In November, an independent team of academics and public-health experts who called themselves the Covid Rapid Response Working Group gathered on Zoom to puzzle over what had by then become the pandemic’s most vexing challenge: how to make all schools safe for full-time, in-person learning as quickly as possible. Schools had not proved to be a hotbed of coronavirus transmission, but beyond that the research was complicated, and communities were divided about how to balance the risks. Some people wanted a full reopening, immediately, no exceptions. Others were terrified to return at all.

So far, there was no national plan for how to move forward. The Centers for Disease Control and Prevention was advising everyone to wear masks and remain six feet apart at all times. But that guidance was a significant impediment to any full-bore reopening, because most schools could not maintain that kind of distance and still accommodate all their students and teachers. It also left many questions unanswered: How did masks and distancing and other strategies like opening windows fit together? Which were essential? Could some measures be skipped if others were followed faithfully?

The C.D.C. seemed incapable of answering these questions. From the pandemic’s earliest days, the agency had been subject to extreme politicization and troubled by what looked, at least from the outside, like pathological clumsiness. Scientists there had been far too slow to detect the virus, to develop an accurate diagnostic test for it or to grasp how fast it was mutating. Their advisories on mask-wearing, quarantine and ventilation had been confusing, inconsistent and occasionally dead wrong. And during the Trump administration, agency leaders stood by while politicians and political appointees repeatedly undermined the agency’s staff. Scientific reports were blocked or altered. Quarantine powers were used to achieve political goals. Dangerous strategies for controlling the virus were not only promoted but actively employed. And state and local leaders were left to fend for themselves — to decide which of the agency’s recommendations to follow or modify or ignore.

The Covid Rapid Response Working Group, at the Edmond J. Safra Center for Ethics at Harvard, was one of several independent organizations that stepped in to help fill the gap. In the last year, these groups, run mostly out of academic centers and private foundations, have transformed reams of raw data — on transmission rates and hospitalization rates and death tolls — into actionable intelligence. They have created county-by-county risk-assessment tools, devised national testing strategies and mapped out national contact-tracing programs. In many if not most cases, they have moved faster than the C.D.C., painting a more accurate picture of the pandemic as it unfolded and offering more feasible solutions to the challenges that state and community leaders were facing.

When it came to the question of school reopenings, the Covid Rapid Response Working Group found itself going in circles. It was possible to control the spread of infections indoors; hospitals did it all the time. But when it came to schools, where the risk was much lower, everyone seemed to be at a loss. Why was that? What, exactly, made hospitals so different? “It makes no sense,” Thomas Tsai, a surgeon in the group, said. “Hospitals are not special. We don’t use magic. We just use basic infection control.” He explained what that meant: Teams of specialists create detailed protocols based on what the risks are and what the evidence says about how to avoid those risks. They update and adjust their practices as information evolves, and they conduct routine trainings with all hospital staff members (not just doctors or administrators) so that everyone knows exactly what to do. It was all very standard, he said. It did not even require an advanced degree, just a basic understanding of disease transmission, an awareness of a given hospital’s particular situation and a few people who knew how to connect the two and could train others to do the same. School systems did not have any of those tools, Danielle Allen, head of the Safra Center, pointed out. Nor did they have a clear path to making those connections. But maybe the group could chart that path for them? What would that take?

From the pandemic’s earliest days, the C.D.C. was subject to extreme politicization and troubled by what looked, at least from the outside, like pathological clumsiness.

Allen and her colleagues had already published at least one report on school safety, but when the Biden administration set a national goal of opening most schools by May 1, they partnered with a larger initiative, the Covid Collaborative, and formed a task force to address the issue of infection control. They parsed research, brought educators and other stakeholders together for sustained dialogue and, by late April, produced a detailed road map: Most schools could remain open for full-time in-person instruction even when the virus was circulating at high levels in the community, as long as they had good infection-control programs. Beyond a few key elements — including masks, proper ventilation and contact tracing — the contours of such programs would depend almost entirely on the individual school. What was the ventilation system like? How many students did it have? Did its windows open easily?

The road map explained how to devise and implement an infection-control plan, making clear who should take charge of what and how to get federal funding and offering suggestions, like establishing “situation rooms,” for managing challenges on the ground. It was, in short, everything that the C.D.C. guidance was not. And it was the product of a strategy that felt obvious and simple: The task force engaged stakeholders in a sustained dialogue, incorporated input from schools and factored practical realities, like the need to move quickly, into its recommendations.

