How Virus Hunters Are Preparing for the Next Pandemic

NSARS-CoV-2 was not something anyone expected. Researchers were trying to get samples of people with mysterious breathing difficulties, fevers and coughs in the beginning stages of the pandemic. Pretty soon, they realized that the disease-causing culprit was a new virus humans hadn’t seen before.

And there was no coordinated international response. Some nations rushed to produce tests against the new coronavirus while others waited. This virus is able to travel freely between continents, countries, and states, making everyone more vulnerable. What is the solution? The solution?

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. Private sector workers 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. The group now has 15 members, with 12 locations. 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. This was quite a change to being completely blindsided by the original 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. As monkeypox was spreading around the globe, in June the network monitored DNA sequences to determine if it originated from one of the two less severe strains of monkeypox endemic in Africa. The network also determined that current vaccines were still effective. Abbott used that information to create a monkeypox-PCR test for research. This is what coalition members use to monitor the spread of the virus within their countries and identify any potential changes in the virus’ genome. APDC is also monitoring a variety of new infectious diseases like Zika, yellow fever, Zika, Zika, Zika, dengue and meningitis. 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. The risk of spreading infectious diseases due to climate change is also increasing as bacteria and viruses spread from one area to another.

Members of the Abbott Pandemic Defense Coalition receive training at AP8 Abbott Park (Ill.).

Courtesy Abbott

COVID-19 proved to be a great proving ground. Scientists at the partner labs analyze genetic sequences taken from COVID-19 victims in order to determine if there are any significant differences. Scientists can quickly identify any differences in sequences and track them down more precisely by comparing existing sequences. 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 partner notices a trend, they share the information with the other partners immediately to see if any others have noticed it. Abbott, the other members and their partners will join hands to confirm that current testing are capable of detecting the new strain. If the test fails, Abbott scientists will begin revising the results. “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. The virus is still being detected in current testing. All concerns are shared with the public-health and government leaders worldwide, as well as at the World Health Organization (WHO), and on public global databases. The ability to predict what is coming will allow health officials to deploy COVID-19 resources such as tests and treatments as well as extra personnel where needed.

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.

The public-health partners are also benefited. 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 has also contributed its expertise in scientific and manufacturing since it has been tracking viruses worldwide for 30 years. This began at the dawn 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 required these partnerships to be formed between foundations and public-health institutions. Collaborations like these are crucial for a swift and efficient response against fast-moving viruses. 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.

This is the only way to prepare for the next pandemic. They are the most effective way to protect against the next major pandemic. “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.”

During a training session at AP8 Abbott Park, Ill., laboratory technicians marked samples.

Courtesy Abbott

APDC member have helped to identify three SARS-CoV-2 variants. Hospitals in South Africa saw a sudden increase in COVID-19 patients as the coalition was formed. This seemed to be out of line with 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. The data obtained from South African hospitals indicated that the affected were younger and were suffering more severe symptoms than the people infected by the older version.

De Oliveira immediately alerted international health officials to the existence of the variant. Public health professionals were able to prepare for potential patient influxes who may need 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 had issued an identical alarm 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. Gamma was the new virus variant that caused significant illness and death throughout the region. 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.

Omicron, the greatest shape-shifting of all the viruses was then performed. South Africa’s lab technician noticed that one of three key proteins missing from the virus, which was the same as the other variants. 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. The same mutation pattern was revealed when the samples were sequenced. De Oliveira, together with WHO, notified South Africa’s president and health minister within 36 hours that there was a new virus.

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.

Many eyes were quickly drawn to the same issue by this collaboration. “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 other members of the center are experts in HIV research and community-based surveillance as well data analysis for 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.”

Labor technicians at AP8 training in Abbott Park (Ill.).

Courtesy Abbott

APDC is a good example of how to build larger networks of virus researchers. “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 supports this kind of squad for virus hunting. He wrote this book in 2022 How to Avoid the Next PandemicHe describes the perfect global epidemic response and mobilization system called GERM. 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 will also send SWAT teams to assist countries affected by disease outbreaks.

A similar system is used by the WHO to monitor emerging public-health risks through its Global Outbreak and Alert Response Network. It provides immediate assistance for countries facing infectious disease epidemics. 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 monitors emerging pathogens and has mobile teams that can fly to assist countries in need.

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.

This investment becomes more important 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 research in America is on hold despite the fact that they were initially successful in their manufacturing and development. 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. Topol states that pharmaceutical companies might be attracted to develop innovative solutions and invest in their testing. However, the funding gap between the government and philanthropic organizations could make it more difficult for them to do so. 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. Some experts like Kallas are optimistic that COVID-19 will prove to governments the importance of collaborations among countries, particularly when it comes down to identifying potential new 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. Brazil would be a great country to have more virus researchers. 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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