Why research labs were drastically unprepared for Covid-19, even after SARS

SARS-CoV-2 isn’t the first coronavirus the government has thrown money at.
SARS-CoV-2 isn’t the first coronavirus the government has thrown money at.
Image: REUTERS/Brendan McDermid
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Back in 2003, Jairam Lingappa was an epidemiologist at the US Centers for Disease Control and Prevention (CDC). When a new coronavirus called SARS emerged in China, he and his CDC colleagues, as well as many researchers around the world, jumped into action. “People were concerned,” Lingappa recalls. “With any epidemic for a new agent, there is a certain amount of fear that just comes from not knowing what the agent’s characteristics are.”

Lingappa co-authored a number of studies about SARS between 2003 and 2004. But then he switched to studying how host genomics affect HIV infection, and started working at the University of Washington, where he is now a professor of global health. In part, he changed focus because the new opportunity allowed him to follow his research interests. But there was a practical concern, too: “Probably the major driver is that SARS was diminishing as a real threat in terms of actual disease occurrence,” he says. “Because of the nature of our funding system, that leads to funding drying up. Our system tends to focus on the thing that hurts now.”

Recently, Lingappa has submitted several grant proposals to study the role of inflammation in infection from a newer coronavirus: SARS-CoV-2. The funding is there. In late March, the US government responded to the novel coronavirus—which by that stage had already claimed more than 42,000 lives globally and tanked the economy—by directing $1.2 billion of its $2.2 trillion economic stimulus package towards scientific research across a number of agencies. That additional money would help researchers at institutions all over the country understand how the virus works in order to develop treatments and vaccines, though some argued it wasn’t enough.

Researchers like Lingappa have seen this before. Coronaviruses as a category have been around for centuries, and science first identified the cold-causing bugs in the 1960s. Since then, new, more dangerous versions have emerged—with extra funding to counter them.

In 2003, to combat SARS, the US National Institute of Allergy and Infectious Diseases (NIAID) increased the amount of funding intended to help study the disease from up to $5 million per year to $51 million, according to STAT News. The National Institutes of Health (NIH) also opened up new opportunities for funding that year. In 2013, soon after MERS emerged in Saudi Arabia, NIAID offered some additional sources of funding for studies to understand the virus causing it and to develop tests and treatments.

Though Congress didn’t throw money at researching those coronaviruses the way they have for SARS-CoV-2, US-based scientists had opportunity to understand how they emerge and how they work. Money could have gone to public health initiatives, with epidemiologists and contact tracers at the ready should a pandemic break out. They might have even been able to create a universal coronavirus vaccine.

Such research could have ended the current pandemic before it even started. So why didn’t it? Why was the scientific community caught so off-guard by SARS-CoV-2?

What labs are able to focus on depends completely on how they’re funded. And the way that money has been allocated makes it really hard to do research that might prepare the world for the next big health crisis.

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Follow the money

In the US today, most virology research in academic labs is funded by grants from the National Institutes of Health (NIH). (The National Science Foundation offers virology researchers another smaller pot of funding, as do pharmaceutical companies.) Using that money, researchers primarily in the US conduct studies into the mechanisms of, and possible treatments for, viruses as far-ranging as the flu, HIV, Zika, Ebola, and any number of animal-borne viruses. The NIH claims to be the largest single public funder of biomedical research in the world; it allocates grants to researchers in the US and internationally.

Scientists at academic institutions write grant proposals for projects they want to undertake, and submit them to the relevant branch of the NIH; a group of scientists known as a “study section” decides who gets the grants. It’s a notoriously competitive process.

Overall, the NIH has $41 billion to allocate for fiscal year 2020, about 80% of which is doled out through grants. A successful grant application can help pay for everything from research materials to scientists’ salaries. Some of that money also goes to the university itself, which it can spend on high-tech equipment or new facilities.

But before all that happens, the researchers writing the proposals have to decide which branch of NIH fits what they want to study. It’s not always straightforward.

There are 27 institutes of the NIH, and in fact, the NIH doesn’t have a department simply focused on “virology.” Virologists have to consider which facet of human health—infectious diseases (NIAID), or if it affects the lungs (National Heart, Lung, and Blood Institute), or if it’s basic research (National Institute of General Medical Sciences)—they could impact with their work, even if it’s not directly relevant to their research. Sometimes scientists may spin a grant application to match a department where they think they stand a better chance of receiving funding.

