then shown to work against SARS-CoV-2 by March 2020.

Consequently, I disagree. I would ask critics if they had identified any broad-spectrum coronavirus drugs prior to the pandemic. Can they point to papers from their laboratories documenting a strategic approach to develop effective pan-coronavirus drugs that turned out to be effective against an unknown emerging pandemic virus?

Unfortunately, remdesivir could only be delivered by intravenous injection. We were moving toward an oral-based delivery formulation, but the covid-19 pandemic emerged. I really wish we’d had an oral-based drug early on. That’s the game-changer that would help people infected in the developing world, as well as citizens in the US.

Molnupiravir is an oral medication, and phase 3 trials demonstrate rapid control of viral infection. It’s been considered for emergency-use authorization in India.

Finally, the work also supported federal policy decisions that prioritized basic and applied research on coronaviruses.

What about vaccines?

Around 2018 to 2019, the Vaccine Research Center at NIH contacted us to begin testing a messenger-RNA-based vaccine against MERS-CoV [a coronavirus that sometimes spreads from camels to humans]. MERS-CoV has been an ongoing problem since 2012, with a 35% mortality rate, so it has real global-health-threat potential.

By early 2020, we had a tremendous amount of data showing that in the mouse model that we had developed, these mRNA spike vaccines were really efficacious in protecting against lethal MERS-CoV infection. If designed against the original 2003 SARS strain, it was also very effective. So I think it was a no-brainer for NIH to consider mRNA-based vaccines as a safe and robust platform against SARS-CoV-2 and to give them a high priority moving forward.

Most recently, we published a paper showing that multiplexed, chimeric spike mRNA vaccines protect against all known SARS-like virus infections in mice. Global efforts to develop pan-sarbecoronavirus vaccines [sarbecoronavirus is the subgenus to which SARS and SARS-CoV-2 belong] will require us to make viruses like those described in the 2015 paper.

So I would argue that anyone saying there was no justification to do the work in 2015 is simply not acknowledging the infrastructure that contributed to therapeutics and vaccines for covid-19 and future coronaviruses.

The work only has value if the benefits outweigh the risks. Are there safety standards that should be applied to minimize those risks?

Certainly. We do everything at BSL-3 plus. The minimum requirements at BSL-3 would be an N95 mask, eye protection, gloves, and a lab coat, but we actually wear impervious Tyvek suits, aprons, and booties and are double-gloved. Our personnel wear hoods with PAPRs [powered air-purifying respirators] that supply HEPA-filtered air to the worker. So not only are we doing all research in a biological safety cabinet, but we also perform the research in a negative-pressure containment facility, which has lots of redundant features and backups, and each worker is encased in their own private personal containment suit.

Another thing we do is to run emergency drills with local first responders. We also work with the local hospital. With many laboratory infections, there’s actually no known event that caused that infection to occur. And people get sick, right? You have to have medical surveillance plans in place to rapidly quarantine people at home, to make sure they have masks and communicate regularly with a doctor on campus.

Is all that standard for other facilities in the US and internationally?

No, I don’t think so. Different places have different levels of BSL-3 containment operations, standard operating procedures, and protective gear. Some of it is dependent on how deep your pockets are and the pathogens studied in the facility. An N95 is a lot cheaper than a PAPR.

Internationally, the US has no say over what biological safety conditions are used in China or any other sovereign nation to conduct research on viruses, be they coronaviruses or Nipah, Hendra, or Ebola.

The Wuhan Institute of Virology was making chimeric coronaviruses, using techniques similar to yours, right?

Let me make it clear that we never sent any of our molecular clones or any chimeric viruses to China. They developed their own molecular clone, based on WIV1, which is a bat coronavirus. And into that backbone they shuffled in the spike genes of other bat coronaviruses, to learn how well the spike genes of these strains can promote infection in human cells.

Would you call that gain-of-function?

A committee at NIH makes determinations of gain-of-function research. The gain-of-function rules are focused on viruses of pandemic potential and experiments that intend to enhance the transmissibility or pathogenesis of SARS, MERS, and avian flu strains in humans. WIV1 is approximately 10% different from SARS. Some argue that “SARS coronavirus” by definition covers anything in the sarbecoronavirus genus. By this definition, the Chinese might be doing gain-of-function experiments, depending on how the chimera behaves. Others argue that SARS and WIV1 are different, and as such the experiments would be exempt. Certainly, the CDC considers SARS and WIV1 to be different viruses. Only the SARS coronavirus from 2003 is a select agent. Ultimately, a committee at the NIH is the final arbiter and makes the decision about what is or is not a gain-of-function experiment.

Definitions aside, we know they were doing the work in BSL-2 conditions, which is a much lower safety level than your BSL-3 plus.

Historically, the Chinese have done a lot of their bat coronavirus research under BSL-2 conditions. Obviously, the safety standards of BSL-2 are different than BSL-3, and lab-acquired infections occur much more frequently at BSL-2. There is also much less oversight at BSL-2.

This year, a joint commission of the World Health Organization and China said it was extremely unlikely that a lab accident had caused SARS-CoV-2. But you later signed a letter with other scientists calling for a thorough investigation of all possible causes. Why was that?

One of the reasons I signed the letter in Science was that the WHO report didn’t really discuss how work was done in the WIV laboratory, or what data the expert panel reviewed to come to the conclusion that it was “very unlikely” that a laboratory escape or infection was the cause of the pandemic.

There must be some recognition that a laboratory infection could have occurred under BSL-2 operating conditions. Some unknown viruses pooled from guano or oral swabs might replicate or recombine with others, so you could get new strains with unique and unpredictable biological features.

And if all this research is being performed at BSL-2, then there are questions that need to be addressed. What are the standard operating procedures in the BSL-2? What are the training records of the staff? What is the history of potential exposure events in the lab, and how were they reviewed and resolved? What are the biosafety procedures designed to prevent potential exposure events?