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The Virus Hunters Trying to Prevent the Next Pandemic

16 minute read

Nobody saw SARS-CoV-2 coming. In the early days of the pandemic, researchers were scrambling to collect samples from people who had mysteriously developed fevers, coughs, and breathing problems. Pretty soon, they realized that the disease-causing culprit was a new virus humans hadn’t seen before.

And the world, lacking a coordinated global response, was unprepared. Some countries acted quickly to develop tests for the novel coronavirus, while others with fewer resources were left behind. With a virus oblivious to national borders, and with travel between countries and continents more common than it had been in previous centuries when past plagues had hit, these inequities meant everyone was vulnerable. The solution? Shutting the world down, closing borders, and asking people to hide from the virus by staying indoors.

It soon became clear that the world would only weather this pandemic by working together, and that governments alone couldn’t necessarily save us. Surveillance into the microbial world was necessary in order to predict coming outbreaks—and, barring that, then at least detect them more quickly after they hit. Some in the private sector saw an opportunity. In 2021, Abbott—the global health care company known for its diagnostic tests—decided to start the Abbott Pandemic Defense Coalition (APDC), the first convergence of public health and academic experts led by a private company. It now includes 15 members based in 12 countries. Its mission: to detect new pathogens that threaten to wreak havoc on the world, share their discoveries by making their findings available publicly, and contain them before it’s too late.

The experiment is just beginning, but it’s already paying off. APDC partners were among the first in the world to spot several dangerous mutations of the COVID-19 virus—including Omicron—just as they were emerging, which put countries on high alert and allowed them to prepare in advance by increasing testing, doubling down on vaccine programs, and advising infected people to isolate. It was a big change from being blindsided by the original version of the virus.

Now, the virus hunters are watching out not only for new versions of SARS-CoV-2, but they’re also continuing their search for other dangerous disease-causing bugs. In June, as monkeypox began infecting people around the world, the network monitored genetic sequences of the virus that showed it came from the less virulent of two monkeypox strains endemic in Africa, and that existing vaccines would continue to be effective. Using that data, Abbott has developed a monkeypox PCR test (for research purposes only) that coalition members are using to track the virus in their respective countries so they can hopefully contain spread of the disease and detect any changes in the viral genome as soon as they appear. APDC also monitors a host of other emerging infectious diseases, including hepatitis, Zika, dengue, meningitis, and yellow fever. These are predicted to become more widespread; as humans continue to encroach on previously wild geographical regions, we’re more likely to come into contact with pathogens that can pose a threat to public health. Climate change also raises the risk of infectious diseases as species that carry viruses or bacteria spread to broader areas.

Laboratory technicians from members of the Abbott Pandemic Defense Coalition undergo training at AP8 in Abbott Park, Ill.
Laboratory technicians from members of the Abbott Pandemic Defense Coalition undergo training at AP8 in Abbott Park, Ill.Courtesy Abbott

COVID-19 has turned out to be an ideal proving ground for this type of coalition. Partner labs in the coalition analyze the genetic sequences of thousands of virus samples collected from COVID-19 patients in their region. The virus is constantly evolving, and by comparing sequences to those from existing samples, scientists can immediately distinguish any noteworthy differences and monitor them more closely. These changes—especially if they are appearing in not just one part of the world but in multiple regions simultaneously—could represent worrying mutations that make it easier for the virus to spread or cause more serious disease.

If one of the partners detects a pattern, they immediately share it with all partners to determine if others are seeing the same trend. If they are, then Abbott and the members join forces to ensure the current tests are still able to detect the new strain. Should the tests fail, then Abbott scientists would get to work revising it. “We are able to build tools like tests and assays that can be distributed to our partners and potentially manufacture them at scale if needed,” says Gavin Cloherty, who leads APDC. (Fortunately, current tests continue to pick up the latest variants of the virus.) The coalition also shares any concerning discoveries with public-health officials and government leaders around the world, including the World Health Organization (WHO), as well as on global public databases. Knowing what might be coming can help health authorities deploy limited COVID-19 resources like testing and treatments, as well as additional personnel, to where they are needed the most.

