Finalist: Staff of The New York Times

A series of missed chances by the federal government to ensure more widespread testing came during the early days of the outbreak, when containment would have been easier.

By Sheri Fink and Mike Baker

Dr. Helen Y. Chu, an infectious disease expert in Seattle, knew that the United States did not have much time.

In late January, the first confirmed American case of the coronavirus had landed in her area. Critical questions needed answers: Had the man infected anyone else? Was the deadly virus already lurking in other communities and spreading?

As luck would have it, Dr. Chu had a way to monitor the region. For months, as part of a research project into the flu, she and a team of researchers had been collecting nasal swabs from residents experiencing symptoms throughout the Puget Sound region.

To repurpose the tests for monitoring the coronavirus, they would need the support of state and federal officials. But nearly everywhere Dr. Chu turned, officials repeatedly rejected the idea, interviews and emails show, even as weeks crawled by and outbreaks emerged in countries outside of China, where the infection began.

By Feb. 25, Dr. Chu and her colleagues could not bear to wait any longer. They began performing coronavirus tests, without government approval.

What came back confirmed their worst fear. They quickly had a positive test from a local teenager with no recent travel history. The coronavirus had already established itself on American soil without anybody realizing it.

“It must have been here this entire time,” Dr. Chu recalled thinking with dread. “It’s just everywhere already.”

In fact, officials would later discover through testing, the virus had already contributed to the deaths of two people, and it would go on to kill 20 more in the Seattle region over the following days.

Federal and state officials said the flu study could not be repurposed because it did not have explicit permission from research subjects; the labs were also not certified for clinical work. While acknowledging the ethical questions, Dr. Chu and others argued there should be more flexibility in an emergency during which so many lives could be lost. On Monday night, state regulators told them to stop testing altogether.

The failure to tap into the flu study, detailed here for the first time, was just one in a series of missed chances by the federal government to ensure more widespread testing during the early days of the outbreak, when containment would have been easier. Instead, local officials across the country were left to work in the dark as the crisis grew undetected and exponentially.

Even now, after weeks of mounting frustration toward federal agencies over flawed test kits and burdensome rules, states with growing cases such as New York and California are struggling to test widely for the coronavirus. The continued delays have made it impossible for officials to get a true picture of the scale of the growing outbreak, which has now spread to at least 36 states and Washington, D.C.

Dr. Robert R. Redfield, director of the Centers for Disease Control and Prevention, said in an interview on Friday that acting quickly was critical for combating an outbreak. “Time matters,” he said.

He insisted that despite the rocky start, there was still time to beat back the coronavirus in the United States. “It’s going to take rigorous, aggressive public health — what I like to say, block and tackle, block and tackle, block and tackle, block and tackle,” he said. “That means if you find a new case, you isolate it.”

But the Seattle Flu Study illustrates how existing regulations and red tape — sometimes designed to protect privacy and health — have impeded the rapid rollout of testing nationally, while other countries ramped up much earlier and faster. Faced with a public health emergency on a scale potentially not seen in a century, the United States has not responded nimbly.

The C.D.C.’s own effort to create a system for monitoring the virus around the country, using established government surveillance networks for the flu, has not yet built steam. And as late as last week, after expanding authorizations for commercial and academic institutions to make tests, administration officials provided conflicting accounts of when a significant increase in tests would be available.

In states like Maine, Missouri and Michigan, where there are few or no known infections, state public health officials say they have more than enough tests to meet demand.

But it remains unclear how many Americans have been tested for the coronavirus. The C.D.C. says approximately 8,500 specimens or nose swabs have been taken since the beginning of the outbreak — a figure that is almost certainly larger than the number of people tested since one person can have multiple swabs. By comparison, South Korea, which discovered its first case around the same time as the United States, has reported having the capacity to test roughly 10,000 people a day since late February.

A prime mission

As soon as the genetic sequence of the coronavirus was published in January, the C.D.C.’s first job was to develop a diagnostic test. “That’s our prime mission,” Dr. Redfield said, “to get eyes on this thing.”

The agency also released criteria for deciding which individuals should be tested for the virus — at first only those who had a fever and respiratory issues and had traveled from the outbreak’s origin in Wuhan, China.

The criteria were so strict that the sick man in the Seattle area who had visited Wuhan did not meet it. Still, worried state health officials pushed to get him checked, and the C.D.C. agreed. Local officials sent a sample to Atlanta and the results came back positive.

Officials monitored 70 people who were in contact with the man, including 50 who consented to getting nose swabs, and none tested positive for the coronavirus. But there was still the possibility that someone had been missed, said Dr. Scott Lindquist, the state epidemiologist for communicable diseases.

Around this time, the Washington State Department of Health began discussions with the Seattle Flu Study already going on in the state.

But there was a hitch: The flu project primarily used research laboratories, not clinical ones, and its coronavirus test was not approved by the Food and Drug Administration. And so the group was not certified to provide test results to anyone outside of their own investigators. They began discussions with state, C.D.C. and F.D.A. officials to figure out a solution, according to emails and interviews.

Dr. Scott F. Dowell, a former high-ranking C.D.C. official and a current deputy director at the Bill & Melinda Gates Foundation, which funds the Seattle Flu Study, asked for help from the leaders of the C.D.C.’s coronavirus response. “Hoping there is a solution,” he wrote on Feb. 10.

Later, Dr. Lindquist, the state epidemiologist in Washington, wrote an email to Dr. Alicia Fry, the chief of the C.D.C.’s epidemiology and prevention branch, requesting the study be used to test for the coronavirus.

C.D.C. officials repeatedly said it would not be possible. “If you want to use your test as a screening tool, you would have to check with F.D.A.,” Gayle Langley, an officer at the C.D.C.’s National Center for Immunization and Respiratory Disease, wrote back in an email on Feb. 16. But the F.D.A. could not offer the approval because the lab was not certified as a clinical laboratory under regulations established by the Centers for Medicare & Medicaid Services, a process that could take months.

Dr. Chu and Dr. Lindquist tried repeatedly to wrangle approval to use the Seattle Flu Study. The answers were always no.

“We felt like we were sitting, waiting for the pandemic to emerge,” Dr. Chu said. “We could help. We couldn’t do anything.”

Sense of exasperation

As Washington State debated with the federal officials over what to do, the C.D.C. confronted the daunting task of testing more widely for the coronavirus.

The C.D.C. had designed its own test as it typically does during an outbreak. Several other countries also developed their own tests.

But when the C.D.C. shipped test kits to public labs across the country, some local health officials began reporting that the test was producing invalid results.

The C.D.C. promised that replacement kits would be distributed within days, but the problem stretched on for over two weeks. Only five state laboratories were able to test in that period. Washington and New York were not among them.

By Feb. 24, as new cases of the virus began popping up in the United States, the state labs were growing frantic.

The Association of Public Health Laboratories made what it called an “extraordinary and rare request” of Dr. Stephen Hahn, the commissioner of the F.D.A., asking him to use his discretion to allow state and local public health laboratories to create their own tests for the virus.

“We are now many weeks into the response with still no diagnostic or surveillance test available outside of C.D.C. for the vast majority of our member laboratories,” Scott Becker, the chief executive of the association, wrote in a letter to Dr. Hahn.

Dr. Hahn responded two days later, saying in a letter that “false diagnostic test results can lead to significant adverse public health consequences” and that the laboratories were welcome to submit their own tests for emergency authorization.

But the approval process for laboratory-developed tests was proving onerous. Private and university clinical laboratories, which typically have the latitude to develop their own tests, were frustrated about the speed of the F.D.A. as they prepared applications for emergency approvals from the agency for their coronavirus tests.

Dr. Alex Greninger, an assistant professor at the University of Washington Medical Center in Seattle, said he became exasperated in mid-February as he communicated with the F.D.A. over getting his application ready to begin testing. “This virus is faster than the F.D.A.,” he said, adding that at one point the agency required him to submit materials through the mail in addition to over email.

New tests typically require validation — running the test on known positive samples from a patient or a copy of the virus genome. The F.D.A.’s process called for five. Obtaining such samples has been hard because most hospital labs have not seen coronavirus cases yet, said Dr. Karen Kaul, chair of the department of pathology and laboratory medicine at NorthShore University HealthSystem in Illinois.

She said she had to scramble to obtain virus RNA from a laboratory in Europe. “Everyone is trying to figure out what we can get to help us gather the data that we need,” she said.

The F.D.A. has disputed that it moved too slowly, saying that it provided emergency authorization for two laboratory-developed tests within 24 hours of a completed submission — one was the C.D.C.’s test and the other a test developed by New York’s Wadsworth laboratory after it had trouble verifying the C.D.C.’s test.

‘What do we do?’

On the other side of the country in Seattle, Dr. Chu and her flu study colleagues, unwilling to wait any longer, decided to begin running samples.

A technician in the laboratory of Dr. Lea Starita who was testing samples soon got a hit.

“I’m like, ‘Oh my God,’” Dr. Starita said. “I just took off running” to the office of the study’s program managers. “We got one,” she told them. “What do we do?”

Members of the research group discussed the ethics of what to do next.

“What we were allowed to do was to keep it to ourselves,” Dr. Chu said. “But what we felt like we needed to do was to tell public health.”

They decided the right thing to do was to inform local health officials.

The case was a teenager, in the same county where the first coronavirus case had surfaced, who had a flu swab just a few days before but had no travel history and no link to any known case.

The state laboratory, finally able to begin testing, confirmed the result the next morning. The teenager, who had recovered from his illness, was located and informed just after he entered his school building. He was sent home and the school was later closed as a precaution.

Later that day, the investigators and Seattle health officials gathered with representatives of the C.D.C. and the F.D.A. to discuss what happened. The message from the federal government was blunt. “What they said on that phone call very clearly was cease and desist to Helen Chu,” Dr. Lindquist remembered. “Stop testing.”

A silent spread

Still, the troubling finding reshaped how officials understood the outbreak. Seattle Flu Study scientists quickly sequenced the genome of the virus, finding a genetic variation also present in the country’s first coronavirus case.

The implications were unnerving. There was a good chance that the virus had been circulating silently in the community for around six weeks, infecting potentially hundreds of people.

On a phone call the day after the C.D.C. and F.D.A. had told Dr. Chu to stop, officials relented, but only partially, the researchers recalled. They would allow the study’s laboratories to test cases and report the results only in future samples. They would need to use a new consent form that explicitly mentioned that results of the coronavirus tests might be shared with the local health department.

They were not to test the thousands of samples that had already been collected.

The same day, the F.D.A. said it would relax its rules and allow clinical labs to begin using their own coronavirus tests as long as they submitted evidence that they worked to the agency. Under that new policy, according to an agency representative on Tuesday, it had heard from 14 labs, with 10 already beginning patient testing.

On March 2, the Seattle Flu Study’s institutional review board at the University of Washington determined that it would be unethical for the researchers not to test and report the results in a public health emergency, Dr. Starita said. Since then, her laboratory has found and reported numerous additional cases, all of which have been confirmed.

As new samples came in, Dr. Starita’s laboratory also worked their way backward through some older samples that had been sitting in the freezers for weeks, finding cases that date back to at least Feb. 20 — seven days before public health officials had any idea the virus was in the community.

The scientists said they believe that they will find evidence that the virus was infecting people even earlier, and that they could have alerted authorities sooner if they had been allowed to test.

But on Monday night, state regulators, enforcing Medicare rules, stepped in and again told them to stop until they could finish getting certified as a clinical laboratory, a process that could take many weeks.

In the days since the teenager’s test, the Seattle region has spun into crisis, with dozens of people testing positive and at least 22 dying — many of them infected in a nursing home that had unknowingly been suffering casualties since Feb. 19.

The availability of testing for coronavirus remains uneven, with some people able to easily obtain tests in certain parts of the country while others have been turned away. Some state officials fear that the virus is spreading far faster than the capacity for testing is increasing.

Looking back, Dr. Chu said she understood why the regulations that stymied the flu study’s efforts for weeks existed. “Those protections are in place for a reason,” she said. “You want to protect human subjects. You want to do things in an ethical way.”

The frustration, she said, was how long it took to cut through red tape to try to save lives in an outbreak that had the potential to explode in Washington State and spread in many other regions. “I don’t think people knew that back then,” she said. “We know it now.”

Reporting was contributed by Nicholas Bogel-Burroughs, Joseph Goldstein, Sheila Kaplan, Michael D. Shear, Knvul Sheikh, Katie Thomas and Noah Weiland.

Government exercises, including one last year, made clear that the U.S. was not ready for a pandemic like the coronavirus. But little was done.

By David E. Sanger, Eric Lipton, Eileen Sullivan and Michael Crowley

WASHINGTON — The outbreak of the respiratory virus began in China and was quickly spread around the world by air travelers, who ran high fevers. In the United States, it was first detected in Chicago, and 47 days later, the World Health Organization declared a pandemic. By then it was too late: 110 million Americans were expected to become ill, leading to 7.7 million hospitalized and 586,000 dead.

That scenario, code-named “Crimson Contagion” and imagining an influenza pandemic, was simulated by the Trump administration’s Department of Health and Human Services in a series of exercises that ran from last January to August.

The simulation’s sobering results — contained in a draft report dated October 2019 that has not previously been reported — drove home just how underfunded, underprepared and uncoordinated the federal government would be for a life-or-death battle with a virus for which no treatment existed.

The draft report, marked “not to be disclosed,” laid out in stark detail repeated cases of “confusion” in the exercise. Federal agencies jockeyed over who was in charge. State officials and hospitals struggled to figure out what kind of equipment was stockpiled or available. Cities and states went their own ways on school closings.

Many of the potentially deadly consequences of a failure to address the shortcomings are now playing out in all-too-real fashion across the country. And it was hardly the first warning for the nation’s leaders. Three times over the past four years the U.S. government, across two administrations, had grappled in depth with what a pandemic would look like, identifying likely shortcomings and in some cases recommending specific action.

In 2016, the Obama administration produced a comprehensive report on the lessons learned by the government from battling Ebola. In January 2017, outgoing Obama administration officials ran an extensive exercise on responding to a pandemic for incoming senior officials of the Trump administration.