Allen disputes the notion that she and her colleagues are doing work that the C.D.C. itself should be doing; in fact, she says, the task force and the federal agency have worked closely together. But she acknowledges that the interdisciplinary approach of the collaborative — it consists not only of doctors and public-health professionals but also of political scientists, economists, lawyers and M.B.A.s — enables it to spot problems that the federal institution can’t necessarily see. Infection control is a good example. “This is not a public-health problem, or even a medical one,” she says. “It’s an issue of organizational capacity.” The C.D.C. is not equipped to identify organizational issues, let alone resolve them.

The agency has made clear improvements under the Biden administration. Among other things, the incoming director, Rochelle Walensky, has made a point of bringing agency guidelines back under the exclusive domain of agency staff members. But those guidelines are still confusing, the agency’s messaging is still deeply muddy and communities across the country — and school districts, especially — are still struggling with next steps. Schools are reopening, but vaccines have yet to be approved for children younger than 12. No one can say for sure how long immunity to the virus might last, or what will happen when it fades.

What is clear, as the second pandemic spring tilts into the second pandemic summer, is that efforts like the Covid Collaborative will be needed for some time to come. “We did not expect to be doing this work once the new administration took over,” Stefanie Friedhoff, a professor of public health at Brown University and a member of the collaborative, told me recently. But as the rest of the nation is learning, the former president was not the C.D.C.’s only — or even its biggest — problem.

For most of the last seven decades, the C.D.C. has stood as the world’s premier public-health institution — so much so that counterpart agencies in other countries are often called C.D.C.s, even when the abbreviation means nothing in their native languages. The agency invented disease surveillance as we know it, helped lead the (successful) quest to eradicate smallpox, initiated the (ongoing) fight against H.I.V. and beat back Ebola — more than once. Its heroics have been the stuff of novels and movies and harrowing nonfiction best sellers. Americans took for granted that the C.D.C. would be engaged and quick in a crisis; that it was well funded and equipped with modern technology; that it had, or could quickly get, comprehensive data on diseases of concern; and that it knew how to translate that data into sound guidance in a crisis. Wasn’t that, at least partly, how bird flu, swine flu and a thousand other nameless plagues were prevented from decimating the American masses?

The agency may be just one cog in the nation’s public-health apparatus, but it is a crucial one. In an ideal world, its edicts would hold sway not only over schools but also nursing homes, prisons and meatpacking plants. It would guide elected officials and private institutions alike through not just global pandemics but all manner of public-health threats: food-borne pathogen outbreaks, the opioid crisis, gun violence. In an ideal world, its efforts would succeed, more often than not, at keeping people safe and helping them stay healthy. This is the C.D.C. we need. But as the last year has made clear, it is not the C.D.C. we have.

The C.D.C. we have is hardly a monolith: Some of its many pockets are bursting with innovation; others are plagued by inertia. But scientists and administrators who have spent decades working with and for the agency say that three problems in particular affect the whole institution: a lack of funding, a lack of authority and a culture that has been warped by both. Some of these problems come down to politics, but most are a result of flaws in the agency’s very foundation.

From its inception in 1946, the agency’s existence hinged on its officers’ ability to sell its services to state leaders who were leery of federal interference, and to lawmakers who often struggled to appreciate the point of epidemiology. They did this by taking on the jobs that no other agency wanted, quickly developing a reputation for being the first to arrive at any given emergency, the last to leave and the one with the most cutting-edge technology. But with each success, a pattern emerged. The agency received an infusion of funding in times of crises, and praise and more responsibility when it saved the day. But it was often starved of resources the rest of the time and rived by internal conflicts over how to apportion the money it did receive. “Everybody was trying to establish his own thing,” the historian Elizabeth Etheridge writes in “Sentinel for Health,” her biography of the agency. Each branch had strong leadership, but none of those strong leaders were great at working together.

Today the C.D.C. is both sprawling in its reach and extremely constrained in what it can do. It consists of more than a dozen centers, institutes and offices and employs more than 11,000 people in all, in a gargantuan roster of public-health initiatives — not just infectious-disease control but also chronic-disease prevention, workplace safety, health equity and more. A majority of that work is concentrated in the agency’s Atlanta headquarters, but there are also C.D.C. labs and programs across the United States and C.D.C. operations around the world. Despite that scope, the agency has little authority. Its officers can’t compel individual states to participate in its initiatives, for example, nor to include C.D.C. scientists in local outbreak investigations, nor to share much data with the agency — even in the middle of a pandemic. It can’t force people to wear masks, or local leaders to close (or open) schools or other establishments. The agency did try to halt evictions during the height of the pandemic, but that edict faced such a barrage of court challenges that its fate remains uncertain even now. Aside from a few quarantine powers, the most the C.D.C. can do is issue guidance, which is unenforceable and — as the past year has repeatedly shown — just as likely to be weaponized as meaningfully employed.

