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Tuesday, April 16, 2024

The Pandemic Revolutionized Disease Surveillance. Now What?

For the past two years, the hottest data set in the United Kingdom has dropped every Friday. Scientists, journalists, and amateur data sleuths all dial up one specific website: The Covid-19 Infection Survey, run by the Office for National Statistics (ONS), an independent government agency. With 180,000 participants who are swabbed every fortnight, it is one of the largest surveys of coronavirus infections and antibodies in the UK. It monitors how many people are infected with Covid at any one time and whether specific regions or age groups are at particular risk. Because it samples such a large and randomized slice of the population, it avoids biases from local changes in testing guidance, individual behavior, or access to tests.

Randomly selected households receive a letter from the ONS that invites them to register for the survey. Once they're registered, a worker visits the home to collect swabs from each volunteer’s throat and nose and ask a few questions. After the first appointment, volunteers have the option to continue taking part in the survey, receiving follow-up appointments that include monthly blood tests. The information gathered will be linked to the participants’ health records to uncover how Covid-19 infection—and vaccination—can affect things like frequency of doctor’s visits or health conditions that may develop after infection.

In return, participants have been remunerated with vouchers for hotels, the cinema, and supermarkets. The survey was said to be “worth its weight in gold” for its role in understanding Covid epidemiology and the ability to respond quickly to new variants—not just in the UK, but around the world. (During times of particularly high demand, the ONS released a midweek preview of Friday’s numbers on Wednesday, like a widely anticipated movie dropping teaser trailers.) “I’m not aware of anything comparable anywhere else in the world, really,” says Colin Angus, a health inequalities modeler at the University of Sheffield. 

The survey’s special ingredient is its randomness. Unlike daily testing data, which is typically collected from people who are showing symptoms or have recently been exposed to Covid, it samples just about anyone. Daily test numbers can also be muddied by social inequities that affect how available tests are and whether there's more testing within any particular age or demographic group. “It's really the only study I know that gives estimates that I would be scientifically confident in, because there's so many problems with trying to do it in the messy real-world data of people who just happen to go get tested,” says Jennifer Beam Dowd, professor of demography and population health at the Leverhulme Center for Demographic Science at the University of Oxford. 

But as the pandemic enters its third year, England has declared it’s time to “live with Covid,” and justifying the costs of such widespread data collection is getting trickier. In late February, the British government announced that the survey will continue, but in a slimmed-down version, likely with fewer participants. The UK government also announced in mid-March that funding for two other major infection surveys will end: Funding for the React study, led by Imperial College London researchers, which randomly tests about 150,000 people across England every month and was responsible for discovering that a third of Covid cases are asymptomatic, will be scrapped at the end of March. The ZOE Covid study, which tracks volunteers’ symptoms via an app, is also losing government funding. Free mass testing is also ending on April 1, with free tests only available to the most vulnerable.

Researchers like Angus warn that relaxing restrictions and surveillance at the same time could be unwise, since these surveys act as early warning systems for new variants or mysterious bumps in cases. With stripped-back restrictions, data is all we’ve got. “It's like sticking your fingers in your ears and going ‘La, la, la—if I don't look for it, then the bad thing must have gone away,’” says Angus. 

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“I don't think now is the time to wind down,” agrees Natalie Dean, a biostatistician at Emory University. “We still have the threat of future waves because there’s the threat of new variants.” 

And for some of the researchers, the loss of funding is a big disappointment. “We believe that not renewing the funding is a huge mistake for the UK and for science. The UKHSA [UK Health Security Agency] have acknowledged that the pandemic isn’t over yet so for them to take this decision is both a surprise and disappointment,” ZOE cofounder Tim Spector, a professor of genetic epidemiology at King’s College London, wrote in a statement to WIRED.

Helen Ward, professor of public health at Imperial and one of the investigators of the React study, took a more pragmatic approach, tweeting that the surveys have “cost lots—probably billions” and that it would now be best for the teams to share what they’ve learned. “Although I’d love our REACT study to continue, I think it’s time to rationalize, building on the best aspects of each [surveillance study],” she wrote.