The full story of the Trump administration’s response to the coronavirus is still playing out. Government officials, health professionals, journalists and historians will spend years looking back on the muddled messages and missed opportunities of the past three months, as President Trump moved from dismissing the coronavirus as a few cases that would soon be “under control” to his revisionist announcement on Monday that he had known all along that a pandemic was on the way.

What the scenario makes clear, however, is that his own administration had already modeled a similar pandemic and understood its potential trajectory.

The White House defended its record, saying it responded to the 2019 exercise with an executive order to improve the availability and quality of flu vaccines, and that it moved early this year to increase funding for the Department of Health and Human Services’ program that focuses on global pandemic threats.

“Any suggestion that President Trump did not take the threat of COVID-19 seriously is false,” said Judd Deere, a White House spokesman.

But officials have declined to say why the administration was so slow to roll out broad testing or to move faster, as the simulations all indicated it should, to urge social distancing and school closings.

Asked at his news briefing on Thursday about the government’s preparedness, Mr. Trump responded: “Nobody knew there would be a pandemic or epidemic of this proportion. Nobody has ever seen anything like this before.”

The work done over the past five years, however, demonstrates that the government had considerable knowledge about the risks of a pandemic and accurately predicted the very types of problems Mr. Trump is now scrambling belatedly to address.

Crimson Contagion, the exercise conducted last year in Washington and 12 states including New York and Illinois, showed that federal agencies under Mr. Trump continued the Obama-era effort to think ahead about a pandemic.

But the planning and thinking happened many layers down in the bureaucracy. The knowledge and sense of urgency about the peril appear never to have gotten sufficient attention at the highest level of the executive branch or from Congress, leaving the nation with funding shortfalls, equipment shortages and disorganization within and among various branches and levels of government.

The October 2019 report in particular documents that officials at the Departments of Homeland Security and Health and Human Services, and even at the White House’s National Security Council, were aware of the potential for a respiratory virus outbreak originating in China to spread quickly to the United States and overwhelm the nation.

“Nobody ever thought of numbers like this,’’ Mr. Trump said on Wednesday, at a news conference.

In fact, they had.

From Ebola, Lessons Learned

As early as the George W. Bush administration, homeland security and health officials focused on big gaps in the American response to a biological attacks and the growing risk of pandemics. The first test came in April 2009, just a few months after the start of President Barack Obama’s first term. A 10-year-old California girl was diagnosed with a contagious disease that would be called swine flu or H1N1, the first flu pandemic in more than 40 years.

The Centers for Disease Control and Prevention estimates that ultimately there were about 60.8 million cases in the United States, along with 274,304 hospitalizations and 12,469 deaths associated with H1N1.

The virus turned out to be less deadly than first expected. But it was a warning shot that officials in the Obama administration said they took seriously, kicking off a planning effort that escalated in early 2014, with the outbreak of Ebola in West Africa and ensuing fear that it could spread to the United States.

Ebola was less contagious than the flu, but far more deadly. It killed 11,000 people in Africa. But it could have been far worse. The United States sent nearly 3,000 troops to Africa to help keep the disease from spreading. While the containment effort was considered a success, inside the White House, officials sensed that the United States had gotten lucky — and that the response had revealed gaps in preparedness.

Christopher Kirchhoff, a national security aide who moved from the Pentagon to the White House to deal with the Ebola crisis, was given the job of putting together a “lessons learned” report, with input from across the government.

The weaknesses Mr. Kirchhoff identified were early warning signals of what has unfolded in the past three months.

His report concluded that the United States assumed more ability on the part of the World Health Organization than the agency actually had.

The United States had its own issues. There was no airplane in the U.S. fleet capable of evacuating an American doctor who was infected while treating patients in Liberia. The Pentagon was largely unprepared for the intervention that Mr. Obama ordered.

While the United States rapidly developed a way to screen air passengers coming into the country — borrowing from intelligence tools developed after the Sept. 11, 2001, attacks to track possible terrorists — Mr. Kirchhoff found deficiencies in even measuring how fast the virus was spreading.

On the plus side, the Obama White House had created an Ebola Task Force, run by Ron Klain, Vice President Joseph R. Biden Jr.’s former chief of staff, before a single case emerged in the United States. Congress allocated $5.4 billion in emergency funding to pay for Ebola treatment and prevention efforts in the United States and West Africa.

The money helped fund a little-known agency inside the Department of Health and Human Services in charge of preparing for future contagious disease outbreaks, the same office that in 2019 ran the Crimson Contagion exercise and other similar events in the years since.

After a man named Thomas Duncan, a Liberian citizen, became the first person given a diagnosis of Ebola on American territory in September 2014, errors resulted in the infection of two nurses and fear of a wider spread in the United States. (Mr. Duncan died, but the two nurses recovered.)

What is striking in reading Mr. Kirchhoff’s account today, however, is how few of the major faults he found in the American response resulted in action — even though the report was filled with department-by-department recommendations.

There were deficiencies “in personal protective equipment use, disinfection” and “social services for those placed under quarantine.”

There was confusion over travel restrictions, and the need “for a smoother sliding scale of escalation of government response, from local authorities acting on their own to local authorities acting with some federal assistance” to the full activation of the federal government.

The report concluded that “a minimum planning benchmark might be an epidemic an order of magnitude or two more difficult than that presented by the outbreak of Ebola in West Africa, with much more significant domestic spread.”

But one big change did come out of the study: The creation of a dedicated office at the National Security Council to coordinate responses and raise the alarm early.

“What I learned most is that we had to stand up a global biosecurity and health directorate, and get it enshrined for the next administration,” said Lisa Monaco, Mr. Obama’s homeland security adviser.

Getting the Trump Team’s Attention

After Mr. Trump’s election, Ms. Monaco arranged an extensive exercise for high-level incoming officials — including Rex W. Tillerson, the nominee for secretary of state; John F. Kelly, designated to become homeland security secretary; and Rick Perry, who would become energy secretary — gaming out the response to a deadly flu outbreak.

She asked Tom Bossert, who was preparing to come in as Mr. Trump’s homeland security adviser, to run the event alongside her.

“We modeled a new strain of flu in the exercise precisely because it’s so communicable,” Ms. Monaco said. “There is no vaccine, and you would get issues like nursing homes being particularly vulnerable, shortages of ventilators.”

Ms. Monaco was impressed by how seriously Mr. Bossert, her successor, appeared to take the threat, as did many of the 30 or so Trump team members who participated in the exercise, details of which were reported by Politico.

But by the time the current crisis hit, almost all of the leaders at the table — Mr. Tillerson, Mr. Kelly and Mr. Perry among them — had been fired or moved on.

In 2018, Mr. Trump’s national security adviser at the time, John R. Bolton, ousted Mr. Bossert and eliminated the National Security Council directorate, folding it into an office dedicated to weapons of mass destruction in what Trump officials called a logical consolidation.

Asked about that shift on March 13, Mr. Trump told a reporter that it was “a nasty question,” before adding: “I don’t know anything about it.” Writing on Twitter the next day, Mr. Bolton lashed out at critics who said the shift had reflected disregard for pandemic threats.

“Claims that streamlining NSC structures impaired our nation’s bio defense are false,” Mr. Bolton tweeted. “Global health remained a top NSC priority.”

In a statement, the National Security Council said it “has directors and staff whose full-time job it is to monitor, plan for, and respond to pandemics, including an infectious disease epidemiologist and a virologist.”

But in testimony to Congress last week, Dr. Anthony S. Fauci, the director of the National Institute of Allergy and Infectious Diseases, suggested that ending the stand-alone directorate was ill-advised. “It would be nice if the office was still there,” he said.

On Feb. 10, nearly three weeks after the first coronavirus case was diagnosed in the United States, Mr. Trump submitted a 2021 budget proposal that called for a $693.3 million reduction in funding for the C.D.C., or about 9 percent, although there was a modest increase for the division that combats global pandemics.

‘Crimson Contagion’

The Crimson Contagion planning exercise run last year by the Department of Health and Human Services involved officials from 12 states and at least a dozen federal agencies. They included the Pentagon, the Department of Veterans Affairs and the National Security Council. Groups like the American Red Cross and American Nurses Association were invited to join, as were health insurance companies and major hospitals like the Mayo Clinic.

The war game-like exercise was overseen by Robert P. Kadlec, a former Air Force physician who has spent decades focused on biodefense issues. After stints on the Bush administration’s Homeland Security Council and the staff of the Senate Intelligence Committee, he was appointed assistant secretary of Health and Human Services for Preparedness and Response.

“He recognized early that we have a big problem and we needed much bigger budgets to prepare,” said Richard Danzig, the secretary of the Navy in the Clinton administration, who had worked with Mr. Kadlec.

The exercise played out in four separate stages, starting in January 2019.

The events were supposedly unspooling in real time — with the worst-case scenario underway as of Aug. 13, 2019 — when, according to the script, 12,100 cases had already been reported in the United States, with the largest number in Chicago, which had 1,400.

The fictional outbreak involved a pandemic flu, which the Department of Health and Human Services says was “very different than the novel coronavirus.” The staged outbreak had started when a group of 35 tourists visiting China were infected and then flew home to Australia, Kuwait, Malaysia, Thailand, Britain and Spain, as well as to the United States, with some developing respiratory symptoms and fevers en route.

A 52-year-old man from Chicago, who was on the tour, had “low energy and a dry cough” upon his return home. His 17-year-old son on that same day went out to a large public event in Chicago, and the chain of illnesses in the United States started.

Many of the moments during the tabletop exercise are now chillingly familiar.

In the fictional pandemic, as the virus spread quickly across the United States, the C.D.C. issued guidelines for social distancing, and many employees were told to work from home.

But federal and state officials struggled to identify which employees were essential and what equipment was needed to effectively work from home.

There also was confusion over how to handle school children. The C.D.C. recommended that states delay school openings — the exercise took place toward the end of the summer. But some school districts decided to go ahead with the start of school while others followed the federal advice, causing the same types of confusion and discrepancies that have marked the response to the coronavirus.

The exercise from last year then went on to predict how the situation on the ground in the United States would worsen as the weeks passed.

Confusion emerged as state governments began to turn in large numbers to Washington for help to address shortages of antiviral medications, personal protective equipment and ventilators. Then states started to submit requests to different branches of the federal government, leading to bureaucratic chaos.

Friction also emerged between the Federal Emergency Management Agency, which is traditionally in charge of disaster response, and the Department of Health and Human Services, another scenario playing out now.

But the problems were larger than bureaucratic snags. The United States, the organizers realized, did not have the means to quickly manufacture more essential medical equipment, supplies or medicines, including antiviral medications, needles, syringes, N95 respirators and ventilators, the agency concluded.

Congress was briefed in December on some of these findings, including the inability to quickly replenish certain medical supplies, given that much of the product comes from overseas.

These concerns turned more urgent at a hearing last Thursday on Capitol Hill, as lawmakers peppered officials with the Department of Health and Human Services with questions that sounded almost as if they had read the script from the fictional exercise, reflecting the shortage of respirators and protective gear.

Senator Mitt Romney, Republican of Utah, said last week that he blamed Congress and prior administrations for not increasing stockpiles of this type of equipment.

“That is an area we ought to consider making an investment in,” he added, making a point, apparently unknown to him, that the administration’s own simulation had made clear five months earlier.

Aggressive screening might have helped contain the coronavirus in the United States. But technical flaws, regulatory hurdles and lapses in leadership let it spread undetected for weeks.

By Michael D. Shear, Abby Goodnough, Sheila Kaplan, Sheri Fink, Katie Thomas and Noah Weiland

WASHINGTON — Early on, the dozen federal officials charged with defending America against the coronavirus gathered day after day in the White House Situation Room, consumed by crises. They grappled with how to evacuate the United States consulate in Wuhan, China, ban Chinese travelers and extract Americans from the Diamond Princess and other cruise ships.

The members of the coronavirus task force typically devoted only five or 10 minutes, often at the end of contentious meetings, to talk about testing, several participants recalled. The Centers for Disease Control and Prevention, its leaders assured the others, had developed a diagnostic model that would be rolled out quickly as a first step.

But as the deadly virus spread from China with ferocity across the United States between late January and early March, large-scale testing of people who might have been infected did not happen — because of technical flaws, regulatory hurdles, business-as-usual bureaucracies and lack of leadership at multiple levels, according to interviews with more than 50 current and former public health officials, administration officials, senior scientists and company executives.

The result was a lost month, when the world’s richest country — armed with some of the most highly trained scientists and infectious disease specialists — squandered its best chance of containing the virus’s spread. Instead, Americans were left largely blind to the scale of a looming public health catastrophe.

The absence of robust screening until it was “far too late” revealed failures across the government, said Dr. Thomas Frieden, the former C.D.C. director. Jennifer Nuzzo, an epidemiologist at Johns Hopkins, said the Trump administration had “incredibly limited” views of the pathogen’s potential impact. Dr. Margaret Hamburg, the former commissioner of the Food and Drug Administration, said the lapse enabled “exponential growth of cases.”

And Dr. Anthony S. Fauci, a top government scientist involved in the fight against the virus, told members of Congress that the early inability to test was “a failing” of the administration’s response to a deadly, global pandemic. “Why,” he asked later in a magazine interview, “were we not able to mobilize on a broader scale?”

Across the government, they said, three agencies responsible for detecting and combating threats like the coronavirus failed to prepare quickly enough. Even as scientists looked at China and sounded alarms, none of the agencies’ directors conveyed the urgency required to spur a no-holds-barred defense.

Dr. Robert R. Redfield, 68, a former military doctor and prominent AIDS researcher who directs the C.D.C., trusted his veteran scientists to create the world’s most precise test for the coronavirus and share it with state laboratories. When flaws in the test became apparent in February, he promised a quick fix, though it took weeks to settle on a solution.

The C.D.C. also tightly restricted who could get tested and was slow to conduct “community-based surveillance,” a standard screening practice to detect the virus’s reach. Had the United States been able to track its earliest movements and identify hidden hot spots, local quarantines might have confined the disease.