Insiders say three problems affect the institution: a lack of funding, a lack of authority and a culture that has been warped by both.

The C.D.C.’s multibillion-dollar annual budget is both too small — it has barely kept pace with inflation in the last two decades — and subject to too many restrictions. Around half of the agency’s domestic budget is funneled to the states, but only after passing through a bureaucratic thicket. There are nearly 200 separate line items in the C.D.C.’s budget. Neither the agency’s director nor any state official has the power to consolidate those line items or shift funds among them. “It ends up being extremely fragmented and beholden to different centers and advocacy groups,” says Tom Frieden, who led the C.D.C. during the Obama administration. That lack of flexibility makes it extremely difficult to adapt to the needs of individual states.

This funding system also hobbles emergency-response efforts, because there is no real budget for the unexpected. When something like swine flu or Zika or Covid-19 emerges, the agency must rely on Congress for additional resources — almost always a large, one-time infusion that can’t be used for longer-term planning — and then deploy those resources, quickly, in the middle of the crisis. Public-health experts like to call this “building the plane while flying the plane.” In the past, they say, it made the C.D.C. scrappy and fostered an esprit de corps among its officers that helped the broader operation thrive. But in recent decades, these privations appear to have done the opposite. “I’d go into a meeting and say, ‘What needs to be done?’” William Darrow, a former chief of the agency’s Behavioral and Prevention Research branch, told me. “And they’d give me a five-point chart. And then I’d ask, ‘Well why aren’t we doing those things?’ And it was all hemming and hawing about whether we could convince the states, or get top leadership to support it, or if it would be controversial.”

The C.D.C. is resistant to change, slow to act and reluctant to innovate, according to critics. The agency’s officers are overly reliant on published studies, which take time to produce; and are incapable of making necessary judgment calls. Agency departments are also deeply siloed. “We are really good at drilling down,” Darrow says. “But terrible at looking up and reaching across.” Ongoing tensions between the C.D.C. and its parent agency, the Department of Health and Human Services, have exacerbated these tendencies, insiders say, and the agency is constantly fending off H.H.S.’s efforts to usurp some of its portfolio. “There are a lot of very good people there,” Bill Hanage, a scientist who studies the evolution of infectious diseases at the Harvard T.H. Chan School of Public Health, says. “But when your resources are constantly constrained like that — when you’re constantly told no — that forces you into a defensive crouch.”

Long before the novel coronavirus began its march across the globe, scientists at the C.D.C. understood that the United States was well behind where it should have been when it came to identifying and monitoring infectious-disease threats. In 2014, the agency created the Office of Advanced Molecular Detection to begin closing this gap, but the effort faced several hurdles. New technology required much more advanced computer infrastructure than the C.D.C. or any of the nation’s public-health labs had. It also required the kind of work force, highly skilled in bioinformatics and genomic analysis, that you had to compete with the private sector to get. And it necessitated a mountain of data-sharing agreements between the C.D.C. and the states that were tricky and laborious to negotiate. “We are talking about a 50-way dialogue,” says Duncan MacCannell, lead scientist at the O.A.M.D. “Anything you want to do or change has to be negotiated with each state separately, and at the end of the day, they can still say no to you.”

Just about every public-health lab in the nation had at least some genomic-surveillance capacity by the time the coronavirus pandemic erupted. But most of that capacity was concentrated in the foodborne-pathogen division, and despite MacCannell’s best efforts, it was difficult to adapt many of those programs to meet the new crisis. Several months into the pandemic, when SARS-CoV-2, the virus that causes Covid-19, was well on its way to becoming the most-sequenced virus in human history, the United States was contributing hardly anything to that effort. And when it came to tracking new variants in the United States, health officials were flying blind.

MacCannell says he did everything he could think of to get a handle on the crisis: He and his team devised protocols to help public-health labs start new sequencing programs; developed plans for partnering with commercial labs, which have much greater capacity overall; and set up a consortium of scientists across the country to collaborate and pool resources. But those efforts were mere stopgaps, he acknowledges, and in any case the approval and funding needed to get them off the ground was delayed for many months. “There was a big gap between what we expected to happen and what we actually saw unfold,” MacCannell says. “Not only at the federal level, but at every step down from there.”

