Uncontrolled spread, p.42
Uncontrolled Spread, page 42
Genomic epidemiology, or “gen epi” as it’s called in the field, has become a powerful tool, and Trevor Bedford helped advance the modern application of this approach as part of the global response to COVID. Bedford’s work with the New York Times was a vivid, albeit small application of these methods for tracing patterns of transmission. When done at a larger scale, these could be powerful tools for evaluating the evolution of an epidemic and uncovering how a virus spreads across a population. As the repository of genomic information expands and our capacity to store and mine this information improves, along with the ability to sequence genetic material faster and more cheaply, it will accelerate our ability to read across viral genomes to identify novel pathogens and detect when a known virus has taken a dangerous evolutionary turn.
“Historians of science sometimes talk about new paradigms, or new modes of thought, that change our collective thinking about what is true or possible. But paradigms often evolve not just when new ideas displace existing ones, but when new tools allow us to do things—or to see things—that would have been impossible to consider earlier,” observed science writer Jon Gertner. The advent of commercial genome sequencing, he says, is one such tool. Its application to the COVID pandemic proved its modern utility to transform whole fields of science.13
As computational power and storage capabilities improve, so will the precision of the sequencing techniques. Critics point out the shortcomings in using large-scale sequencing as a way to identify emerging pathogens, chief among them the limitations on what can be deduced from sequence data alone. However, as it becomes easier, less costly, and more routine to sequence respiratory samples; as we build a bigger global repository of this information and expand open-source platforms that allow these data to be easily shared; and as genetic features are correlated with more and better clinical and experimental evidence to give us added insight into how aspects of a virus’s sequence change the way it behaves, the usefulness of these approaches will continue to quickly expand. A committee of the National Academy of Medicine, writing on steps to modernize our pandemic response, reflected on the application of gen epi to COVID, observing that “advances in the speed, granularity, affordability, and portability of genomic sequencing technologies have created transformative potential for widespread rapid genomic surveillance during infectious disease outbreaks, particularly when data from genomic sequencing are integrated with and analyzed alongside patient-based clinical and population-based epidemiological data.”14
The public repository of sequences had made it possible to use the genetic features of the strain found at the White House, to track its migration around the globe and into the West Wing. With the virus that infected the president lifted off the two journalists and placed in those same public databases, scientists can now trace infections that have descended from the White House cluster.15 If other people got sick as a result of the outbreak, and if scientists happen to sequence those subsequent infections, then they may be able to identify the future travels of the strain.
This ability to track the spread of a virus using sequencing information, to deduce insights about its risk based on its genetic features, and to use these data to derive fully synthetic drugs and vaccines on an expedited timetable—all these marked a new inception in the use of science to uncover biological risk and fashion ways to counter it. We’ve crossed a threshold between two states of science, entering a post-pandemic paradigm where genomic information will drive more of our public health response.
The emergence of SARS-CoV-2 and the pandemic that it caused marked a historical turning point in many aspects of our society and culture, and the application of genomics was one visible crossroad. The scientific advances we achieved in combating COVID gave us one of our few bright spots in this tragic event. The pandemic defined other historical inflection points, in other areas of our life, in addition to its impact on our use of science to advance public health. Among them was a turning point for how we must view our public health preparedness as a matter of national security and a crossroad for how we must address protracted social ills that leave us more vulnerable to health threats. COVID exposed wounds of inequity that plague our nation, and one hopes it will start a cycle of profound change for how we address them.
On the technology: With COVID, America embraced a genomically driven public health response, leaning heavily on gene-based approaches to track and trace the spread of SARS-CoV-2, target our mitigation, and develop synthetically derived drugs and vaccines directly from the sequence of the virus’s genetic code. Bedford’s integration of sequencing with traditional epidemiology helped redefine how outbreaks are traced, allowing us to more accurately reveal patterns of spread so we can better inform our tactics for breaking chains of transmission. It allowed us to identify and track new variants in the winter that posed heightened risks, and then develop vaccines and antibody drugs that target them.16
The speed by which companies like Pfizer, Moderna, Regeneron, Johnson & Johnson, and Eli Lilly were able to develop countermeasures to the SARS-CoV-2 threat owed in large part to this same genomic transformation. This scientific aptitude was one of the inspirations in the US response. We developed a safe and effective vaccine against a completely novel target in less than a year—a record time. Before COVID, the fastest that we had ever developed a vaccine was the original preparations against mumps, a process that took about four years.17 The new speed turned largely on our ability to deploy novel approaches for developing vaccines, where the initial constructs were derived entirely from the virus’s genome. This enabled us to use pieces of synthetic genetic material that could be made quickly available as the vaccine starting point. The application of these tools transformed the way we develop vaccines against a novel viral target. After COVID, these approaches will be routine.