Dr. Stephen Hahn, 60, the commissioner of the Food and Drug Administration, enforced regulations that paradoxically made it tougher for hospitals, private clinics and companies to deploy diagnostic tests in an emergency. Other countries that had mobilized businesses were performing tens of thousands of tests daily, compared with fewer than 100 on average in the United States, frustrating local health officials, lawmakers and desperate Americans.

Alex M. Azar II, who led the Department of Health and Human Services, oversaw the two other agencies and coordinated the government’s public health response to the pandemic. While he grew frustrated as public criticism over the testing issues intensified, he was unable to push either agency to speed up or change course.

Mr. Azar, 52, who chaired the coronavirus task force until late February, when Vice President Mike Pence took charge, had been at odds for months with the White House over other issues. The task force’s chief liaison to the president was Mick Mulvaney, the acting White House chief of staff, who was being forced out by Mr. Trump. Without high-level interest — or demands for action — the testing issue festered.

At the start of that crucial lost month, when his government could have rallied, the president was distracted by impeachment and dismissive of the threat to the public’s health or the nation’s economy. By the end of the month, Mr. Trump claimed the virus was about to dissipate in the United States, saying: “It’s going to disappear. One day — it’s like a miracle — it will disappear.”

By early March, after federal officials finally announced changes to expand testing, it was too late. With the early lapses, containment was no longer an option. The tool kit of epidemiology would shift — lockdowns, social disruption, intensive medical treatment — in hopes of mitigating the harm.

Now, the United States has more than 100,000 coronavirus cases, the most of any country in the world. Deaths are rising, cities are shuttered, the economy is sputtering and everyday life is upended. And still, many Americans sickened by the virus cannot get tested.

In a statement, Judd Deere, a White House spokesman, said that “any suggestion that President Trump did not take the threat of Covid-19 seriously or that the United States was not prepared is false.” He added that at Mr. Trump’s direction, the administration had “expanded testing capacities.”

Dr. Bruce Aylward, a senior adviser at the World Health Organization, led an expert team to China last month to research the mysterious new virus. Testing, he said, was “absolutely vital” for understanding how to defeat a disease — what distinguishes it from others, the spectrum of illness and, most important, its path through populations.

“You want to know whether or not you have it,” Dr. Aylward said. “You want to know whether the people around you have it. Because you know what? Then you could stop it.”

“You can’t stop it,” he warned, “if you can’t see it.”

A Startling Setback

The first time Dr. Robert Redfield heard about the severity of the virus from his Chinese counterparts was around New Year’s Day, when he was on vacation with his family. He spent so much time on the phone that they barely saw him. And what he heard rattled him; in one grim conversation about the virus days later, George F. Gao, the director of the Chinese Center for Disease Control and Prevention, burst into tears.

Dr. Redfield, a longtime AIDS researcher, had never run a government agency before his appointment to lead the C.D.C. in 2018. Until then, his biggest priorities had been fighting the opioid epidemic and the spread of H.I.V. Suddenly, a man who preferred treating patients in Haiti or Africa to being in the public glare was facing a new pandemic threat.

At first, Dr. Redfield’s agency moved quickly.

On Jan. 7, the C.D.C. created an “incident management system” for the coronavirus and advised travelers to Wuhan to take precautions. By Jan. 20, just two weeks after Chinese scientists shared the genetic sequence of the virus, the C.D.C. had developed its own test, as usual, and deployed it to detect the country’s first coronavirus case.

“That’s our prime mission,” Dr. Redfield said later in an interview, “to get eyes on this thing.”

Assessing the virus would prove challenging. It was so new that scientists had little information to work with. China provided limited data, and rebuffed an early attempt by Mr. Azar and Dr. Redfield to send C.D.C. experts there to learn more. That the virus could cause no symptoms and still spread — something not initially known — made it all the more difficult to understand.

To identify the virus, the C.D.C. test used three small genetic sequences to match up with portions of a virus’s genome extracted from a swab. A German-developed test that the W.H.O. was distributing to other countries used just two, potentially making it less precise.

But soon after the F.D.A. cleared the C.D.C. to share its test kits with state health department labs, some discovered a problem. The third sequence, or “probe,” gave inconclusive results. While the C.D.C. explored the cause — contamination or a design issue — it told those state labs to stop testing.

The startling setback stalled the C.D.C.’s efforts to track the virus when it mattered most. By mid-February, the nation was testing only about 100 samples per day, according to the C.D.C.’s website.

Dr. Redfield played down the problem in task force meetings and conversations with Mr. Azar, assuring him it would be fixed quickly, several administration officials said.

With capacity so limited, the C.D.C.’s criteria for who was tested remained extremely narrow for weeks to come: only people who had recently traveled to China or had been in contact with someone who had the virus.

The lack of tests in the states also meant local public health officials could not use another essential epidemiological tool: surveillance testing. To see where the virus might be hiding, nasal swab samples from people screened for the common flu would also be checked for the coronavirus.

The C.D.C. announced a plan on Feb. 14 to perform the screening in five high-risk cities: New York, Chicago, Los Angeles, San Francisco and Seattle. An agency official said it could provide “an early warning signal to trigger a change in our response strategy.” But most of the cities could not carry it out.

“Had we had done more testing from the very beginning and caught cases earlier,” said Dr. Nuzzo, of Johns Hopkins, “we would be in a far different place.”

The consequences became clear by the end of February. For the first time, someone with no known exposure to the virus or history of travel tested positive, in the Seattle area, where the U.S.’s first case had been detected more than a month earlier. The virus had probably been spreading there and elsewhere for weeks, researchers later concluded. Without a more complete picture of who had been infected, public health workers could not do “contact tracing” — finding all those with whom any contagious people had interacted and then quarantining them to stop further transmission.

The C.D.C. gave little thought to adopting the test being used by the W.H.O. The C.D.C.’s test was working in its own lab — still processing samples from states — which gave agency officials confidence. Dr. Anne Schuchat, the agency’s principal deputy director, would later say that the C.D.C. did not think “we needed somebody else’s test.”

And the German-designed W.H.O. test had not been through the American regulatory approval process, which would take time.

Throughout February, Dr. Redfield shuttled between Atlanta, where the C.D.C. is based, and Washington, holding multiple calls every day with Mr. Azar and participating in the coronavirus task force.

Mr. Azar’s take-charge style contrasted with the more deliberative manner of Dr. Redfield, who lacked the kind of commanding television presence that impressed Mr. Trump. He was “a consensus person,” as one colleague described him, who sought to avoid conflict. He relied heavily on some of the C.D.C.’s career scientists, like Dr. Schuchat and Dr. Nancy Messonnier, the director of the agency’s National Center for Immunization and Respiratory Diseases.

Under scrutiny from Congress, Dr. Redfield offered reassurances. Responding on Feb. 24 to a letter from 49 members of Congress about the need for testing in the states, he wrote, “CDC’s aggressive response enables us to identify potential cases early and make sure that they are properly handled.”

Days later, his agency provided a workaround, telling state and local health department labs that they could finally begin testing. Rather than awaiting replacements, they should use their C.D.C. test kits and leave out the problematic third probe.

Meanwhile, the agency’s epidemiologists were growing more concerned as the virus spread in South Korea and Italy. On Feb. 25, Dr. Messonnier gave a briefing with a much blunter warning than usual. “Disruption to everyday life might be severe,” she said.

Mr. Trump, returning from a trip to India, was furious, according to senior administration officials. Later that day, Mr. Azar seemed to be tamping down the level of concern. All Dr. Messonnier had meant, he said at a news conference, was that people should “start thinking about, in their own lives, what that might involve.”

“Might,” Mr. Azar repeated emphatically. “Might involve.”

Barriers to Testing

Dr. Stephen Hahn’s first day as F.D.A. commissioner came just six weeks before Mr. Azar declared a public health emergency on Jan. 31. A radiation oncologist and researcher who helped turn around MD Anderson in Houston, one of the nation’s leading cancer centers, Dr. Hahn had come to Washington to oversee a sprawling federal agency that regulates everything from lifesaving therapies to dog food.

But overnight, his mission — to manage 15,000 employees in a culture defined by precision and caution — was upended. A pathogen that Mr. Trump would later call the “invisible enemy” was hurtling toward the United States. It would fall to the newly arrived Dr. Hahn to help build a huge national capacity for testing by academic and private labs.

Instead, under his leadership, the F.D.A. became a significant roadblock, according to current and former officials as well as researchers and doctors at laboratories around the country.

Private-sector tests were supposed to be the next tier after the C.D.C. fulfilled its obligation to jump-start screening at public labs. In other countries hit hard by the coronavirus, governments acted quickly to speed tests to their populations. In South Korea, for example, regulators in early February summoned executives from 20 medical manufacturers, easing rules as they demanded tests.

But Dr. Hahn took a cautious approach. He was not proactive in reaching out to manufacturers, and instead deferred to his scientists, following the F.D.A.’s often cumbersome methods for approving medical screening.

Even the nation’s public health labs were looking for the F.D.A.’s help. “We are now many weeks into the response with still no diagnostic or surveillance test available outside of C.D.C. for the vast majority of our member laboratories,” Scott Becker, chief executive of the Association of Public Health Laboratories, wrote to Mr. Hahn in late February. “We believe a more expeditious route is needed at this time.”

Ironically, it was Mr. Azar’s emergency declaration that established the rules Dr. Hahn insisted on following. Designed to make it easier for drugmakers to pursue vaccines and other therapies during a crisis, such a declaration lets the F.D.A. speed approvals that could otherwise take a year or more.

But the emergency announcement created a new barrier for hospitals and laboratories that wanted to create their own tests to diagnose the coronavirus. Usually, they faced minimal federal regulation. But once Mr. Azar took action, they were subject to an F.D.A. process called an “emergency use authorization.”

Even though researchers around the country quickly began creating tests that could diagnose Covid-19, many said they were hindered by the F.D.A.’s approval process. The new tests sat unused at labs around the country.

Stanford was one of them. Researchers at the world-renowned university had a working test by February, based on protocols published by the W.H.O. The organization had already delivered more than 250,000 of the German-designed tests to 70 laboratories around the world, and doctors at the Stanford lab wanted to be prepared for a pandemic.

“Even if it didn’t come, it would be better to be ready than not to be ready,” said Dr. Benjamin Pinsky, the lab’s medical director.

But in the face of what he called “relatively tight” rules at the F.D.A., Dr. Pinsky and his colleagues decided against even trying to win permission. The Stanford clinical lab would not begin testing coronavirus samples until early March, when Dr. Hahn finally relaxed the rules.

Executives at bioMérieux, a French diagnostics company, had a similar experience. The company makes a countertop testing system, BioFire, that is routinely used to check for the flu and other respiratory illnesses in 1,700 hospitals around the country. It can provide results in about 45 minutes.

“A lot of us said, you know, your typical E.U.A. is just much too demanding,” said Dr. Mark Miller, the company’s chief medical officer, referring to the emergency approval. “It’s going to take much too much time. And can’t you do something to shorten that?”

Officials at the F.D.A. tried to be responsive, Dr. Miller said. But rather than throw out the rules, the agency only modified the regulatory requirements, still requiring weeks of discussions and negotiations.

After conversations with the F.D.A. in mid-February, the company received emergency approval for its BioFire test on March 24. (The company also began talking to the F.D.A. in January about another type of test, but decided not to pursue it in the United States for now.) Dr. Miller said that while he was ultimately satisfied with the F.D.A.’s actions, the overall response by the government was too slow, especially when it came to logistical questions like getting enough testing supplies to those who needed them.

“You’ve got other countries — and I’m sorry, unfortunately, the U.S. is one of those — where they’ve been slow, disorganized,” he said. “There are still not enough tests available there to test everybody who needs it.”

In an emailed statement, Dr. Hahn maintained that his agency had moved as quickly as it safely could to ensure that tests would be accurate. “Since the early days of this pandemic,” he said, “the F.D.A.’s doors have always been and still remain open to test developers.”

A Lack of Trust

Alex Azar had sounded confident at the end of January. At a news conference in the hulking H.H.S. headquarters in Washington, he said he had the government’s response to the new coronavirus under control, pointing out high-ranking jobs he had held in the department during the 2003 SARS outbreak and other infectious threats.

“I know this playbook well,” he told reporters.

A Yale-trained lawyer who once served as the top attorney at the health department, Mr. Azar had spent a decade as a top executive at Eli Lilly, one of the world’s largest drug companies. But he caught Mr. Trump’s attention in part because of other credentials: After law school, Mr. Azar was a clerk for some of the nation’s most conservative judges, including Justice Antonin Scalia of the Supreme Court. And for two years, he worked as Ken Starr’s deputy on the Clinton Whitewater investigation.

As Mr. Trump’s second health secretary, confirmed at the beginning of 2018, Mr. Azar has been quick to compliment the president and focus on the issues he cares about: lowering drug prices and fighting opioid addiction. On Feb. 6 — even as the W.H.O. announced that there were more than 28,000 coronavirus cases around the globe — Mr. Azar was in the second row in the White House’s East Room, demonstrating his loyalty to the president as Mr. Trump claimed vindication from his impeachment acquittal the day before and lashed out at “evil” lawmakers and the F.B.I.’s “top scum.”

As public attention on the virus threat intensified in January and February, Mr. Azar grew increasingly frustrated about the harsh spotlight on his department and the leaders of agencies who reported to him, according to people familiar with the response to the virus inside the agencies.

Described as a prickly boss by some administration officials, Mr. Azar has had a longstanding feud with Seema Verma, the Medicare and Medicaid chief, who recently became a regular presence at Mr. Trump’s televised briefings on the pandemic. Mr. Azar did not include Dr. Hahn on the virus task force he led, though some of the F.D.A. commissioner’s aides participated in H.H.S. meetings on the subject.

And tensions grew between the secretary and Dr. Redfield as the testing issue persisted. Mr. Azar and Dr. Redfield have been on the phone as often as a half-dozen times a day. But throughout February, as the C.D.C. test faltered, Mr. Azar became convinced that Dr. Redfield’s agency was providing him with inaccurate information about testing that the secretary repeated publicly, according to several administration officials.

In one instance, Mr. Azar appeared on Sunday morning news programs and said that more than 3,600 people had been tested for the virus. In fact, the real number was much smaller because many patients were tested multiple times, an error the C.D.C. had to correct in congressional testimony that week. One health department official said Mr. Azar was repeatedly assured that the C.D.C.’s test would be widely available within a week or 10 days, only to be given the same promise a week later.