Genomic surveillance is one of many shortcomings plaguing the disease-surveillance system over which the C.D.C. presides. Those shortcomings have been invisible to anyone not working in the field, because at first blush the system makes sense. Public-health emergencies that are identified at the local level are reported up to state health departments and then, when necessary, passed on to the C.D.C., where officials analyze the information, issue guidelines and coordinate federal response efforts. There’s a special system for the 120 or so “notifiable diseases” — like Lyme disease and hepatitis — which everyone agrees are serious enough to warrant immediate action, and another for “syndromic surveillance,” in which epidemiologists can search real-time emergency-room data for symptoms of concern. But beneath that broad structure, chaos often reigns.

As the coronavirus grew into a full-blown pandemic, C.D.C. scientists struggled to answer even basic questions about what the disease looked like or where or how it was spreading.

The system itself is deeply disjointed, and the technology that underpins it is less sophisticated than that found in many American households. State health departments are not connected to one another in any meaningful way, nor are hospitals, clinics, laboratories and local health agencies. The C.D.C. maintains more than 100 separate disease-specific computer systems (a byproduct of the agency’s funding silos), and many of those can’t interface with one another. Crucial data is often shepherded from health care facilities to health departments through a tortured process that can involve handwritten notes, manual spreadsheets, fax machines and snail mail. It’s not uncommon for basic information like race, ethnicity, age or address to be missing from clinical reports. It’s also not uncommon for those reports to languish at the state or local level without ever making their way to federal officials. Even the most serious diseases, which are supposed to be logged within 24 hours of detection and reported to the C.D.C. in a timely way, are not necessarily sent up that chain in any systematic manner. “It depends on the jurisdiction,” Janet Hamilton, executive director of the Council for State and Territorial Epidemiologists, told me recently. “Some regions have robust public health departments and good reporting records, and others don’t.”

Disease monitoring is also hampered by the uneven patchwork of surveillance programs across the country and the need to negotiate data sharing and other agreements separately with each state. Antibiotic resistance, respiratory infections and other pathogens are tracked robustly in some areas and very poorly or not at all in others (respiratory infections, for example, are more heavily monitored in the Four Corners region than in other places), in part because the agency does not have the ability, or authority, to get all the data it needs from every community. Hanage likens the entire apparatus to a Rube Goldberg machine. “There’s no central anything,” he says. “Random patchwork collaborations were initiated and transformed and now have an outsize impact on our understanding of public health. That’s not to criticize the people who made those things, because the alternative might have been nothing. But the result is something with no rational plan behind it.”

The gaps make it difficult to track even well-known diseases and nearly impossible to get a handle on new ones. During a recent E. coli outbreak involving romaine lettuce, officials were forced to base billion-dollar, life-or-death decisions about which products to pull from which shelves in which regions of the country on data that was being screen-shotted and text-messaged to epidemiologists and health officials. During the vaping injury (or Evali) outbreak in 2019, doctors faxed hundreds of pages of medical records, for some cases, directly to local health departments. Epidemiologists could barely process the data in that format, let alone parse it for clues. “There is no ready-made process for when something like vaping injury or Zika or SARS-CoV-2 pops up,” Hamilton says. “There are 64 separate public-health jurisdictions in this country, and each one will have its own ideas about what information to collect and how to share it.”

In 2020, as the coronavirus grew from a few isolated outbreaks into a full-blown pandemic, C.D.C. scientists struggled to answer even basic questions about what the disease itself looked like or where or how it was spreading. “We were being asked who is being hospitalized, who are the severe cases, what are the characteristics, and it was so frustrating,” Anne Schuchat, the agency’s deputy director, told a panel of colleagues last fall. “People were going out to manually review charts. I felt like, well, the health care sector has this data. It’s sitting in their system. Can we work with them?” The agency could not keep reliable track of testing or case rates across the country. It also struggled to update hospital data, which includes things like bed availability and ventilator supply; the Trump administration hired a private contractor to assemble that data, amid accusations of political favoritism. And when multiple vaccines were finally deployed, the agency was not able to monitor supplies or accurately keep tabs on waste.

Covid is the biggest crisis the C.D.C. has faced, by far, in all its history. It is exactly the kind of threat for which the agency was created in the first place. But when it finally arrived, by most accounts, officials there had very little to meet it with.