The coalition may seem self-serving for a company like Abbott, which has a long history of providing diagnostic tests for pathogens—including its popular BinaxNOW COVID-19 rapid at-home test kits. Being the first to hear of any changes in SARS-CoV-2 samples around the world gives Abbott’s scientists a running start at modifying diagnostics, should the need arise. Finding more variants and more viruses means more tests—which makes good business sense.

But the public-health partners benefit, too. It’s an expensive operation to run: Abbott wholly funds the coalition, providing its partners with state-of-the-art equipment, training, and lab supplies to collect samples and conduct genetic sequencing. Abbott also shares its scientific and manufacturing expertise, since it has been surveilling viruses globally for the last 30 years, from the start of the HIV/AIDS epidemic. That ongoing global surveillance program is the predecessor to APDC; it monitors known pathogens—instead of new or emerging ones—for mutations that might affect diagnostic tests and treatments. APDC was created to concentrate on diseases that couldn’t be explained by existing microbes. For the members, joining the coalition also links otherwise isolated public health labs around the world—from places including Africa, Central America, and Asia—into a tight-knit community that can quickly disseminate information about any new pathogens they discover, or aberrations they find in the genetic sequences of viruses.

“Although it is a private company, and diagnostic kits are to be sold, what I see is an effort to bring down scientific borders and increase communication across the globe,” says Esper Kallas, professor of infectious and parasitic diseases at the University of Sao Paulo, which is a coalition partner.

Such worldwide collaborations aren’t entirely new, and most have been initiated by philanthropic groups. The Rockefeller Foundation’s Pandemic Prevention Institute, for example, which recently partnered with the Pasteur Institute, is a philanthropy-led group of 33 members that act as sentinels for emerging infectious diseases that could become public health threats.

COVID-19 forced these types of partnerships between public-health facilities, foundations, and private companies, which have the financial resources to develop new tests or treatments. Such collaborations are increasingly essential for mounting a quick and efficient response against a fast-moving virus. Perhaps the best example of the power of such alliances was the U.S.’s ability to develop, test, manufacture, and distribute millions of COVID-19 vaccines in under a year. The feat never would have been possible if the U.S. government had not funded pharmaceutical companies’ costs in developing and manufacturing these vaccines; doing so helped not only the U.S., but also the world benefit from the revolutionary mRNA shots that had never before been used against a virus.

The only way to be truly prepared for the next pandemic is to make such coalitions the norm. Sustaining them between public health threats is among the best ways to defend against the next big one. “Public-private partnerships are essential for [disease] surveillance, testing, treatments, you name it,” says Dr. Eric Topol, director and founder of the Scripps Research Translational Institute. “We do better if those groups are working together.”

Laboratory technicians from members of the Abbott Pandemic Defense Coalition mark samples during a training at AP8 in Abbott Park, Ill.
Laboratory technicians mark samples during a training at AP8 in Abbott Park, Ill.Courtesy Abbott

So far, APDC members have contributed to identifying three major SARS-CoV-2 variants. In June and July 2020, as the coalition was being formed, hospitals in South Africa noticed a rapid uptick in patients admitted with COVID-19 that seemed out of proportion to previous trends. A research team at the Center for Epidemic Response and Innovation (CERI) at Stellenbosch University in South Africa—which was already collaborating with Abbott on tracking HIV—analyzed samples from patients at 200 clinics when they found the mutation that the WHO later designated as Beta. “We found the exact same variant in samples from clinics that were hundreds of kilometers away, so we knew it was widespread and that we potentially had a new variant,” says Tulio de Oliveira, who leads CERI. Data from the South African hospitals suggested that younger people were the most affected, and that they were getting sicker than people who had been infected with the earlier version of the virus.