Asked about criticism of his agency’s response to the pandemic, Dr. Redfield said: “I’m personally not focused on whether they’re pointing fingers here or there. We’re focused on doing all we can to get through this outbreak as quickly as possible and keep America safe.”

For all Mr. Azar’s complaints, however, he continued to defer to the scientists at the two agencies, according to several administration officials. Mr. Azar’s allies said he was told by Dr. Redfield and Dr. Fauci that the C.D.C. had the resources it needed, that there was no reason to believe the virus was spreading through the country from person to person and that it was important to test only people who met certain criteria.

But even in the face of a crescendo of complaints from doctors and health care researchers around the country, Mr. Azar failed to push those under him to do the one thing that could have helped: broader testing.

In a statement, Caitlin Oakley, Mr. Azar’s spokeswoman, said that the secretary had “empowered and followed the guidance of world-renowned U.S. scientists” on the testing issue. “Any insinuation that Secretary Azar did not respond with needed urgency to the response or testing efforts,” she said, “are just plain wrong and disproven by the facts.”

By Feb. 26, Dr. Fauci was concerned that the stalled testing had become an urgent issue that needed to be addressed. He called Brian Harrison, Mr. Azar’s chief of staff, and asked him to gather the group of officials overseeing screening efforts.

Around noon on Feb. 27, Dr. Hahn, Dr. Redfield and top aides from the F.D.A. and H.H.S. dialed in to a conference call. Mr. Harrison began with an ultimatum: No one leaves until we resolve the lag in testing. We don’t have answers and we need them, one senior administration official recalled him saying. Get it done.

By the end of the day, the group agreed that the F.D.A. should loosen regulations so that hospitals and independent labs could move forward quickly with their own tests.

But the evening before, Mr. Azar had been effectively removed as the leader of the task force when Mr. Trump abruptly put Mr. Pence in charge, a decision so last-minute that even the top health officials in the White House learned of it while watching the announcement.

A Tacit Acknowledgment

Previous presidents have moved quickly to confront disease threats from inside the White House by installing a “czar” to manage the effort.

During an outbreak of the Ebola virus in 2014, President Barack Obama tapped Ron Klain, his vice president’s former chief of staff, to direct the response from the West Wing. Mr. Obama later created an office of global health security inside the National Security Council to coordinate future crises.

“If you look historically in the United States when it is challenged with something like this — whether it’s H.I.V. crises, whether it’s pandemic, whether it’s whatever — man, they pull out all the stops across the system and they make it work,” said Dr. Aylward, the W.H.O. epidemiologist.

But faced with the coronavirus, Mr. Trump chose not to have the White House lead the planning until nearly two months after it began. Mr. Obama’s global health office had been disbanded a year earlier. And until Mr. Pence took charge, the task force lacked a single White House official with the power to compel action.

Since then, testing has ramped up quickly, with nearly 100 labs at hospitals and elsewhere performing it. On Friday, the health care giant Abbott said it had received emergency approval for a portable test that could detect the virus in five minutes.

The president boasted on Tuesday that the United States had “created a new system that now we are doing unbelievably big numbers” of tests for the virus. The U.S., he said, had done more testing for the coronavirus in the last eight days than South Korea had done in eight weeks.

Yet hospitals and clinics across the country still must deny tests to those with milder symptoms, trying to save them for the most serious cases, and they often wait a week for results. In tacit acknowledgment of the shortage, Mr. Trump asked South Korea’s president on Monday to send as many test kits as possible from the 100,000 produced there daily, more than the country needs.

Public health experts reacted positively to the increased capacity. But having the ability to diagnose the disease three months after it was first disclosed by China does little to address why the United States was unable to do so sooner, when it might have helped reduce the toll of the pandemic.

“Testing is the crack that split apart the rest of the response, when it should have tied everything together,” said Dr. Nahid Bhadelia, the medical director of the Special Pathogens Unit at Boston University School of Medicine.

“It seeps into every other aspect of our response, touches all of us,” she said. “The delay of the testing has impacted the response across the board.”

Eric Lipton contributed reporting from Washington and Choe Sang-Hun from Seoul, South Korea.

An examination reveals the president was warned about the potential for a pandemic but that internal divisions, lack of planning and his faith in his own instincts led to a halting response.

By Eric Lipton, David E. Sanger, Maggie Haberman, Michael D. Shear, Mark Mazzetti and Julian E. Barnes

WASHINGTON — “Any way you cut it, this is going to be bad,” a senior medical adviser at the Department of Veterans Affairs, Dr. Carter Mecher, wrote on the night of Jan. 28, in an email to a group of public health experts scattered around the government and universities. “The projected size of the outbreak already seems hard to believe.”

A week after the first coronavirus case had been identified in the United States, and six long weeks before President Trump finally took aggressive action to confront the danger the nation was facing — a pandemic that is now forecast to take tens of thousands of American lives — Dr. Mecher was urging the upper ranks of the nation’s public health bureaucracy to wake up and prepare for the possibility of far more drastic action.

“You guys made fun of me screaming to close the schools,” he wrote to the group, which called itself “Red Dawn,” an inside joke based on the 1984 movie about a band of Americans trying to save the country after a foreign invasion. “Now I’m screaming, close the colleges and universities.”

His was hardly a lone voice. Throughout January, as Mr. Trump repeatedly played down the seriousness of the virus and focused on other issues, an array of figures inside his government — from top White House advisers to experts deep in the cabinet departments and intelligence agencies — identified the threat, sounded alarms and made clear the need for aggressive action.

The president, though, was slow to absorb the scale of the risk and to act accordingly, focusing instead on controlling the message, protecting gains in the economy and batting away warnings from senior officials. It was a problem, he said, that had come out of nowhere and could not have been foreseen.

Even after Mr. Trump took his first concrete action at the end of January — limiting travel from China — public health often had to compete with economic and political considerations in internal debates, slowing the path toward belated decisions to seek more money from Congress, obtain necessary supplies, address shortfalls in testing and ultimately move to keep much of the nation at home.

Unfolding as it did in the wake of his impeachment by the House and in the midst of his Senate trial, Mr. Trump’s response was colored by his suspicion of and disdain for what he viewed as the “Deep State” — the very people in his government whose expertise and long experience might have guided him more quickly toward steps that would slow the virus, and likely save lives.

Decision-making was also complicated by a long-running dispute inside the administration over how to deal with China. The virus at first took a back seat to a desire not to upset Beijing during trade talks, but later the impulse to score points against Beijing left the world’s two leading powers further divided as they confronted one of the first truly global threats of the 21st century.

The shortcomings of Mr. Trump’s performance have played out with remarkable transparency as part of his daily effort to dominate television screens and the national conversation.

But dozens of interviews with current and former officials and a review of emails and other records revealed many previously unreported details and a fuller picture of the roots and extent of his halting response as the deadly virus spread:

• The National Security Council office responsible for tracking pandemics received intelligence reports in early January predicting the spread of the virus to the United States, and within weeks was raising options like keeping Americans home from work and shutting down cities the size of Chicago. Mr. Trump would avoid such steps until March.
• Despite Mr. Trump’s denial weeks later, he was told at the time about a Jan. 29 memo produced by his trade adviser, Peter Navarro, laying out in striking detail the potential risks of a coronavirus pandemic: as many as half a million deaths and trillions of dollars in economic losses.
• The health and human services secretary, Alex M. Azar II, directly warned Mr. Trump of the possibility of a pandemic during a call on Jan. 30, the second warning he delivered to the president about the virus in two weeks. The president, who was on Air Force One while traveling for appearances in the Midwest, responded that Mr. Azar was being alarmist.
• Mr. Azar publicly announced in February that the government was establishing a “surveillance” system in five American cities to measure the spread of the virus and enable experts to project the next hot spots. It was delayed for weeks. The slow start of that plan, on top of the well-documented failures to develop the nation’s testing capacity, left administration officials with almost no insight into how rapidly the virus was spreading. “We were flying the plane with no instruments,” one official said.
• By the third week in February, the administration’s top public health experts concluded they should recommend to Mr. Trump a new approach that would include warning the American people of the risks and urging steps like social distancing and staying home from work. But the White House focused instead on messaging and crucial additional weeks went by before their views were reluctantly accepted by the president — time when the virus spread largely unimpeded.

When Mr. Trump finally agreed in mid-March to recommend social distancing across the country, effectively bringing much of the economy to a halt, he seemed shellshocked and deflated to some of his closest associates. One described him as “subdued” and “baffled” by how the crisis had played out. An economy that he had wagered his re-election on was suddenly in shambles.

He only regained his swagger, the associate said, from conducting his daily White House briefings, at which he often seeks to rewrite the history of the past several months. He declared at one point that he “felt it was a pandemic long before it was called a pandemic,” and insisted at another that he had to be a “cheerleader for the country,” as if that explained why he failed to prepare the public for what was coming.

Mr. Trump’s allies and some administration officials say the criticism has been unfair. The Chinese government misled other governments, they say. And they insist that the president was either not getting proper information, or the people around him weren’t conveying the urgency of the threat. In some cases, they argue, the specific officials he was hearing from had been discredited in his eyes, but once the right information got to him through other channels, he made the right calls.

“While the media and Democrats refused to seriously acknowledge this virus in January and February, President Trump took bold action to protect Americans and unleash the full power of the federal government to curb the spread of the virus, expand testing capacities and expedite vaccine development even when we had no true idea the level of transmission or asymptomatic spread,” said Judd Deere, a White House spokesman.

There were key turning points along the way, opportunities for Mr. Trump to get ahead of the virus rather than just chase it. There were internal debates that presented him with stark choices, and moments when he could have chosen to ask deeper questions and learn more. How he handled them may shape his re-election campaign. They will certainly shape his legacy.

The Containment Illusion

By the last week of February, it was clear to the administration’s public health team that schools and businesses in hot spots would have to close. But in the turbulence of the Trump White House, it took three more weeks to persuade the president that failure to act quickly to control the spread of the virus would have dire consequences.

When Dr. Robert Kadlec, the top disaster response official at the Health and Human Services Department, convened the White House coronavirus task force on Feb. 21, his agenda was urgent. There were deep cracks in the administration’s strategy for keeping the virus out of the United States. They were going to have to lock down the country to prevent it from spreading. The question was: When?

There had already been an alarming spike in new cases around the world and the virus was spreading across the Middle East. It was becoming apparent that the administration had botched the rollout of testing to track the virus at home, and a smaller-scale surveillance program intended to piggyback on a federal flu tracking system had also been stillborn.

In Washington, the president was not worried, predicting that by April, “when it gets a little warmer, it miraculously goes away.” His White House had yet to ask Congress for additional funding to prepare for the potential cost of wide-scale infection across the country, and health care providers were growing increasingly nervous about the availability of masks, ventilators and other equipment.

What Mr. Trump decided to do next could dramatically shape the course of the pandemic — and how many people would get sick and die.

With that in mind, the task force had gathered for a tabletop exercise — a real-time version of a full-scale war gaming of a flu pandemic the administration had run the previous year. That earlier exercise, also conducted by Mr. Kadlec and called “Crimson Contagion,” predicted 110 million infections, 7.7 million hospitalizations and 586,000 deaths following a hypothetical outbreak that started in China.

Facing the likelihood of a real pandemic, the group needed to decide when to abandon “containment” — the effort to keep the virus outside the U.S. and to isolate anyone who gets infected — and embrace “mitigation” to thwart the spread of the virus inside the country until a vaccine becomes available.

Among the questions on the agenda, which was reviewed by The New York Times, was when the department’s secretary, Mr. Azar, should recommend that Mr. Trump take textbook mitigation measures “such as school dismissals and cancellations of mass gatherings,” which had been identified as the next appropriate step in a Bush-era pandemic plan.

The exercise was sobering. The group — including Dr. Anthony S. Fauci of the National Institutes of Health; Dr. Robert R. Redfield of the Centers for Disease Control and Prevention, and Mr. Azar, who at that stage was leading the White House Task Force — concluded they would soon need to move toward aggressive social distancing, even at the risk of severe disruption to the nation’s economy and the daily lives of millions of Americans.

If Dr. Kadlec had any doubts, they were erased two days later, when he stumbled upon an email from a researcher at the Georgia Institute of Technology, who was among the group of academics, government physicians and infectious diseases doctors who had spent weeks tracking the outbreak in the Red Dawn email chain.

A 20-year-old Chinese woman had infected five relatives with the virus even though she never displayed any symptoms herself. The implication was grave — apparently healthy people could be unknowingly spreading the virus — and supported the need to move quickly to mitigation.

“Is this true?!” Dr. Kadlec wrote back to the researcher. “If so we have a huge whole on our screening and quarantine effort,” including a typo where he meant hole. Her response was blunt: “People are carrying the virus everywhere.”

The following day, Dr. Kadlec and the others decided to present Mr. Trump with a plan titled “Four Steps to Mitigation,” telling the president that they needed to begin preparing Americans for a step rarely taken in United States history.

But over the next several days, a presidential blowup and internal turf fights would sidetrack such a move. The focus would shift to messaging and confident predictions of success rather than publicly calling for a shift to mitigation.

These final days of February, perhaps more than any other moment during his tenure in the White House, illustrated Mr. Trump’s inability or unwillingness to absorb warnings coming at him. He instead reverted to his traditional political playbook in the midst of a public health calamity, squandering vital time as the coronavirus spread silently across the country.

Dr. Kadlec’s group wanted to meet with the president right away, but Mr. Trump was on a trip to India, so they agreed to make the case to him in person as soon as he returned two days later. If they could convince him of the need to shift strategy, they could immediately begin a national education campaign aimed at preparing the public for the new reality.

A memo dated Feb. 14, prepared in coordination with the National Security Council and titled “U.S. Government Response to the 2019 Novel Coronavirus,” documented what more drastic measures would look like, including: “significantly limiting public gatherings and cancellation of almost all sporting events, performances, and public and private meetings that cannot be convened by phone. Consider school closures. Widespread ‘stay at home’ directives from public and private organizations with nearly 100% telework for some.”