By mid-May of this year, the nation had cleared what felt like a dangerous bottleneck. The dreaded fourth surge in cases had not materialized, even as it became clear that more-contagious variants were spreading across the country. Vaccination rates were climbing steadily, despite vaccine-hesitancy; and case counts, hospitalizations and daily death counts were trending downward just about everywhere. Yet the C.D.C. struggled to grasp this new reality. Agency officials were exceedingly slow to update guidelines, and then conservative, awkward and confusing when they finally did. They waited months before saying anything at all about the impact that vaccination might have on various restrictions. When they finally allowed that people who were fully vaccinated could resume overseas travel, Walensky, the agency’s director, undermined that advice almost immediately by saying that personally, she advised against it.

A few weeks later the agency updated its mask guidelines: Fully vaccinated people should wear masks in all indoor settings and in some outdoor ones, and unvaccinated people should wear masks almost all the time, including outside, except for when walking or jogging alone. At summer camp, the agency said, everyone should wear a mask, at all times, except when swimming or eating. Critics were both bewildered and frustrated by these edicts. It had been clear for many months that outdoor transmission was exceedingly rare, and most experts agreed that fully vaccinated people were highly unlikely to contract the virus and even less likely to pass it on to others if they did. Why was it taking the C.D.C., the supposed leader in global public health, so long to acknowledge what everyone else could see so clearly?

Lawmakers — Republicans especially — denounced Walensky over the lag. At one hearing, Bill Cassidy of Louisiana warned that the agency was at risk of becoming completely irrelevant to the American public. “I always considered the C.D.C. to be the gold standard,” Senator Susan Collins of Maine told Walensky at the same hearing. “I don’t anymore.” A few days later — just weeks after the C.D.C. had told everyone to keep their masks on — the agency announced yet another update: People who were fully vaccinated could ditch their masks in most settings, including in most indoor settings.

Critics took issue with this move too. The old guidelines were too strict, they said, but these were too lenient and failed to factor in the realities of human behavior. How would retail workers distinguish among vaccinated and unvaccinated patrons? What should immunocompromised people do, especially in workplaces where masks and distancing would not be enforced? And what would happen now in communities with very low vaccination rates? Even the C.D.C.’s staunchest defenders wondered aloud why the agency had not taken a more sensible middle path between the two extremes. Why not suggest scrapping outdoor mandates altogether, given how rare outdoor transmission seemed to be? And then maintain indoor masking edicts or tie them to vaccination rates, or even transmission levels, in individual communities?

It’s unclear how or whether any of these more practical questions factored into the C.D.C.’s decision-making. The Washington Post reported that White House officials pressed the agency about the implications such guidelines would have for businesses and people who could not be vaccinated, but could not get satisfactory answers. With some 35,000 new cases and more than 600 deaths still being logged nationwide every day, some of the agency’s own staff members had wanted to hold off on the update, according to the paper. Many scientists and public-health experts seemed to agree that it made sense to lift masking advisories as the agency had done, but even to them, the agency seemed to be operating inside a black box.

Why was it taking the C.D.C., the supposed leader in global public health, so long to acknowledge what everyone else could see so clearly?

Walensky maintained that as with all of the agency’s guidelines, its position on masks changed as the science behind them evolved. She cited a roster of new studies that she said had tipped the balance of evidence away from outdoor masking, and toward loosening restrictions for the fully vaccinated. And the C.D.C. pointed out that not even President Biden had been notified of the agency’s decision until a few hours before the announcement — proof that it was not being swayed by political considerations.

But even if the agency was governed exclusively by science, at least some of that science was flawed. Far fewer than 1 percent of coronavirus cases — fewer than one-tenth of 1 percent, by some estimates — have been contracted outdoors. The C.D.C. puts the risk at less than 10 percent, an order of magnitude higher. Walensky says the higher number comes from an aggregation of high-​quality peer-reviewed research. But, as The New York Times has reported, those studies rely on an overly liberal interpretation of the term “outdoors.” They included almost any setting that had an outdoor component: Workplaces and educational settings counted as outdoors if people sometimes went outside to a courtyard or play area.