On our public health system: COVID revealed dangerous gaps in the US public health preparedness, medical infrastructure, and healthcare system. We lacked the public health capacity and resiliency we thought we had. In the most advanced healthcare system in the world, we ran out of medical masks. We had to retrofit anesthesia machines and turn them into respirators. We didn’t have enough swabs to collect samples from patients’ noses.
Our system was set up well to handle singular, technology-intensive, and complex problems like developing a novel vaccine or antibody drugs. We do this better than anyone. But it faltered when we were faced with more mundane problems like manufacturing those vaccines in bulk, deploying testing centers, or making nose swabs to collect respiratory samples. When we finally developed safe and effective therapeutics and vaccines that could treat or prevent infection, we couldn’t manufacture enough of them in time to supply the nation for the winter surge. We had to set up elaborate rationing schemes. Then, we were unable to establish an efficient distribution plan. Antibody drugs went unused because we couldn’t deliver them. It took more than a month after the authorization of the first vaccine to begin vaccinating the 1.34 million residents of US nursing homes, where the most COVID deaths were occurring.18 It took even longer to set up mass delivery sites to the general public. The vaccine was our only backstop against a relentless surge of infection in winter 2021, and we failed to amplify its timely use.
The CDC couldn’t deploy a test to screen for the virus, allowing the nation to become heavily seeded with infection before it was detected. This was a historic failure that we would never overcome. By the fall, testing still couldn’t keep up with demand. With millions of infections occurring in the US, the CDC didn’t systematically collect and report information on the clinical outcomes. It didn’t deploy sequencing as a tool to detect and evaluate new variants in time to uncover their spread, and it didn’t use the tracking and tracing of sick patients to firmly establish the social compartments where spread was most likely to occur, or to identify the circumstances that were contributing to transmission. Public health authorities overestimated the role of fomites because collectively US agencies underestimated the impact of asymptomatic spread. The virus proved how underfunded our public health system really was.
On our social ills: COVID had a particularly devastating impact on communities of color in the United States. Infectious diseases often hit especially hard those communities that already lack access to good medical care and are overlooked or face bias. Black, Hispanic, and indigenous Americans bore a disproportionately heavy burden from the virus, as it crept through wounds of inequity and racism that have long plagued our society and our medical system. This increased vulnerability sprung from social factors that were made more glaring by this public health crisis. When we look at the unequal impact COVID had on communities of color, the epidemic revealed broader injustices we have to resolve.
This is one piece of a much larger problem of inequity and intolerance. Often Black and Hispanic communities had higher rates of COVID disease because of low income and related factors: overcrowded housing, a reliance on public transportation, the need to work in lower-wage but essential jobs interacting with the public. Many people couldn’t do their work over Zoom or socially distance on their job site. They couldn’t easily isolate themselves at home when they became infected, because they lived in crowded multigenerational homes where, if one member of a family got sick, others were made excessively vulnerable. Too many Americans didn’t have the social equity at work to demand proper protective equipment and safer working conditions.
In many cases, Black and Hispanic Americans also faced delays in diagnosis of COVID, difficulties in getting access to testing, and more barriers in acquiring care. And when people from communities of color got sick, they also suffered higher rates of serious disease and death. Years of inequity in healthcare—poor access to medical services, distrust of the healthcare system, and sometimes discrimination in how care is delivered—as well as higher rates of chronic diseases like diabetes and hypertension, which also owed in part to the inequities in income, environment, and access to medical care, were all aggravated by COVID’s advance. The virus struck hardest those who were most vulnerable. Some were vulnerable by age. Others were made vulnerable by a system that left them behind. Stopping the next pandemic will depend on making sure we address the reasons why some communities were more likely to experience suffering and death from COVID-19. The social unrest of the summer of 2020 was a defining moment that brought these inequities into sharp focus. The hope is that it will be a turning point in how we address them.
Our political union also turned out to be socially fragile. We fought over the collective action we needed to take to reduce spread, perpetuated by an often-false dichotomy between the exercise of liberty and the application of public health. Masks became one unfortunate flashpoint. However, some of that anger and opposition was born of understandable frustrations. The mitigation measures we took had unduly hard impacts on certain segments of society: small business owners who ran restaurants, parents who couldn’t work unless their kids could go to school, kids who depended on schools for meals. Just as the virus would disproportionately sicken some segments of society, the steps taken to control infection would also excessively burden certain people. Yet here again, we failed to take special measures to help those most affected. Debate and division over some of these actions were understandable, but over others, like the wearing of masks, such rancor was inexcusable. We couldn’t even agree on the easy stuff.
The pandemic also exposed weaknesses in the international conventions and scientific collaboration that were supposed to help safeguard us from a global pandemic. COVID crushed the global order that governed public health cooperation by revealing that the established conventions were unenforceable in a moment of crisis. Many thought that China had been chastened after SARS-1.19 In response, nations signed agreements and created institutions, with a promise to share information about new contagions so countries would be alerted earlier to novel threats. When COVID appeared, those conventions crumpled. Whether early notice would have made a difference in the global response to COVID is debatable. In the US, we made plenty of our own mistakes, downplaying the risk of the threat for too long and failing to get testing in place despite ample warning. However, the proof that even after SARS-1, countries like China would still sidestep many of these international commitments, underscored a simple orthodoxy. In a moment of crisis, every country will follow its own self-interest.