The memo did not advocate an immediate national shutdown, but said the targeted use of “quarantine and isolation measures” could be used to slow the spread in places where “sustained human-to-human transmission” is evident.

Within 24 hours, before they got a chance to make their presentation to the president, the plan went awry.

Mr. Trump was walking up the steps of Air Force One to head home from India on Feb. 25 when Dr. Nancy Messonnier, the director of the National Center for Immunization and Respiratory Diseases, publicly issued the blunt warning they had all agreed was necessary.

But Dr. Messonnier had jumped the gun. They had not told the president yet, much less gotten his consent.

On the 18-hour plane ride home, Mr. Trump fumed as he watched the stock market crash after Dr. Messonnier’s comments. Furious, he called Mr. Azar when he landed at around 6 a.m. on Feb. 26, raging that Dr. Messonnier had scared people unnecessarily. Already on thin ice with the president over a variety of issues and having overseen the failure to quickly produce an effective and widely available test, Mr. Azar would soon find his authority reduced.

The meeting that evening with Mr. Trump to advocate social distancing was canceled, replaced by a news conference in which the president announced that the White House response would be put under the command of Vice President Mike Pence.

The push to convince Mr. Trump of the need for more assertive action stalled. With Mr. Pence and his staff in charge, the focus was clear: no more alarmist messages. Statements and media appearances by health officials like Dr. Fauci and Dr. Redfield would be coordinated through Mr. Pence’s office. It would be more than three weeks before Mr. Trump would announce serious social distancing efforts, a lost period during which the spread of the virus accelerated rapidly.

Over nearly three weeks from Feb. 26 to March 16, the number of confirmed coronavirus cases in the United States grew from 15 to 4,226. Since then, nearly half a million Americans have tested positive for the virus and authorities say hundreds of thousands more are likely infected.

The China Factor

The earliest warnings about coronavirus got caught in the crosscurrents of the administration’s internal disputes over China. It was the China hawks who pushed earliest for a travel ban. But their animosity toward China also undercut hopes for a more cooperative approach by the world’s two leading powers to a global crisis.

It was early January, and the call with a Hong Kong epidemiologist left Matthew Pottinger rattled.

Mr. Pottinger, the deputy national security adviser and a hawk on China, took a blunt warning away from the call with the doctor, a longtime friend: A ferocious, new outbreak that on the surface appeared similar to the SARS epidemic of 2003 had emerged in China. It had spread far more quickly than the government was admitting to, and it wouldn’t be long before it reached other parts of the world.

Mr. Pottinger had worked as a Wall Street Journal correspondent in Hong Kong during the SARS epidemic, and was still scarred by his experience documenting the death spread by that highly contagious virus.

Now, seventeen years later, his friend had a blunt message: You need to be ready. The virus, he warned, which originated in the city of Wuhan, was being transmitted by people who were showing no symptoms — an insight that American health officials had not yet accepted. Mr. Pottinger declined through a spokesman to comment.

It was one of the earliest warnings to the White House, and it echoed the intelligence reports making their way to the National Security Council. While most of the early assessments from the C.I.A. had little more information than was available publicly, some of the more specialized corners of the intelligence world were producing sophisticated and chilling warnings.

In a report to the director of national intelligence, the State Department’s epidemiologist wrote in early January that the virus was likely to spread across the globe, and warned that the coronavirus could develop into a pandemic. Working independently, a small outpost of the Defense Intelligence Agency, the National Center for Medical Intelligence, came to the same conclusion. Within weeks after getting initial information about the virus early in the year, biodefense experts inside the National Security Council, looking at what was happening in Wuhan, started urging officials to think about what would be needed to quarantine a city the size of Chicago.

By mid-January there was growing evidence of the virus spreading outside China. Mr. Pottinger began convening daily meetings about the coronavirus. He alerted his boss, Robert C. O’Brien, the national security adviser.

The early alarms sounded by Mr. Pottinger and other China hawks were freighted with ideology — including a push to publicly blame China that critics in the administration say was a distraction as the coronavirus spread to Western Europe and eventually the United States.

And they ran into opposition from Mr. Trump’s economic advisers, who worried a tough approach toward China could scuttle a trade deal that was a pillar of Mr. Trump’s re-election campaign.

With his skeptical — some might even say conspiratorial — view of China’s ruling Communist Party, Mr. Pottinger initially suspected that President Xi Jinping’s government was keeping a dark secret: that the virus may have originated in one of the laboratories in Wuhan studying deadly pathogens. In his view, it might have even been a deadly accident unleashed on an unsuspecting Chinese population.

During meetings and telephone calls, Mr. Pottinger asked intelligence agencies — including officers at the C.I.A. working on Asia and on weapons of mass destruction — to search for evidence that might bolster his theory.

They didn’t have any evidence. Intelligence agencies did not detect any alarm inside the Chinese government that analysts presumed would accompany the accidental leak of a deadly virus from a government laboratory. But Mr. Pottinger continued to believe the coronavirus problem was far worse than the Chinese were acknowledging. Inside the West Wing, the director of the Domestic Policy Council, Joe Grogan, also tried to sound alarms that the threat from China was growing.

Mr. Pottinger, backed by Mr. O’Brien, became one of the driving forces of a campaign in the final weeks of January to convince Mr. Trump to impose limits on travel from China — the first substantive step taken to impede the spread of the virus and one that the president has repeatedly cited as evidence that he was on top of the problem.

In addition to the opposition from the economic team, Mr. Pottinger and his allies among the China hawks had to overcome initial skepticism from the administration’s public health experts.

Travel restrictions were usually counterproductive to managing biological outbreaks because they prevented doctors and other much-needed medical help from easily getting to the affected areas, the health officials said. And such bans often cause infected people to flee, spreading the disease further.

But on the morning of Jan. 30, Mr. Azar got a call from Dr. Fauci, Dr. Redfield and others saying they had changed their minds. The World Health Organization had declared a global public health emergency and American officials had discovered the first confirmed case of person-to-person transmission inside the United States.

The economic team, led by Treasury Secretary Steven Mnuchin, continued to argue that there were big risks in taking a provocative step toward China and moving to curb global travel. After a debate, Mr. Trump came down on the side of the hawks and the public health team. The limits on travel from China were publicly announced on Jan. 31.

Still, Mr. Trump and other senior officials were wary of further upsetting Beijing. Besides the concerns about the impact on the trade deal, they knew that an escalating confrontation was risky because the United States relies heavily on China for pharmaceuticals and the kinds of protective equipment most needed to combat the coronavirus.

But the hawks kept pushing in February to take a critical stance toward China amid the growing crisis. Mr. Pottinger and others — including aides to Secretary of State Mike Pompeo — pressed for government statements to use the term “Wuhan Virus.”

Mr. Pompeo tried to hammer the anti-China message at every turn, eventually even urging leaders of the Group of 7 industrialized countries to use “Wuhan virus” in a joint statement.

Others, including aides to Mr. Pence, resisted taking a hard public line, believing that angering Beijing might lead the Chinese government to withhold medical supplies, pharmaceuticals and any scientific research that might ultimately lead to a vaccine.

Mr. Trump took a conciliatory approach through the middle of March, praising the job Mr. Xi was doing.

That changed abruptly, when aides informed Mr. Trump that a Chinese Foreign Ministry spokesman had publicly spun a new conspiracy about the origins of Covid-19: that it was brought to China by U.S. Army personnel who visited the country last October.

Mr. Trump was furious, and he took to his favorite platform to broadcast a new message. On March 16, he wrote on Twitter that “the United States will be powerfully supporting those industries, like Airlines and others, that are particularly affected by the Chinese Virus.”

Mr. Trump’s decision to escalate the war of words undercut any remaining possibility of broad cooperation between the governments to address a global threat. It remains to be seen whether that mutual suspicion will spill over into efforts to develop treatments or vaccines, both areas where the two nations are now competing.

One immediate result was a free-for-all across the United States, with state and local governments and hospitals bidding on the open market for scarce but essential Chinese-made products. When the state of Massachusetts managed to procure 1.2 million masks, it fell to the owner of the New England Patriots, Robert K. Kraft, a Trump ally, to cut through extensive red tape on both sides of the Pacific to send his own plane to pick them up.

The Consequences of Chaos

The chaotic culture of the Trump White House contributed to the crisis. A lack of planning and a failure to execute, combined with the president’s focus on the news cycle and his preference for following his gut rather than the data cost time, and perhaps lives.

Inside the West Wing, Mr. Navarro, Mr. Trump’s trade adviser, was widely seen as quick-tempered, self-important and prone to butting in. He is among the most outspoken of China hawks and in late January was clashing with the administration’s health experts over limiting travel from China.

So it elicited eye rolls when, after initially being prevented from joining the coronavirus task force, he circulated a memo on Jan. 29 urging Mr. Trump to impose the travel limits, arguing that failing to confront the outbreak aggressively could be catastrophic, leading to hundreds of thousands of deaths and trillions of dollars in economic losses.

The uninvited message could not have conflicted more with the president’s approach at the time of playing down the severity of the threat. And when aides raised it with Mr. Trump, he responded that he was unhappy that Mr. Navarro had put his warning in writing.

From the time the virus was first identified as a concern, the administration’s response was plagued by the rivalries and factionalism that routinely swirl around Mr. Trump and, along with the president’s impulsiveness, undercut decision making and policy development.

Faced with the relentless march of a deadly pathogen, the disagreements and a lack of long-term planning had significant consequences. They slowed the president’s response and resulted in problems with execution and planning, including delays in seeking money from Capitol Hill and a failure to begin broad surveillance testing.

The efforts to shape Mr. Trump’s view of the virus began early in January, when his focus was elsewhere: the fallout from his decision to kill Maj. Gen. Qassim Suleimani, Iran’s security mastermind; his push for an initial trade deal with China; and his Senate impeachment trial, which was about to begin.

Even after Mr. Azar first briefed him about the potential seriousness of the virus during a phone call on Jan. 18 while the president was at his Mar-a-Lago resort in Florida, Mr. Trump projected confidence that it would be a passing problem.

“We have it totally under control,” he told an interviewer a few days later while attending the World Economic Forum in Switzerland. “It’s going to be just fine.”

Back in Washington, voices outside of the White House peppered Mr. Trump with competing assessments about what he should do and how quickly he should act.

The efforts to sort out policy behind closed doors were contentious and sometimes only loosely organized.

That was the case when the National Security Council convened a meeting on short notice on the afternoon of Jan. 27. The Situation Room was standing room only, packed with top White House advisers, low-level staffers, Mr. Trump’s social media guru, and several cabinet secretaries. There was no checklist about the preparations for a possible pandemic, which would require intensive testing, rapid acquisition of protective gear, and perhaps serious limitations on Americans’ movements.

Instead, after a 20-minute description by Mr. Azar of his department’s capabilities, the meeting was jolted when Stephen E. Biegun, the newly installed deputy secretary of state, announced plans to issue a “level four” travel warning, strongly discouraging Americans from traveling to China. The room erupted into bickering.

A few days later, on the evening of Jan. 30, Mick Mulvaney, the acting White House chief of staff at the time, and Mr. Azar called Air Force One as the president was making the final decision to go ahead with the restrictions on China travel. Mr. Azar was blunt, warning that the virus could develop into a pandemic and arguing that China should be criticized for failing to be transparent.

Mr. Trump rejected the idea of criticizing China, saying the country had enough to deal with. And if the president’s decision on the travel restrictions suggested that he fully grasped the seriousness of the situation, his response to Mr. Azar indicated otherwise.

Stop panicking, Mr. Trump told him.

That sentiment was present throughout February, as the president’s top aides reached for a consistent message but took few concrete steps to prepare for the possibility of a major public health crisis.

During a briefing on Capitol Hill on Feb. 5, senators urged administration officials to take the threat more seriously. Several asked if the administration needed additional money to help local and state health departments prepare.

Derek Kan, a senior official from the Office of Management and Budget, replied that the administration had all the money it needed, at least at that point, to stop the virus, two senators who attended the briefing said.

“Just left the Administration briefing on Coronavirus,” Senator Christopher S. Murphy, Democrat of Connecticut, wrote in a tweet shortly after. “Bottom line: they aren’t taking this seriously enough.”

The administration also struggled to carry out plans it did agree on. In mid-February, with the effort to roll out widespread testing stalled, Mr. Azar announced a plan to repurpose a flu-surveillance system in five major cities to help track the virus among the general population. The effort all but collapsed even before it got started as Mr. Azar struggled to win approval for $100 million in funding and the C.D.C. failed to make reliable tests available.

The number of infections in the United States started to surge through February and early March, but the Trump administration did not move to place large-scale orders for masks and other protective equipment, or critical hospital equipment, such as ventilators. The Pentagon sat on standby, awaiting any orders to help provide temporary hospitals or other assistance.

As February gave way to March, the president continued to be surrounded by divided factions even as it became clearer that avoiding more aggressive steps was not tenable.

Mr. Trump had agreed to give an Oval Office address on the evening of March 11 announcing restrictions on travel from Europe, where the virus was ravaging Italy. But responding to the views of his business friends and others, he continued to resist calls for social distancing, school closures and other steps that would imperil the economy.

But the virus was already multiplying across the country — and hospitals were at risk of buckling under the looming wave of severely ill people, lacking masks and other protective equipment, ventilators and sufficient intensive care beds. The question loomed over the president and his aides after weeks of stalling and inaction: What were they going to do?

The approach that Mr. Azar and others had planned to bring to him weeks earlier moved to the top of the agenda. Even then, and even by Trump White House standards, the debate over whether to shut down much of the country to slow the spread was especially fierce.

Always attuned to anything that could trigger a stock market decline or an economic slowdown that could hamper his re-election effort, Mr. Trump also reached out to prominent investors like Stephen A. Schwarzman, the chief executive of Blackstone Group, a private equity firm.

“Everybody questioned it for a while, not everybody, but a good portion questioned it,” Mr. Trump said earlier this month. “They said, let’s keep it open. Let’s ride it.”

In a tense Oval Office meeting, when Mr. Mnuchin again stressed that the economy would be ravaged, Mr. O’Brien, the national security adviser, who had been worried about the virus for weeks, sounded exasperated as he told Mr. Mnuchin that the economy would be destroyed regardless if officials did nothing.