De Oliveira immediately alerted global health authorities to the new variant, which allowed public health experts to prepare for a potential wave of patients who might need more intensive hospital care. Back in Chicago at Abbott’s headquarters, scientists quickly determined that, based on the variant sequences, the company’s existing PCR and recently authorized at-home rapid tests for SARS-CoV-2 could still detect the new variant.

Brazilian researchers issued a similar alarm several months later. Researchers at the University of Sao Paulo had worked with Oxford scientists during Brazil’s 2015 Zika outbreak to develop a mobile, compact machine to process virus samples; later using it to scan COVID-19 samples, they noticed unusual sequences coming from northern Brazil in the Amazon Basin, centered around the city of Manaus. The changes to the viral genome turned out to signal a new variant, Gamma, that would go on to cause significant disease and death in the area. But as tragic as Gamma’s local effects were, early detection likely prevented it from causing even more disease and death elsewhere in the country and world, says Kallas, whose team helped to identify Gamma. “What would have happened if Gamma would not have been discovered until it reached a big city such as Sao Paulo, of 20 million people?” he says. “We would have been caught completely off guard.” Luckily, coalition scientists confirmed that existing rapid tests also worked to detect Gamma, just as they had for Beta.

Then came the most stunning shape-shifting the virus had undergone yet: Omicron. A lab technician in South Africa was conducting routine genetic sequencing of random SARS-CoV-2 samples and noticed that the virus was missing one of three hallmark proteins that all of the previous variants had. The technician tipped off de Oliveira’s group, which conducted a more detailed analysis showing that the virus had picked up a shocking 30 or so mutations—most of them in the spike protein, the region that vaccine and drug makers targeted. In the span of six hours, hundreds of samples from more than 100 clinics from different cities in South Africa arrived at de Oliveira’s labs in Stellenbosch. Sequencing those samples revealed the same pattern of mutations. Within 36 hours, de Oliveira notified the health minister and president of South Africa, along with the WHO, that a new version of the virus was brewing.

Within days of confirming the findings, de Oliveira also shared them with coalition partners around the world—in the U.S., India, Thailand, Brazil, and Columbia, as well as throughout the continent of Africa—to give countries a head start in looking for the genetic changes signaling the Omicron variant, just as they had done with Beta and Gamma.

The collaboration quickly put lots of different eyes on the same urgent problem. “Each of us brings a different skill set,” says Dr. Sunil Solomon, assistant professor of medicine in infectious diseases at Johns Hopkins and director of YRG Care in Chennai, India, one of the coalition partners. Solomon and others at the center have extensive experience researching HIV, for example, and now community-based surveillance and data analysis of SARS-CoV-2. “Sometimes you can get siloed, and people can go down rabbit holes thinking what they are working on is important, so they forget what the bigger picture is. The coalition is focused on translating what all of us find for clinical relevance to make sure that whatever we are doing is tailored toward improving the public’s health.”

Laboratory technicians during a training at AP8 in Abbott Park, Ill.
Laboratory technicians during a training at AP8 in Abbott Park, Ill.Courtesy Abbott

Coalitions like APDC could serve as a model for standing up more extensive networks of virus hunters. “Our efforts are intended to augment and add to the overall global efforts, with the philosophy of networking different networks together,” says Cloherty. “Viruses move very fast. We also need to be moving very fast by working with our partners.” Cloherty says he shares the APDC’s findings with teams at the WHO, the U.S. Centers for Disease Control and Prevention (CDC), and the Bill and Melinda Gates Foundation in order to better coordinate programs and work together efficiently.

Gates is a big proponent of this type of virus-hunting squad. In his 2022 book, How to Prevent the Next Pandemic, he describes the ideal global infectious disease monitoring system, which he dubs GERM, for Global Epidemic Response and Mobilization. The idea is to maintain a network of scientists whose sole mission is to scan the world’s databases of infectious disease cases and raise alerts if new, unexplained infections are bubbling up anywhere in the world. GERM would also be responsible for sending SWAT teams of experts to help countries where outbreaks are occurring contain and control the spread of disease.