It was not until late this spring that the agency finally acknowledged that the virus was airborne and that people did not necessarily need to be in close contact to infect or be infected by one another, something many scientists, not to mention average citizens, had long since concluded. Here, too, the delay came down to a flawed interpretation of published studies and a blind eye toward real-world experience. For the better part of a year, C.D.C. scientists relied on research that tried to culture the virus from air samples — a notoriously difficult feat, even for viruses like measles that are known to be airborne. In the meantime, they overlooked ample evidence — including multiple superspreader events that its own epidemiologists had tracked — that the virus could be carried on air currents well beyond six feet.

This belated acknowledgment of how the virus is transmitted has huge implications for pandemic-response efforts: For an airborne virus, health officials should prioritize ventilation, especially in factories, congregate facilities and other high-risk settings. But the agency’s update was made with very little fanfare and did not come with new instructions for how any of those entities should proceed. “They fuss over outdoor masks, which most of us agree have zero impact on public health or safety,” says Céline Gounder, an infectious-disease doctor and former member of Biden’s transition Covid advisory board, “but ignore this other very obvious, much more pressing thing.”

This spring, the Biden administration issued a proposed budget that included the C.D.C.’s biggest funding increase in nearly two decades. And in recent months, the agency received billions of dollars in Covid-19 supplemental funding that has been used for long-overdue data-modernization and genomic-surveillance initiatives. Since at least February, Walensky has appeared at multiple press briefings each week, as a key member of the president’s Covid-19 response team. She has also held a series of “all-hands meetings” with C.D.C. staff members where attendees say she renewed the agency’s commitment to health equity and hinted at the need for broader reforms within the agency. “It feels like we’re finally starting to move forward,” a senior C.D.C. official, who asked not to be named discussing the agency, told me in April.

But the pall of the previous year still lingered. Not only did the public messaging flubs — and the public backlash against them — persist, but there also seemed to be no plan to fully reckon with the agency’s biggest missteps and mistakes, many of which were still coming to light. In her assessment of the C.D.C.’s Trump-era coronavirus guidelines, Schuchat identified several that were either written outside the agency or considerably watered down before publication, or both. But her report did not say who was responsible for that interference, nor parse the leadership failures that allowed it to happen, nor offer any real plan for preventing similar mistakes in the future. Those questions need to be answered, too. “What we really need is a truth-and-reconciliation commission,” the senior C.D.C. official told me. “But we need someone at the very top to make that happen.”

In May, both Schuchat and Nancy Messonnier, the long-serving director of the C.D.C.’s immunization center, resigned from the C.D.C. Some agency staff members and alumni I spoke with lamented these departures. Schuchat especially had attained an aura of celebrity in her 30 years with the United States Public Health Service. She had served as deputy director under three administrations and presided over scores of high-profile outbreak investigations, and her institutional memory is unrivaled. But some said that such resignations were necessary for the C.D.C. to move forward, and that if anything, a greater purge of top leadership was warranted. How could the agency reform itself if the people who built its current culture and set its institutional priorities were still running things?

Others pointed out that personnel changes were no substitute for the much bigger fixes that were needed — starting with the agency’s own culture. “For years, we have managed to muddle through crisis after crisis, thanks to some luck and to some of the truly brilliant people that we have here,” the senior official told me earlier this year. “But those wins have been a double-edged sword, because now our reputation exceeds our capacity, and people think we can do all these things that we can’t actually do. And we have sort of internalized that and become deluded ourselves, instead of reflecting on how we need to improve.” Like other agency insiders I spoke with, he was deeply anxious about the C.D.C.’s future and adamant that any reckoning would have to go beyond the obvious crisis of the previous administration. “We have a chance to rebuild this institution so that it works the way we want it to,” he said. “But we have to start by acknowledging what’s really broken.”

Many scientists I spoke with insisted that the biggest barrier to modernizing the C.D.C. was the agency’s own lack of imagination. New technologies capable of tracking pandemic disease through wastewater, for instance, or through human blood are promising and could revolutionize the fight against global disease threats — if only agency scientists would open their minds and embrace them. But such technologies are difficult to imagine in a system that still relies on fax machines.

‘You can’t starve and neglect something over and over for decades and then expect it to function perfectly in a crisis.’

Each fresh crisis brings new resolve to modernize the system, but that resolve usually evaporates before progress can be made. And when funds are available, public health tends to lose out to other interests. In 2010, for example, when Congress appropriated billions of dollars through the Affordable Care Act to upgrade the nation’s electronic medical record systems, just about all of the money went to health care providers, not public-health departments. In 2019, when a consortium of public-health groups asked Congress for $1 billion to be routed through the C.D.C. over the next 10 years to upgrade the public-health data system, lawmakers gave them $50 million. By then, the novel coronavirus had almost certainly made its way into several states, but owing partly to insufficient surveillance efforts, it would be months before anyone realized it.