Soon after the Oval Office address, Dr. Scott Gottlieb, the former commissioner of the Food and Drug Administration and a trusted sounding board inside the White House, visited Mr. Trump, partly at the urging of Jared Kushner, the president’s son-in-law. Dr. Gottlieb’s role was to impress upon the president how serious the crisis could become. Mr. Pence, by then in charge of the task force, also played a key role at that point in getting through to the president about the seriousness of the moment in a way that Mr. Azar had not.

But in the end, aides said, it was Dr. Deborah L. Birx, the veteran AIDS researcher who had joined the task force, who helped to persuade Mr. Trump. Soft-spoken and fond of the kind of charts and graphs Mr. Trump prefers, Dr. Birx did not have the rough edges that could irritate the president. He often told people he thought she was elegant.

On Monday, March 16, Mr. Trump announced new social distancing guidelines, saying they would be in place for two weeks. The subsequent economic disruptions were so severe that the president repeatedly suggested that he wanted to lift even those temporary restrictions. He frequently asked aides why his administration was still being blamed in news coverage for the widespread failures involving testing, insisting the responsibility had shifted to the states.

During the last week in March, Kellyanne Conway, a senior White House adviser involved in task force meetings, gave voice to concerns other aides had. She warned Mr. Trump that his wished-for date of Easter to reopen the country likely couldn’t be accomplished. Among other things, she told him, he would end up being blamed by critics for every subsequent death caused by the virus.

Within days, he watched images on television of a calamitous situation at Elmhurst Hospital Center, miles from his childhood home in Queens, N.Y., where 13 people had died from the coronavirus in 24 hours.

He left the restrictions in place.

Mark Walker contributed reporting from Washington, and Mike Baker from Seattle. Kitty Bennett contributed research.

The technology was old, the data poor, the bureaucracy slow, the guidance confusing, the administration not in agreement. The coronavirus shook the world’s premier health agency, creating a loss of confidence and hampering the U.S. response to the crisis.

By Eric Lipton, Abby Goodnough, Michael D. Shear, Megan Twohey, Apoorva Mandavilli, Sheri Fink and Mark Walker

WASHINGTON — Americans returning from China landed at U.S. airports by the thousands in early February, potential carriers of a deadly virus who had been diverted to a handful of cities for screening by the Centers for Disease Control and Prevention.

Their arrival prompted a frantic scramble by local and state officials to press the travelers to self-quarantine, and to monitor whether anyone fell ill. It was one of the earliest tests of whether the public health system in the United States could contain the contagion.

But the effort was frustrated as the C.D.C.’s decades-old notification system delivered information collected at the airports that was riddled with duplicative records, bad phone numbers and incomplete addresses. For weeks, officials tried to track passengers using lists sent by the C.D.C., scouring information about each flight in separate spreadsheets.

“It was insane,” said Dr. Sharon Balter, a director at the Los Angeles County Department of Public Health. When the system went offline in mid-February, briefly halting the flow of passenger data, local officials listened in disbelief on a conference call as the C.D.C. responded to the possibility that infected travelers might slip away.

“Just let them go,” two of the health officials recall being told.

The flawed effort was an early revelation for some health departments, whose confidence in the C.D.C. was shaken as it confronted the most urgent public health emergency in its 74-year history — a pathogen that has penetrated much of the nation, killing more than 100,000 people.

The C.D.C., long considered the world’s premier health agency, made early testing mistakes that contributed to a cascade of problems that persist today as the country tries to reopen. It failed to provide timely counts of infections and deaths, hindered by aging technology and a fractured public health reporting system. And it hesitated in absorbing the lessons of other countries, including the perils of silent carriers spreading the infection.

The agency struggled to calibrate its own imperative to be cautious and the need to move fast as the coronavirus ravaged the country, according to a review of thousands of emails and interviews with more than 100 state and federal officials, public health experts, C.D.C. employees and medical workers. In communicating to the public, its leadership was barely visible, its stream of guidance was often slow and its messages were sometimes confusing, sowing mistrust.

“They let us down,” said Dr. Stephane Otmezguine, an anesthesiologist who treated coronavirus patients in Fort Lauderdale, Fla. Richard Whitley, the top health official in Nevada, wrote to the C.D.C. director about a communication “breakdown” between the states and the agency. Gov. J.B. Pritzker of Illinois lashed out at the agency over testing, saying that the government’s response would “go down in history as a profound failure.”

“The C.D.C. is no longer the reliable go-to place,” said Dr. Ashish Jha, the director of the Harvard Global Health Institute.

Even as the virus tested the C.D.C.’s capacity to respond, the agency and its director, Dr. Robert R. Redfield, faced unprecedented challenges from President Trump, who repeatedly wished away the pandemic. His efforts to seize the spotlight from the public health agency reflected the broader patterns of his erratic presidency: public condemnations on Twitter, a tendency to dismiss findings from scientists, inconsistent policy or decision-making and a suspicion that the “deep state” inside the government is working to force him out of office.

Mr. Trump and his top aides have grown increasingly bitter about perceived leaks from the C.D.C. they say were designed to embarrass the president and to build support for decisions that ignore broader concerns about the country’s vast social and economic dislocation. At the same time, some at the C.D.C. have bristled at what they see as pressure to bend evidence-based recommendations to help Mr. Trump’s political standing.

Located in Atlanta, the C.D.C. is encharged with protecting the nation against public health threats — from anthrax to obesity — and serving as the unassailable source of information about fighting them. Given its record and resources, the agency might have become the undisputed leader in the global fight against the virus.

Instead, the C.D.C. made missteps that undermined America’s response.

“Here is an agency that has been waiting its entire existence for this moment,” said Dr. Peter Lurie, a former associate commissioner at the Food and Drug Administration who for years worked closely with the C.D.C. “And then they flub it. It is very sad. That is what they were set up to do.”

The agency’s allies say it is just one part of a vast network of state and local health departments, hospitals, government agencies and suppliers that were collectively unprepared for the speed, scope and ferocity of the pandemic. They also point out that lawmakers have long failed to adequately prioritize funding for the kind of crisis the country now faces.

Dr. Amy Ray, an infectious disease specialist in Cleveland, said the C.D.C. did not “get enough credit,” adding, “They are learning at the same time the world is learning, by watching how this disease manifests.”

The agency, which declined repeated requests for interviews with its top officials, said in a statement: “C.D.C. is at the table as part of the larger U.S. government response, providing the best, most current data and scientific understanding we have.”

“It’s important to remember that this is a global emergency — and it’s impacting the entire U.S.,” the agency said. “That means it requires an all-of-government response.”

‘Not Our Culture to Intervene’

In early March, Dr. Redfield led Mr. Trump on a V.I.P. tour of the high-tech labs at the C.D.C.’s Atlanta headquarters, standing off to the side as the president spoke.

Wearing a red “Keep America Great” cap, Mr. Trump falsely asserted that “anybody that wants a test can get a test,” claimed he had a “natural ability” for science and noted that he might hold campaign rallies even as the virus spread.

“Thank you for your decisive leadership in helping us, you know, put public health first,” Dr. Redfield told the president as they posed for the cameras.

The moment underscored the challenge for the director and his agency. To combat the virus, he would have to manage the mercurial demands of the president who appointed him and the expectations of the career scientists he leads.

The sensibilities could not be more different. At one point that month, administration officials asked the agency to provide feedback on possible logos — including “Make America Healthy Again” — for cloth face masks they hoped to distribute to millions of Americans. The plan fell through, but not before C.D.C. leaders agreed to the request, according to one person familiar with the discussions.

White House aides saw Dr. Redfield, 68, as an ally, but as the coronavirus crisis intensified, his meandering manner in television appearances and congressional hearings irritated a president drawn to big personalities and assertive defenders of his administration.

A former military virologist who specialized in H.I.V., Dr. Redfield was Mr. Trump’s second choice after his first C.D.C. director resigned. He had no experience leading a government agency — though he had been considered for jobs in previous Republican administrations — and often told associates that he was happiest treating patients in Africa or Haiti.

Dr. Robert C. Gallo, who founded the Institute of Human Virology at the University of Maryland School of Medicine with Dr. Redfield in 1996, said he had warned him against taking the C.D.C. post, describing it as “massive public health, lots of politics, lots of pressure.”

While praising his friend as “a terrific, dedicated infectious disease doctor,” Dr. Gallo, who also co-founded the Global Virus Network, said in an interview that Dr. Redfield “can’t do anything communication-wise.” He added, “He’s reticent, never wanting the front of anything — maybe it’s extreme humility.”

The C.D.C., established in the 1940s to control malaria in the South, has the feel of an academic institution. There, experts work “at the speed of science — you take time doing it,” said Dr. Georges C. Benjamin, executive director of the American Public Health Association.

The agency, a division of the Department of Health and Human Services with 11,000 employees, cannot make policy, but it guides federal and state public health systems and advises government leaders.

The C.D.C.’s most fabled experts are the disease detectives of its Epidemic Intelligence Service, rapid responders who investigate outbreaks. But more broadly, according to current and former employees and others who worked closely with the agency, the C.D.C. is risk-averse, perfectionist and ill suited to improvising in a quickly evolving crisis — particularly one that shuts down the country and paralyzes the economy.

“It’s not our culture to intervene,” said Dr. George Schmid, who worked at the agency off and on for nearly four decades. He described it as increasingly bureaucratic, weighed down by “indescribable, burdensome hierarchy.”

The exacting culture shaped its scientists’ ambitions; it also locked some into a fixed way of thinking, former officials said. And it helped produce the C.D.C.’s most consequential failure in the crisis: its inability early on to provide state laboratories around the country with an effective diagnostic test.

The C.D.C. quickly developed a successful test in January designed to be highly precise, but it was more complicated to use and turned out to be no better than versions produced overseas. And in manufacturing test kits to send to the states, the C.D.C. contaminated many of them through sloppy lab practices. That, along with the administration’s failure to quickly ramp up commercial and academic labs, delayed the rollout of tests and limited their availability for months.

In late January, the agency sent epidemiologists to Seattle to help local health officials learn whether what was then the country’s first known patient — a 35-year-old man who had visited Wuhan, China — had infected others.

After an initial round of tests, the agency imposed restrictive testing standards. When doctors in Washington State and elsewhere forwarded the names of about 650 people in January who might have been infected — they had contact with a confirmed patient, had been admitted to a hospital or had other risk factors — the C.D.C. agreed to test only 256. That group consisted primarily of people traveling from Wuhan and their contacts.

In part because of capacity issues, the agency typically did not recommend testing people without symptoms — even though Chinese doctors were reporting that people could spread the virus without ever feeling ill. Dr. Redfield mentioned the possibility of asymptomatic spread in a CNN interview in February, but the C.D.C. did not emphasize such transmission until late March.

In mid-February, C.D.C. officials announced plans for a national surveillance effort — by testing samples from people with flulike symptoms — to determine whether the virus was spreading undetected. The effort was to begin in Seattle, New York and three other cities, but after disagreements over how to proceed, it did not start.

Later that month, public health officials across the country were increasingly concerned about visitors streaming into the United States from South Korea, Japan, Italy and other European countries engulfed by the virus.

On phone calls with the C.D.C., worried state officials kept asking: “Are there plans to expand the travel monitoring?” The response, according to a participant from New York, was always the same: “We’re still actively considering that.”

Mr. Trump announced a European travel ban on March 11, a few days after meeting with Dr. Redfield and others. But it was too late. Genomic tracing would later show that European travelers had brought the virus into New York as early as mid-February; it multiplied there and elsewhere in the country. In Seattle, a strain from China had struck nursing homes in late February.

“If we were able to test early, we would have recognized earlier” the scale of the outbreak, said Dr. Jeffrey Duchin, the chief health officer in King County, Wash. “We would have been able to put prevention measures in place earlier and had fewer cases.”

Part of the C.D.C.’s start-up troubles, current and former employees said, was that the group in charge of the response initially — the Division of Viral Diseases — is smaller and has far less staff focused on contagious respiratory diseases than the C.D.C.’s Influenza Division, which eventually took a more leading role. “They were very quickly overwhelmed by what they had to do,” said Dr. Pierre Rollin, a virologist who left last year.

Now, more than 3,000 C.D.C. employees are aiding the coronavirus response, analyzing data, performing lab work and deploying to cities where local health departments need help. While other federal agencies are also involved — including the F.D.A., which has speeded the use of antibody tests; the Federal Emergency Management Agency, which has worked to get ventilators and other supplies; and the National Institutes of Health, which has studied vaccines and possible treatments — the C.D.C. is the reigning expert.

Even before the current crisis, Dr. Redfield had kept a low profile. Some days he could be spotted in a corner of the cafeteria, sipping coffee alone.

Although he is on the White House coronavirus task force, Dr. Redfield found himself eclipsed by Dr. Anthony S. Fauci, the nation’s most famous infectious disease specialist, and Dr. Deborah Birx, an AIDS expert and former C.D.C. physician.

Meanwhile, his bonds with some of his own staff have frayed. One associate recounted him saying that the agency’s scientists had a “myopic” view of their roles, and characterized his relationship with his top deputy, Dr. Anne Schuchat, a career C.D.C. scientist deeply respected in the agency, as growing strained.

He has not been in Atlanta recently, shuttling instead between his home in Baltimore and the West Wing. One person familiar with his thinking described Dr. Redfield as feeling “a little bit on an island.”

The C.D.C. still has many defenders who say it has done the best it could battling a stealthy, previously unknown virus. “When they do release something, it does what C.D.C. ought to do — retain the voice of credibility,” said Dr. James A. Town, medical director of the intensive care unit at Harborview Medical Center in Seattle. “Even if it’s coming at a slower pace, which can be frustrating, I think they’re pretty thoughtful and trying to make even-keeled investigations.”

Dr. Redfield declined to comment for this article. But in a recent interview with The Hill, he said, “I would say C.D.C. has never been stronger.”

In a briefing last week, he acknowledged that the nation must work to improve its systems to track disease outbreaks, though he disputed that the agency was somehow unable to detect when the coronavirus started to spread in the United States. “We were never really blind to the introduction of this virus,” he said.