“When I was a postdoc, we were working on the genetics and signaling of a particular immune gene,” says Brianne Barker, a biologist at Drew University. “One of our collaborators had shown there had seemed to be polymorphisms in asthma patients”—that is, that it’s a virus that also has an effect on the lungs. So instead of sending their grants to the most logical choice, the NIAID, Barker recalls sending grants to the NHLBI, playing up the gene’s relationship to asthma. Her advisor had said the NHLBI funded a higher percent of applications, and with more money, than NIAID. She still didn’t get the grant, she says.

That kind of bottleneck has made it more difficult for basic coronavirus research to continue in the years between major outbreaks. “In the 10 years between the emergence of SARS and the emergence of MERS, you definitely had to be thinking about a broader context for your research for it to seem significant to the general public and to the NIH, when writing grants,” Lisa Gralinski, a researcher at University of North Carolina, told STAT News.

It’s important to study the diseases that cause the most human suffering, of course. But a focus on science’s direct applications means that basic, fundamental research has suffered.

“We have a pattern in our medical research landscape in which outbreaks lead to a surge in research investment, and if and when those outbreaks wane, as they invariably do, other priorities take their place,” Jason Schwartz, a professor at the Yale School of Public Health, told NBC News. “As a result, you lose those opportunities to capitalize on that initial investment, and the cycle starts over again.”

In 1997, Congress, in an effort to make the US more competitive in medical innovation, voted to double the NIH’s budget, a huge boon for researchers. But up until about 2017, the budget has remained relatively flat. Just when coronavirus research had a great excuse to become a priority, grant funding got even tighter. In the decades that funding remained flat, cutting-edge equipment has become more necessary (and expensive) for researchers, and the number of scientists has continued to grow. That’s created a very competitive funding environment.

Vincent Racaniello, a microbiologist at Columbia University who studies how viruses affect the immune system, recalls what getting funding was like when he first started doing NIH-funded research, in 1979: “Back then, it was relatively easy to get an NIH grant, and you could [use it to] do just about anything that was interesting. Then over the years, the money got tighter as it got siphoned off into other things,” he says.

As a result, scientific funding can become yet another partisan issue, subject to the short-sighted perspective of politics. In April, for example, the NIH abruptly terminated a grant used to fund a lab in Wuhan, China that was studying how coronaviruses move from bats to humans, after the Trump administration made it known that it suspected that SARS-CoV-2 might have originated there.

“We do need a shift in the way science is supported in this country. Right now it’s at the whim of politicians who don’t understand it,” Racaniello says.

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An unclear future

You’d think a crisis as disruptive and as global as SARS-CoV-2 might prompt a call to change the way science is funded. Instead of waiting for a disease to emerge before allocating billions of dollars into research, why not spread scientific funding across a wider range of disciplines and fields? Understanding the basics that underlie many different diseases could help prepare for the next emergent disease, the next pandemic.

Some researchers across scientific fields have been calling for change for years before this crisis hit. Lingappa emphasizes the need to fund independent investigators—academic researchers who aren’t beholden to the research goals of large consortiums and can instead follow their own curiosity. But how exactly to get researchers like that the funding they need is up for debate. In one proposal, the NIH would dole out money via lottery; another calls for scientists to vote on which grants get funding. It’s unclear if the NIH or any other major scientific bodies have taken any of these proposals seriously.

Even those resigned to the current system are skeptical that the coronavirus crisis will bring about the reform needed to prepare for the future. “I think this will be forgotten as soon as it’s over. Congress will say ‘We don’t need money for these coronaviruses.’ The smart thing to do would be invest in drugs and vaccines and have stuff ready for the next pandemic,” Racaniello says.

Instead, scientists are getting creative with where they source their funding. They’re looking into non-traditional sources such as global health nonprofits and even the US military, through agencies like the US Defense Threat Reduction Agency.

“Every one of these epidemics is a unique opportunity to understand our biology and how we relate to pathogens,” Lingappa says. “Every dark cloud has its silver lining. Here it’s that, with proper focus on diversity of research, we will really be able to identify facets of other health conditions and how to treat them better.”