One thing most experts seem to agree on is that the agency’s budget — both the amount of money it receives and the mechanisms by which it is allocated — needs an overhaul. Fiscal insecurity makes it difficult for the agency to be bold or innovative, to build strong relationships or to lead in a crisis. But the history of attempts to fix these problems is long and littered with failure. In 1983, William Foege, the agency’s director at the time, advised Congress to index a portion of total health care spending and reserve it for public health. Lawmakers did not heed his advice. In the early 2000s, Julie Gerberding tried to change the agency’s funding structure so that states could have more flexibility in how they spent C.D.C. dollars, to no avail. And a decade later, Frieden tried to do the same. The only thing he accomplished, he says, was to “make everyone really angry” with him. “Each of those line items is protected by a fierce constituency that fought to get it there in the first place,” Gerberding says. New suggestions are again percolating. Almost every former director I spoke with had at least one proposal or plan for how to fortify the agency by revising its funding structure. But it remains to be seen whether any of them can gain currency.

Many have also argued that the agency should be granted more authority — during public-health emergencies, at least. If the C.D.C. could compel states to share key data through a central, standardized system, or to sequence a certain portion of viral genomes, the nation might be able to develop a picture of a given crisis much more quickly and accurately. And if the agency could enforce certain edicts at the outset of an outbreak, officials might be able to stave off a full-blown epidemic. “We need to come up with a set of no-regret interventions,” Hanage says. “Like, if you have credible evidence of a virus with certain properties, you enact certain measures, like enforced quarantines, regardless. Not to stomp it out, but to slow it down long enough to get other measures in place.” The politics of such a shift might prove insurmountable. “If there was a proposal to give C.D.C. all the same powers that states have for public-health emergencies, 50 governors would immediately oppose it,” Foege told me (in fact, several states are pressing right now to curb the powers of public-health agencies, not expand them). But the specter of 50 separate coronavirus responses, and more than half a million deaths nationwide, has convinced some public-health professionals that it’s time to give the idea serious consideration.

In truth, the C.D.C. and the states each deserve a share of the blame for the disconnect between them. “State and local health departments often feel like C.D.C. is clueless about the challenges they face and the realities of their work,” Frieden says. “And they are not entirely wrong in that.” But while state leaders complain that the C.D.C. is clueless, and occasionally make a show of flouting the agency’s guidelines, some can also be obstinate about sharing data and communicating with the agency — even when it’s in their own best interest. “Sometimes we ask for info, and they just say they can’t give it to us,” the senior C.D.C. official told me. “We don’t know if they are underresourced, or they just don’t want to, or what — because they don’t tell us.”

Frieden, who served as New York City health commissioner before his stint as C.D.C. director, says that one way to bridge this divide might be to create an exchange program of sorts, where thousands of C.D.C. staff members are embedded in state and local health departments for two-to-five-year periods. “In time, you’d have a whole cadre of public-health experts, and a common vision between the C.D.C. and state health departments,” he says. “You’d also have a much stronger public-health system overall.”

Of course, true reform will require more than money or new laws or even a revived spirit of innovation. It will require a reconciliation of sorts: The C.D.C. will have to regain the nation’s trust. The nation will have to acknowledge the limits it imposed on the agency, both implicitly and explicitly, from the outset. And both sides will have to reckon with a fundamental but inconvenient truth: Public health can never fully divorce itself from politics, because public health is an inherently political endeavor. It involves more judgment calls than absolutes and requires trade-offs and public acceptance to work.

In other words, not every failure of pandemic response can be pinned on the C.D.C. “There has been a real pile-on against the C.D.C. in the past few months,” Frieden told me in early June. “Did they fall down on some things? Yes. But they have also done a lot of good work that’s been overlooked. And you can’t starve and neglect something over and over for decades and then expect it to function perfectly in a crisis.”

In retrospect, it seems clear that only a strong C.D.C. — a well-funded, well-run federal authority, grounded in science and resistant to political pressure but also mindful of lived reality — could have rescued American policymakers from the worst of their Covid confusion. And only a stronger C.D.C. stands a chance of correcting these errors when the next pandemic comes along. But the federal agency is just one part of a much larger system, and other components of that system must work properly — and together. For much of the last year, they have not.