The pandemic also illustrated that sequencing the virus’s genome to look for mutations has been vital to showing how it is evolving, helping vaccine makers update formulations as new variants arise. Andrew Page, a bioinformatician at the Quadram Institute, a research institute in the UK, says that scientists previously knew they could and should be doing real-time genomic sequencing but had been trapped in bureaucratic hell. “Within our academic community, we've been saying: ‘This is the thing that's coming soon,’ but it was always getting stuck in academia,” he says. Yet after the World Health Organization declared a pandemic in early 2020, the Covid-19 Genomics UK Consortium was set up within a few days to sequence samples from sources including the free community testing program and the ONS and React surveys. Within a week, Page and his team were sequencing coronavirus samples from their local hospital. The Wall Street Journal promptly dubbed the UK the “World Leader in Sequencing the Coronavirus Genome.”

But with the end of mass free testing, the pool of samples to sequence will be far smaller. Page’s lab, a consortium member that draws its samples from the React survey and hospital admissions, is going to stop its operations in mid-April. “We're kind of relieved that we're starting to wind down,” he says. But he acknowledges there will be a reduction in how quickly a problem gets spotted: “It's a trade-off, unfortunately.”

In a statement, a spokesperson for the UK Health Security Agency wrote that even without government funding, “As we begin a new phase of living with the virus, we will continue to monitor Covid-19 through our world-leading studies and many data sources. We will also be continuing genome sequencing of cases to provide further insights. We now know more than ever before about the virus, and we are extremely grateful for the valuable insights that the REACT study has provided, which alongside other surveillance studies, has informed decision-making throughout the pandemic. We thank all participants for supporting our surveillance work during the most demanding public health crisis in living memory.” 

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It’s not clear yet what a scaled-back ONS survey will look like. In response to a request from WIRED, an agency spokesperson offered a short statement: “The Government is clear that ongoing surveillance will be critical in this next phase of the response to the virus. We will continue to track the virus, including identifying any variants. We’ve written to all participating households to say we’ll be continuing to gather vital information on the virus and its impacts.  Further details will be announced in due course.”   

Page reckons a curtailed version of the ONS Infectious Survey might still provide enough samples to keep an eye on how Sars-CoV-2 is changing. “And while the focus is on just Covid, at the moment, it's trivial to move it over to flu or something else,” Page says, “so I think it is going to be a very good legacy.”

Angus agrees it will continue to be useful. “You could still maintain a lot of the value of it with a much smaller version of it,” says Angus. Plus, he adds, if it needs to be scaled back up in the future, “it's much easier to scale up a thing that you've already got running than it is to bring a new thing into the world.”

Meanwhile, the team behind the ZOE tracking app has pledged to keep going, even without government money. In a March 15 press release, they urged participants to keep uploading their data daily. “The ZOE COVID Study is committed to continue running even without government funding and has confirmed that our parent company, ZOE, the personalized nutrition company, will fund it in the short term, whilst we look for other ways to keep the study running,” Spector wrote in his statement to WIRED. “With the help and support of our loyal loggers, we will continue to track both the symptoms and spread of the Covid pandemic, as well as investigate other chronic health conditions.”

The leaps and bounds made in disease surveillance during the pandemic may have a lasting impact on how we track other diseases in the future. This month, the UK government announced plans to study the genomic sequencing of Covid and apply any lessons to other diseases. Wastewater surveillance, used to estimate Covid prevalence in a region, is being studied as a way to track other diseases. And that’s important, because while deaths from influenza and pneumonia were almost nonexistent in the UK for the past two years, compared to the usual 30,000 or so annual deaths that predated the pandemic, those diseases will rebound, and others will arise. We could, for example, gain a better understanding of the flu’s transmission dynamics, pinning down who is getting it and spreading it and how well vaccines are working. 

And if—or when—another pandemic threat arrives, that infrastructure will still exist in some way, ready to be scaled up. It’s important, Dean says, that “you're maintaining some infrastructure that's adding value, even in inter-epidemic times, that you can then build upon in the future.” 

Dowd hopes that what researchers have learned from Covid will translate to lowering the overall burden of infection. “This could just be a renaissance in our understanding of infectious disease transmission in the population, and how population immunity interacts with that,” she says. “This would be opening up a whole new world.”


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