The Data Pipeline

Inside Building 21, the C.D.C.’s gleaming 12-story headquarters, nothing has been more critical than getting fast, accurate information on how the virus is spreading, who is getting sick, how best to treat them and how quickly the country can reopen.

But that has proved difficult for the agency’s antiquated data systems, many of which rely on information assembled by or shared with local health officials through phone calls, faxes and thousands of spreadsheets attached to emails. The data is not integrated, comprehensive or robust enough, with some exceptions, to depend on in real time.

The C.D.C. could not produce accurate counts of how many people were being tested, compile complete demographic information on confirmed cases or even keep timely tallies of deaths.

The result is an agency that had blind spots at just the wrong moment, limited in its ability to gather and process information about the pathogen or share it with those who needed it most: front-line medical workers, government health officials and policymakers.

“That specific, granular data has huge implications,” said Julie Fischer, a professor of microbiology at Georgetown University who studies community preparedness for emerging diseases. “We lost precious time in decision-making and putting public health resources to use.”

When C.D.C. officials urged states to track travelers from China in February for possible infection, the agency turned to a computer network called Epi-X. It sent emails to state officials, one at a time, for each arriving flight so they could download a list of targeted passengers.

In California, state health officers received as many as 146 notification emails a day, forcing them to spend time forwarding them to the appropriate local health departments. In some cases, the information, collected for the C.D.C. by the Department of Homeland Security, listed incorrect dates or times; in other cases, passenger data was sent to the wrong state or came more than a week after the travelers had entered the United States.

“We got crappy data,” said Fran Phillips, Maryland’s deputy health secretary. “We would call them up and people would say, ‘Well, I was in China, but that was three years ago.’”

On Feb. 11, Mr. Whitley, Nevada’s top health official, complained to Dr. Redfield in a letter about “the breakdown” in “communication the states have received from the C.D.C.” The agency had said three travelers from China could “go along with their normal day-to-day business” — advice that conflicted with the C.D.C.’s message to monitor such passengers and make sure they were in self-quarantine.

One week later, the C.D.C.’s Epi-X system stopped sending notices entirely, even though flights kept coming. The agency had temporarily shut the system down to “improve data quality,” it told state officials in an email.

The travel-monitoring program screened at least 268,000 passengers through mid-April. A C.D.C. report cited 14 Covid cases that were traced back to those passengers, but lapses and errors in the data made that tally far from conclusive. The agency went on to say that the program did not stop the disease from being introduced to California, where incomplete information, high travel volume and the possibility of asymptomatic spread made it ineffective.

Once coronavirus cases started developing in earnest in the United States in March, federal and state officials began demanding information to make key decisions. Among them: where to move ventilators from the national stockpile and where to build temporary hospitals.

State and local officials were quickly overwhelmed trying to document hospitals’ needs. Staff at the Los Angeles County Public Health Department, for example, called each of the 94 county hospitals in the early weeks of the outbreak, asking nurses how many coronavirus patients were in intensive care units and how many were on ventilators.

The C.D.C. tried to repurpose one of its data systems to collect the information directly from hospitals, but it had significant gaps. Finally, the Department of Health and Human Services in April also enlisted a private contractor, TeleTracking Technologies, only to have hospitals struggle to log on to the system.

Hospital executives resorted to finding aid themselves. Scott Malaney, head of Blanchard Valley Health System in Ohio, got a phone call from an official at a Michigan health care system that was running short on beds and equipment. It was asking neighboring facilities to share supplies or take in overflow patients if necessary.

“She said they were looking up the phone book up and down Highway 75 to see if there were other places that could help,” Mr. Malaney recalled.

The disconnects in the public health record-keeping system delayed sharing critical data that could help patients, said Dr. Thomas Inglesby, director of the Center for Health Security at the Johns Hopkins Bloomberg School of Public Health.

Hospitals look to the C.D.C. for that information. “Is it higher risk to be a healthy person at age 75 with coronavirus or a diabetic with the disease at age 45?” Dr. Inglesby said. “We should have the data to know the answer to this question quickly, and we should be using it to make better decisions.”

As the number of suspected cases — and deaths — mounted, the C.D.C. struggled to record them accurately. The agency rushed to hire extra workers to process incoming emails from hospitals. Still, many officials turned to Johns Hopkins University, which became the primary source for up-to-date counts. Even the White House cited its numbers instead of the C.D.C.’s lagging tallies.

Some staff members were mortified when a Seattle teenager managed to compile coronavirus data faster than the agency itself, creating a website that attracted millions of daily visitors. “If a high schooler can do it, someone at C.D.C. should be able to do it,” said one longtime employee.

For years, federal and state governments have not invested enough money to insure that the nation’s public health system would have critical data needed to respond in a pandemic. Since 2010, for example, grants to help hospitals and states prepare for emergencies have declined.

In 2019, more than 100 public health groups pressed congressional leaders to allocate $1 billion over a decade to upgrade the infrastructure. The C.D.C. received $50 million toward the effort this year. Then, as coronavirus cases and deaths mounted in March, the federal government committed to $500 million under the emergency CARES Act.

“The crisis has highlighted the need to continue efforts to modernize the public health data systems that C.D.C. and states rely on,” Dr. Redfield told a Senate committee on May 12. “Timely and accurate data are essential as C.D.C. and the nation work to understand the impact of Covid-19 on all Americans.”

Data is one of the essential tools of public health; Mr. Trump, though, often appears to see it as a weapon against him. He has suggested that testing is “overrated” and that it makes the United States look bad by increasing the number of confirmed cases. He has seized on lower-end projections of the virus’s toll, only to see them eclipsed as the cases and deaths rose.

Recently, the C.D.C. drew criticism after media reports disclosed that in tracking how many Americans had been tested, the agency had breached standard practice by combining data from antibody tests, which can indicate past infections, with diagnostic tests. The agency said it was caused by confusion in overworked state and local health officials reporting results, but the mistake muddied the picture of the pandemic.

“The scientists at the C.D.C. are still great,” Dr. Jha said. “It’s very puzzling to all of us why C.D.C. performance has been so poor.”

A Strained Relationship

Late in the evening on March 15, the C.D.C. put a bold statement on its website: All gatherings of more than 50 people should be canceled, the agency said, effectively calling for an end to large public events.

Inside the West Wing, the president’s top aides were stunned. Meeting in the Situation Room, the coronavirus task force was just putting the finishing touches on its own guidance. It limited gatherings to no more than 10 people — a fact that C.D.C. officials, including Dr. Redfield, knew from participating in days of debate on the issue.

Reporters soon were peppering the White House with questions about whether it was overruling the C.D.C. Some of Mr. Trump’s aides shrugged it off as a miscommunication. But others viewed it as the C.D.C. insisting it knew best.

The episode underscored the strained relationship between the health agency and the White House. Veteran officials at the C.D.C. were not unfamiliar with the ways of Washington. But they had never dealt with a president like Mr. Trump or a White House like his.

Already under siege for problems with the agency’s diagnostic test, C.D.C. officials watched with growing alarm as Mr. Trump, facing criticism for his administration’s response, repeatedly undermined the agency.

Though the task force was occasionally ahead of the C.D.C. in its cautions to the public, Mr. Trump and his aides often expressed extraordinary skepticism about the coronavirus and the steps required to combat it. He said the virus would disappear “like a miracle” even as C.D.C. scientists described it as a real threat. When the C.D.C. urged Americans to wear masks, he said, “I don’t see it for myself.”

And when Dr. Redfield told The Washington Post that a second wave of the virus could be “even more difficult” than the first, Mr. Trump insisted that he publicly claim to have been misquoted during a White House briefing. Dr. Redfield, with the president standing next to him, scowling, said he had been misunderstood.

At one point, Mr. Trump even complained about the agency to his 80 million Twitter followers, saying, “For decades the @CDCgov looked at, and studied, its testing system, but did nothing about it.”

“There comes a time,” said Dr. Jeffrey Koplan, who served as C.D.C. director in the Clinton and Bush administrations, “when it makes it very hard to operate effectively, when things are being suggested, requested, ordered that you think are contrary to the containment of the pandemic.”

The president and his aides viewed the civil servants at the C.D.C. — many of whom had worked under presidents from both parties — as disloyal liberals eager to wound Mr. Trump politically by leaking to the press. In private, some senior administration officials began referring to agency scientists as members of the “deep state,” according to several people who participated in the conversations but requested anonymity to discuss the meetings.

As the crisis deepened, tensions between Washington and Atlanta increased.

In late February, Dr. Nancy Messonnier, who oversees the C.D.C.’s respiratory diseases center and had been leading the agency’s emergency response, was sidelined after she issued a stark public warning that the virus would disrupt American lives. The comments sent stocks tumbling and infuriated Mr. Trump, who had not been told in advance. Public health officials, inside and outside the agency, saw her forced retreat as an effort to silence the truth.

Often, the clashes have centered on the economic consequences of shutdowns, which have forced 40 million people into unemployment, companies into bankruptcy and fueled resentment across the country.

In early April, the C.D.C. posted an extension of its “no sail” order for cruise ships, forbidding them from operating through August and warning that the ban could become indefinite. The White House had supported the original order, but privately objected to an indefinite ban, fearing lasting harm to an industry that employs tens of thousands of people.

The posting quickly came down, replaced by an order ending the ban in July. “Those things aren’t helpful,” Dr. Redfield would tell his colleagues when disputes between the C.D.C. and the task force erupted.

The White House was soon put on the defensive when USA Today cited internal emails about the pressure. “Sorry to do this, but the Office of the Vice President has instructed us to pull the No Sail Order Extension from the website immediately,” the paper quoted a C.D.C. official as writing to agency colleagues.

To the president’s aides, one of the most frustrating moments came on May 1, when Dr. Schuchat published one of the agency’s regular reports on morbidity and mortality without giving the White House any notice, according to two of Mr. Trump’s advisers.

Written in dry, scientific language, the report offered a blunt assessment of the virus’s spread, showing how travel from Europe and mass gatherings had accelerated it. Dr. Schuchat went further when interviewed for an Associated Press article — “Health Official Says U.S. Missed Some Chances to Slow Virus” — saying that “taking action earlier could have delayed further amplification.”

As the president pushed governors to “liberate” their states from virus lockdowns, top C.D.C. officials in April delivered a draft of new guidance full of caveats about lifting the restrictions. In it, the agency urged schools, churches, child care centers, day camps, restaurants and bars to take numerous precautions and move slowly.

Trump aides were furious when they saw the draft. To them, it was more evidence that the C.D.C. refused to consider political, economic and social effects in weighing how and when to reopen the country. The agency’s recommendations for houses of worship particularly annoyed some aides, who resisted the advice that churches stop giving communion.

When the White House sat on the draft guidance for weeks, a copy was leaked.

While the C.D.C. delayed posting the draft guidance that would allow churches to reopen, Mr. Trump all but ordered it to do so. During a visit to Michigan on May 21, the president — who the next day would explain, “In America, we need more prayer, not less” — made it clear the C.D.C. no longer had any choice.

“I said, ‘You better put it out,’” Mr. Trump told reporters. “And they’re doing it.”

A suggestion in the guidance that houses of worship “consider suspending” the use of choirs and congregant singing because it “may contribute to transmission” was removed. Two federal officials said it had not been cleared by the White House.

Lawrence Gostin, the director of a legal center at the World Health Organization, and a former C.D.C. official, chided the White House for exerting undue pressure on the C.D.C. throughout the crisis.

“Public health is politics. But this is different,” he said. “It’s criticizing its public health agencies in public. It’s rejecting guidelines it puts out. It tells them you can’t even put guidelines out.”

“I would expect the C.D.C. to coordinate with the White House,” he added. “But this is not team work. This is not coordination. This is confrontation.”

Where’s the Guidance?

As the battle against the coronavirus stretches into summer and the United States lurches toward restarting its economy, the mayor of Miami Beach wants to know what to do if Covid-19 cases explode after the city’s famous beaches open again.

Doctors and nurses remain desperate for updates on how to protect themselves. School superintendents and college presidents need to decide how to hold classes in the fall. And employers want advice about whether to test all of their workers before returning to business as usual.

The C.D.C. is where they expect to get answers. As the national clearinghouse for critical public health information, it has dual missions: to provide medical guidance to health workers while offering easy-to-understand information for political leaders, business executives and the general public.

But many say the agency has struggled at times to provide clear and timely guidance.

At Margaret Mary Community Hospital in rural Batesville, Ind., doctors and nurses got sick after following C.D.C. guidance in mid-March that masks were necessary only when treating patients with respiratory symptoms or fever. The first patients who tested positive for Covid-19 there instead showed up with headaches, fatigue, nausea and diarrhea.

“This virus made it halfway around the world without us having a heads-up to our providers that this is how the disease can present,” said Tim Putnam, the hospital’s chief executive. “Over two months after the disease surfaced, I would have expected better.”

Front-line doctors and nurses have long relied on the agency for advice on clinical best practices, and many said in interviews that they were satisfied with the C.D.C.’s advisories, especially given the novelty of the coronavirus.

The agency has issued 114 advisory documents for disaster and homeless shelters, retirement communities, taxis, pediatric clinics and other venues. “We have issued countless guidance and recommendations based on the best available science and data,” an agency press officer said. Its experts have also held about a dozen calls for clinicians about caring for Covid patients, and other calls for medical groups.

But in interviews with medical practitioners across the country, many said they now look elsewhere for detailed recommendations about how to safely care for infected patients, posing questions about the new virus on mailing lists or scouring online research articles.

In a crisis, one of the C.D.C.’s main roles is to explain its guidance and reasoning, provide a rationale for when its thinking changes and acknowledge what it does not know. The agency’s routine in past emergencies was to hold press briefings almost daily; Dr. Thomas Frieden, Dr. Redfield’s predecessor, was highly visible during the Ebola and Zika crises. But in this case, medical workers and the public were left to make sense of often-opaque postings on the C.D.C.’s website after its leadership stopped holding regular briefings on March 9.

“Right now, they only have the PDFs that are out there, without any kind of a conversation,” said Dr. Jennifer Nuzzo, an epidemiologist at Johns Hopkins. “That is a real shortcoming.”