Federal agencies like the Department of Education have not stepped in to help schools confront the challenges of infection control, for example. And while many communities have made heroic efforts to beat the virus back, state and local officials have not always done as much as they could to build trust or secure community support for needed measures. Too often, they fell prey to political bickering and wielded data points as weapons instead of as tools to improve safety. Fear and frustration have prevailed as a result, even as the pandemic wanes — and especially when it comes to schools. While some parents rage over mask mandates and contact-tracing regimes, others say they won’t return or send their children back, even with every precaution in place, until every last person is vaccinated. The fault lines of this divide are familiar, but somehow knowing where they lie has not helped the nation avoid them.

The C.D.C.’s institutional cautiousness and muddy messaging have not helped. “The C.D.C. is like an elephant turning around in a camp tent,” Allen says. “It does not realize that when it turns all these other things have to turn around it.” But the problem is much bigger than messaging or guidelines. The U.S. public-health apparatus is vast and unwieldy. Its components are supposed to work closely together but are instead disconnected from one another, and there is little awareness of this problem or of the impact it has on broader response efforts. Neither the C.D.C. nor the entities it serves seem to have an understanding of what federal disease control is supposed to do, or what the limits of the current system actually are. “C.D.C. updates its guidelines, and half of America thinks that means the rules have changed,” Allen says. “But C.D.C. does not make the rules, states and cities do.”’

Only a stronger C.D.C. stands a chance of correcting these errors when the next pandemic comes along.

Without that basic understanding, nuanced discussion has been difficult, and rare. “We’ve spent a whole year debating things like six feet versus three feet, and masks versus no masks,” Friedhoff, from the Covid Collaborative, told me. “But the answers to these questions are totally context-dependent. The way you layer infection-control measures in a school depends on what your building looks like, how many students you have and so on.” That, she says, is the understanding that public-health groups need to instill in educators, business owners and average people. But so far, it has been lost in all the noise.

A perfect case study is Manatee County, in western Florida, which decided to open its school doors to full-time in-person instruction in January. Kevin Chapman, the district’s strategic planning director, relied heavily on the C.D.C.’s guidance. “It was the only thing we had to go by, the only authority or expertise we could lean on,” he says. The guidelines were hardly perfect: They appeared to have been written by medical professionals who had never set foot in a school. And the district had no meaningful support when it came to translating them. The state’s governor, Ron DeSantis, routinely undermined the C.D.C. in his remarks, which by extension seemed to throw the efforts of Chapman and his colleagues under suspicion too. But the team did the best they could. They set up an operations center, educated themselves in the delicate science of contact-tracing and worked with their local health department to hew as closely as possible to what the federal agency had laid out.

They managed to keep the virus at bay. There were no school outbreaks and no closures between January, when schools reopened, and late May, when the school year finally ended. But even so, the district plans to abandon almost all of its current protocols when the next school year begins: no masks, no contact tracing and none of the other edicts that have helped keep the virus in check. Chapman worries that this is too much, too soon, but his team has little recourse. DeSantis has lifted the state mask mandate, and for weeks, a contingent of vocal parents crowded into school-board meetings to demand that the school district follow suit. Never mind that the C.D.C. quickly clarified that its loosened guidelines didn’t apply to schools. “They yell and threaten us,” Chapman says. “They tell us that it doesn’t matter what the C.D.C. says. That if DeSantis has lifted the mask mandate, schools should do the same.”

Friedhoff worries that with schools opening or staying closed based on political considerations, a broader opportunity is being missed. “We have a chance right now to make good infection control and healthier buildings a part of school culture,” she says, “the same way that mental health and healthy eating have become part of that culture.” But that will only happen if school officials can absorb the right lessons from the last year.

The same is true of state and local governments, and of lawmakers who set the C.D.C.’s funding and determine its powers. As the pandemic fades into the background of American life, it’s unclear whether the necessary changes will take place. Public attention and political resolve are likely to fade quickly as vaccination rates increase and case counts decline. That prospect troubles those who believe in the C.D.C.’s mission and who still have hope for its future. “I think the very worst thing that could happen now,” the senior C.D.C. official told me recently, “is for all of this to be forgotten and for everything to just go back to business as usual.”

Jeneen Interlandi is a staff writer for the magazine and a member of The Times’s editorial board. She last wrote for the magazine about how the underfunding of public health put America on track for the worst coronavirus response in the developed world. Brian Rea is an artist based in Stockholm. He is the former art director for The Times’s Opinion section, and his drawings can be seen each week with the paper’s Modern Love column.