The WHO has a similar system to track emerging public-health threats through its Global Outbreak and Alert Response Network (GOARN), which provides emergency assistance to countries confronting infectious disease outbreaks. But GOARN’s responsibilities extend beyond such outbreaks to include crises in food safety, natural and manmade disasters, and the release of chemical toxins. The CDC also conducts surveillance for emerging pathogens, and maintains teams abroad as well as mobile groups ready to fly anywhere around the world to provide assistance if countries ask for it.

But historically, the enthusiasm for maintaining these types of systems ramps up during outbreaks—such as during Ebola in the 2010s, and now COVID-19—only to die down when the threat retreats, along with funding. More resources and personnel are deployed during urgent needs, but they aren’t maintained between crises, which experts say is crucial to a strong surveillance system. Gates calculates that it would cost the world about $1 billion to support 3,000 full-time “virus hunters” in a sustained war against invisible marauders—less than one-thousandth what nations currently spend on defense, to protect themselves against potential wars with one another. The funding, Gates says, shouldn’t come from solely philanthropists or foundations like his, but from governments, which need to commit to and invest in preparing for public-health threats in the same way they shore their defenses against other threats, and from private companies, which can provide much-needed experience and resources in the form of tests and agile manufacturing capabilities if new tests or therapies are required, to make the process more efficient.

Such investment is becoming more critical with every year. Coronaviruses alone have caused significant outbreaks several times over recent decades—and that’s just one family of viruses. As the world learned with COVID-19, by the time a pandemic hits, it’s already too late to start creating relationships and building networks among different countries to efficiently share real-time information about a dynamic disease and ever-evolving virus. And the network’s potential is only as extensive as its reach; the more partners linking together, the more likely it is that the world will benefit from any alarming findings, such as an emerging infectious disease, that a partner discovers. COVID-19 also made clear that monitoring for changes in existing pathogens and keeping a lookout for new ones isn’t a job for governments and global health groups alone. Industry can play important roles in controlling health outbreaks, but there often aren’t financial incentives for businesses to do so. “I don’t see enough companies who have made billions of dollars using some of that great profit to do things that are not in their self interest,” says Topol. Instead, the world is left with a patchwork system of public-health sentinels that’s riddled with enough holes for pathogens like coronaviruses to slip through undetected, giving them enough time to spread before diagnostic tests, vaccines, or treatments can be developed. “It’s out of sight, out of mind,” says Sumit Chanda, professor of immunology and microbiology at Scripps Research, of the existing preparedness strategy.

Even COVID-19 vaccine development in the U.S. is currently stalled following the initial success of their development and manufacturing. With more transmissible variants of SARS-CoV-2 circulating, and with low uptake of the shots in many parts of the world, new vaccine designs—including nasal shots that might provide stronger and more durable protection against respiratory viruses like SARS-CoV-2—haven’t moved beyond the research and early testing stages because of a lack of funding. Pharmaceutical companies could be enticed to invest in testing and developing innovative solutions like these if the government or philanthropic groups matched the funds industry partners put into development, Topol says, so no one group is left subsidizing the entire cost. But so far, those investments aren’t forthcoming.

Systemic changes—like sustained funding—are also needed in order to be prepared for the next pandemic. Until we make those types of commitments, the world’s ability to see viruses coming will continue to be limited. But some experts, like Kallas, are hopeful that COVID-19 proves to governments how critical collaborations between countries can be, especially when it comes to identifying new potential health threats.

“Some people call the Amazon Brazil a hot zone, a place where diversity in flora and fauna are so [rich] that the chances of a bug jumping from one species into humans is high,” he says. A country like Brazil, then, would benefit greatly from having more virus hunters. Gamma, after all, won’t be the last virus to emerge from there. “We need a cultural change in mindset,” he says, “one that sees the value to society in investing in science to decrease suffering and make us a better society.”

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