We had already gotten a glimpse of this reality in 2009, during the H1N1 swine flu pandemic. Friendly nations like Canada and Australia refused to ship to the US vaccine that had been purchased by our government and manufactured at our behest but made at facilities in those two nations. Only after Canada had satisfied the needs of its own citizens did it allow American products to flow to the US for American patients.20 With COVID, the same behaviors would reoccur. Italy exercised its export control regulations under European Union rules to block the shipment of 250,000 doses of the AstraZeneca vaccine that was bound for Australia, on the grounds that Australia had controlled its epidemic and was in less immediate need of the doses.21 It was the first time that these EU regulations had ever been invoked.22 A few weeks later, the EU implemented new emergency legislation that gave it broad powers to curb exports of COVID vaccines that were manufactured in facilities located in member nations. The rules hit Britain especially hard, since the country was far ahead of other European nations in vaccinating its population at the time and was dependent on shipments from other European countries to keep up its vaccination campaign.23 The European Union was putting its interests first. The same tenets influenced US policy. In May 2021, even as the US developed a surplus of COVID vaccine—stockpiling as many as 100 million vaccine doses by the beginning of the month—the Biden administration wouldn’t allow those doses to be shipped to Brazil, which was experiencing an uncontrolled epidemic. We were vaccinating healthy and low-risk sixteen-year-olds in the US while hospitals in India and Brazil were running out of oxygen for patients hospitalized with the disease.
For those who still cling to the gauzy hope that nations will join hands to better identify and coordinate around global risks, the gloomy truth was revealed by the collective international response to COVID—the application of trade and travel barriers as a way to isolate the virus and the nations that hosted it; the nationalization of production facilities that made critical medical products; the deliberate withholding of drugs and equipment needed for the global response.
If anything, COVID normalized the breakdowns in a global order that it was presumed, perhaps naively, would protect us, just as COVID pierced our own perception of domestic resiliency, cooperation, and fortitude. By implementing global travel bans, we made it clear that any country that’s host to a novel pathogen in the future will quickly find itself isolated. Our hasty decision to pull out of the WHO, and then rejoin it just as quickly, with no preconditions for its reform, hardened these lessons. No matter what steps we take to rebuild international alliances, the overarching lesson will be the one proven by the crisis. In the future, when even friendly nations become host to an outbreak of a new and worrisome respiratory pathogen, we shouldn’t expect them to raise their hand so easily.
These harsh, practical lessons won’t be quickly unwound by sanguine rhetoric about international cooperation and gratifying agreements signed in COVID’s aftermath. Already, the Biden administration is focused on strengthening the International Health Regulations that govern global cooperation around outbreaks as a safeguard against future pandemics. It’s a sound effort, and we need to improve our multilateral relationships and the capacity for sharing information and supporting nations that are host to outbreaks, but we shouldn’t rely on these efforts alone.
The virus made clear that we’ll need to fundamentally alter the way we approach all of these risks. If we don’t, our society will remain excessively vulnerable. For starters, we’ll have to lean much more on our intelligence agencies, and in a different fashion. International agreements alone haven’t provided us with the information we need about emerging threats. There’s little reason to believe they’ll perform much better in the future. The devastation caused by the pandemic proved that these risks, and our preparedness for them, is a matter of national security on par with other threats. We’re going to have to build the capacity to seek out the information we need to protect ourselves. Sometimes that will demand that we avail ourselves of the tools and tradecraft of our clandestine services. The challenge will be to maintain collaboration and multilateral efforts even as we turn more heavily toward intelligence services to guard against the risk of new contagions. We manage to walk this line in other nonmilitary areas of national security. We’ll have to make a similar posture work when it comes to global public health.
Going forward, extending an approach to public health preparedness that views these risks through a lens of national security protection also means building more resilience into our public health infrastructure. It means expanding our healthcare system’s capacity to deal with a crisis, particularly our ability to conduct massive diagnostic testing and to implement large-scale manufacturing of biologicals. It also means reexamining the global supply chain that has left us vulnerable to shortages when every country that we depend on was suddenly hoarding the same equipment. It means we need a no-regrets ethos when it comes to pandemic preparedness. There must be no repentances or recriminations if we overinvest in preparedness when a new pathogen emerges only to see the virus fizzle out rather than explode into the next pandemic.24
Finally, it means bringing back to the US more of the manufacturing of critical healthcare components and finished goods. To do this, we may have to pay higher prices for these parts and services to make sure that we maintain a reliable domestic capacity. There’s a reason why much of this manufacturing left the US in the first place. It was cheaper to produce overseas. But we can no longer afford the luxury of valuing low price for these goods above all else.