Medical specialty and public health organizations have sometimes taken it on themselves to identify and highlight updates for their members.

“It would be awesome if C.D.C. could actually announce significant changes rather than bury it on their website and assume it is done,” Jim Collins, Michigan’s director of communicable diseases, complained to his colleagues in an email on Jan. 31.

The C.D.C., some medical workers complain, has provided limited guidance on how children transmit the virus, when to ventilate patients and how to prioritize use of isolation rooms. And it took until April 27 for the agency to expand its list of possible symptoms to include more than a dozen signs of illness that some medical specialty societies had reported weeks earlier.

To many anxious doctors and nurses, some of the C.D.C.’s clinical guidance often seemed driven by the nationwide shortages of personal protective equipment, not the best interests of health care workers.

Initially, the C.D.C. recommended that all doctors and nurses coming in contact with coronavirus patients wear N95 respirators, which filter out 95 percent of all airborne particles. But on March 10, with supplies dwindling, the C.D.C. announced that less protective surgical masks were “an acceptable alternative” except during procedures that might aerosolize the virus. Days later, the agency said health workers could even wear “homemade masks (e.g., bandanna, scarf) for care of patients with COVID-19 as a last resort.”

“Mistrust crept in,” said Lori Freeman, chief executive of the National Association of County and City Health Officials. “‘Are we really being protected?’”

The relaxed guidance on protective equipment matched advice from the World Health Organization on surgical masks. But the C.D.C. did not highlight that fact in its update and gave no public explanation other than acknowledging the worsening shortages. An analysis published this week suggests that N95 and other respirator masks are superior to surgical or cloth masks in protecting medical workers against the virus.

Leaders of schools, businesses and other organizations also said they were confused by the C.D.C.’s advice, which sometimes conflicted with that of the White House coronavirus task force.

In one such instance on March 16, the White House urged limiting gatherings to no more than 10 people and “schooling from home whenever possible” for at least the next 15 days. But days earlier, the C.D.C. had recommended that schools close only if someone in the building tested positive or there was evidence of “substantial community transmission.”

On March 17, nearly 2,500 superintendents from around the country were hoping to get some clarity during an online seminar with the C.D.C. Why was the C.D.C. recommending most schools could remain open?

But just 40 minutes before the seminar was to start, the C.D.C. canceled it without explanation and never rescheduled. The agency later told reporters it had decided “to fully adapt to the new guidance from White House” before addressing the superintendents.

In Miami Beach, densely packed with tourists, older residents and service workers, Mayor Dan Gelber dreads the prospect of new outbreaks. While he appreciated the reopening guidance that the C.D.C. published recently, Mr. Gelber, a Democrat, said he wished the agency would also lay out specific steps to follow if cases surge again.

“It’s almost as if they just said, ‘Open up and figure out whether it’s a good idea or not afterward,’” he said of the C.D.C. “We don’t have a net here.”

Noah Weiland contributed reporting.

The roots of the nation’s current inability to control the pandemic can be traced to mid-April, when the White House embraced overly rosy projections to proclaim victory and move on.

By Michael D. Shear, Noah Weiland, Eric Lipton, Maggie Haberman and David E. Sanger

WASHINGTON — Each morning at 8 as the coronavirus crisis was raging in April, Mark Meadows, the White House chief of staff, convened a small group of aides to steer the administration through what had become a public health, economic and political disaster.

Seated around Mr. Meadows’s conference table and on a couch in his office down the hall from the Oval Office, they saw their immediate role as practical problem solvers. Produce more ventilators. Find more personal protective equipment. Provide more testing.

But their ultimate goal was to shift responsibility for leading the fight against the pandemic from the White House to the states. They referred to this as “state authority handoff,” and it was at the heart of what would become at once a catastrophic policy blunder and an attempt to escape blame for a crisis that had engulfed the country — perhaps one of the greatest failures of presidential leadership in generations.

Over a critical period beginning in mid-April, President Trump and his team convinced themselves that the outbreak was fading, that they had given state governments all the resources they needed to contain its remaining “embers” and that it was time to ease up on the lockdown.

In doing so, he was ignoring warnings that the numbers would continue to drop only if social distancing was kept in place, rushing instead to restart the economy and tend to his battered re-election hopes.

Casting the decision in ideological terms, Mr. Meadows would tell people: “Only in Washington, D.C., do they think that they have the answer for all of America.”

For scientific affirmation, they turned to Dr. Deborah L. Birx, the sole public health professional in the Meadows group. A highly regarded infectious diseases expert, she was a constant source of upbeat news for the president and his aides, walking the halls with charts emphasizing that outbreaks were gradually easing. The country, she insisted, was likely to resemble Italy, where virus cases declined steadily from frightening heights.

On April 11, she told the coronavirus task force in the Situation Room that the nation was in good shape. Boston and Chicago are two weeks away from the peak, she cautioned, but the numbers in Detroit and other hard-hit cities are heading down.

A sharp pivot soon followed, with consequences that continue to plague the country today as the virus surges anew.

Even as a chorus of state officials and health experts warned that the pandemic was far from under control, Mr. Trump went, in a matter of days, from proclaiming that he alone had the authority to decide when the economy would reopen to pushing that responsibility onto the states. The government issued detailed reopening guidelines, but almost immediately, Mr. Trump began criticizing Democratic governors who did not “liberate” their states.

Mr. Trump’s bet that the crisis would fade away proved wrong. But an examination of the shift in April and its aftermath shows that the approach he embraced was not just a misjudgment. Instead, it was a deliberate strategy that he would stick doggedly to as evidence mounted that, in the absence of strong leadership from the White House, the virus would continue to infect and kill large numbers of Americans.

He and his top aides would openly disdain the scientific research into the disease and the advice of experts on how to contain it, seek to muzzle more authoritative voices like Dr. Anthony S. Fauci and continue to distort reality even as it became clear that his hopes for a rapid rebound in the economy and his electoral prospects were not materializing.

Mr. Trump had missed or dismissed mounting signals of the impending crisis in the early months of the year. Now, interviews with more than two dozen officials inside the administration and in the states, and a review of emails and documents, reveal previously unreported details about how the White House put the nation on its current course during a fateful period this spring.

Key elements of the administration’s strategy were formulated out of sight in Mr. Meadows’s daily meetings, by aides who for the most part had no experience with public health emergencies and were taking their cues from the president. Officials in the West Wing saw the better-known White House coronavirus task force as dysfunctional, came to view Dr. Fauci as a purveyor of dire warnings but no solutions and blamed officials from the Centers for Disease Control and Prevention for mishandling the early stages of the virus.

Dr. Birx was more central than publicly known to the judgment inside the West Wing that the virus was on a downward path. Colleagues described her as dedicated to public health and working herself to exhaustion to get the data right, but her model-based assessment nonetheless failed to account for a vital variable: how Mr. Trump’s rush to urge a return to normal would help undercut the social distancing and other measures that were holding down the numbers.

The president quickly came to feel trapped by his own reopening guidelines. States needed declining cases to reopen, or at least a declining rate of positive tests. But more testing meant overall cases were destined to go up, undercutting the president’s push to crank up the economy. The result was to intensify Mr. Trump’s remarkable public campaign against testing, a vivid example of how he often waged war with science and his own administration’s experts and stated policies.

Mr. Trump’s bizarre public statements, his refusal to wear a mask and his pressure on states to get their economies going again left governors and other state officials scrambling to deal with a leadership vacuum. At one stage, Gov. Gavin Newsom of California was told that if he wanted the federal government to help obtain the swabs needed to test for the virus, he would have to ask Mr. Trump himself — and thank him.

Not until early June did White House officials even begin to recognize that their assumptions about the course of the pandemic had proved wrong. Even now there are internal divisions over how far to go in having officials publicly acknowledge the reality of the situation.

Judd Deere, a White House spokesman, said the president had imposed travel restrictions on China early in the pandemic, signed economic relief measures that have provided Americans with critical assistance and dealt with other issues including supplies of personal protective equipment, testing capacity and vaccine development.

“President Trump and his bold actions from the very beginning of this pandemic stand in stark contrast to the do-nothing Democrats and radical left who just complain, criticize and condemn anything this president does to preserve this nation,” he said.

At a briefing on April 10, Mr. Trump predicted that the number of deaths in the United States from the pandemic would be “substantially” fewer than 100,000. As of Saturday, the death toll stood at 139,186, the pace of new deaths was rising again and the country, logging a seven-day average of 65,790 new cases a day, had more confirmed cases per capita than any other major industrial nation.

Trump’s Choice

The president had a decision to make.

It was the end of March and his initial, 15-day effort to slow the spread of the virus by essentially shutting down the country was expiring in days. Sitting in front of the Resolute Desk in the Oval Office were Drs. Fauci and Birx, along with other top officials. Days earlier, Mr. Trump had said he envisioned the country being “opened up and raring to go” by Easter, but now he was on the verge of announcing that he would keep the country shut down for another 30 days.

“Do you really think we need to do this?” the president asked Dr. Fauci. “Yeah, we really do need to do it,” Dr. Fauci replied, explaining again the federal government’s role in making sure the virus did not explode across the country.

Mr. Trump’s willingness to go along — driven in part by grim television images of bodies piling up at Elmhurst Hospital Center in New York City — was a concession that federal responsibility was crucial to defeating a virus that did not respect state boundaries. In a later Rose Garden appearance, he appeared resigned to continuing the battle.

“Nothing would be worse than declaring victory before the victory is won,” Mr. Trump said.

But even as the president was acknowledging the need for tough decisions, he and his aides would soon be looking to do the opposite — build a public case that the federal government had completed its job and unshackle the president from ownership of the response.

The hub of the activity was the working group assembled by Mr. Meadows, who had just taken over as chief of staff.

Joe Grogan, the domestic policy adviser, had come around to Mr. Trump’s view that the reaction to the virus was overblown, a position shared at that point by Marc Short, Vice President Mike Pence’s chief of staff and a frequent participant in the meetings. Russell T. Vought, the president’s acting budget director, was there to address the pandemic’s mounting costs.

Chris Liddell, a deputy chief of staff, and Jared Kushner, the president’s senior adviser and son-in-law, acted as the group’s procurement and supply-chain experts.

Hope Hicks, the protector of Mr. Trump’s brand, was a regular participant. Kevin A. Hassett, a top economic adviser, came at times to help assess the numbers and also participated in a 9 a.m. meeting three times a week with Mr. Meadows and Treasury Secretary Steven Mnuchin on the economic aspects of the pandemic.

Then there was Dr. Birx, the response coordinator of the coronavirus task force. Unlike Dr. Fauci, who only stopped by the White House to attend meetings, she was given an office near the Situation Room and freely roamed the West Wing, fully embracing her role as a member of the president’s team.

By mid-April, Mr. Trump had grown publicly impatient with the stay-at-home recommendations he had reluctantly endorsed. Weekly unemployment claims made clear the economy was cratering and polling was showing his campaign bleeding support. Republican governors were agitating to lift the lockdown and the conservative political machinery was mobilizing to oppose what it saw as constraints on individual freedom.

At the meetings in Mr. Meadows’s office, the issue was clear: How much longer do we keep this up?

To answer that, they focused on two more questions: Had the virus peaked? And had the government given the states the tools they needed to manage the remaining problems?

On the first question, Dr. Birx and Mr. Hassett were optimistic: Mitigation was working, they insisted, even as many outside experts were warning that the nation would remain at great risk if it let up on social distancing and moved prematurely to reopen.

Mr. Meadows thought of himself as a data-driven decision maker, and in addition to models and infection numbers from the states and the C.D.C., they looked at traffic on the New Jersey Turnpike (the volume of cars coming in and out of New York City was down by 95.2 percent); payroll and credit card data, and the number of people who were reporting to have self-quarantined.

If the point was to sustain a monthlong lockdown, the numbers told them, the administration succeeded. If it was to squelch the virus to containable levels, later events would show the officials were oblivious to how widely it was already spreading.

The members of his group believed they had succeeded on the second question, too, although shortages of protective gear continued in some places (and would flare again months later).

A one-time anticipated shortage of more than 100,000 ventilators had been overcome; now there was enough of a surplus that the United States could lend them to other countries. A ban on elective surgeries meant there was plenty of bed space — and no more need for the Navy’s hospital ships.

The group thought governors should no longer have trouble getting what they needed for hospitals, doctors and first responders. And they grew increasingly frustrated by what they saw as politically motivated complaining about a lack of federal help and the inability of some states to make effective use of the supplies they were receiving.

Enraged by criticism from New York’s Democratic politicians about not being able to find a shipment of ventilators from the federal government, Mr. Grogan, the domestic policy chief, angrily told Mr. Kushner that they should put more ventilators on eighteen-wheelers, drive them into New York City and invite news helicopters to record it all — just to embarrass Gov. Andrew Cuomo and Mayor Bill de Blasio.

On April 14, the country passed what the group saw as a milestone, administering its three millionth test. Inside the West Wing, Mr. Kushner was insistent on that point: Given their assumption that infections would not surge again until the fall, there was enough testing ability out there.

Those outside experts who disagreed were largely brushed off. In mid-April, Dr. Ashish K. Jha, director of the Harvard Global Health Institute, urged a top administration official to embrace his call for conducting 500,000 coronavirus tests a day — far more than was happening at the time.

The official, Adm. Brett P. Giroir, the administration’s testing czar, who had been delivering upbeat descriptions of the nation’s growing testing capacity, eventually conceded to Dr. Jha that his plan seemed to be needed. But he made clear the federal government was not prepared to get there quickly.

“At some point down the road,” is what Dr. Jha said Admiral Giroir told him.

“My take is that Jared Kushner believes that this is not something that the White House should get too involved in,” Dr. Jha recalled. “And then the president believes that it is better left up to the states.”

Their critics notwithstanding, White House officials came to feel that they had in fact accomplished their job: giving governors the tools they needed to deal with remaining outbreaks as infections ebbed.

The wind down of the federal government’s response would play out over the next several weeks. The daily briefings with Mr. Trump ended on April 24. The Meadows team started barring Dr. Fauci from making most television appearances, lest he go off message and suggest continued high risk from the virus.

By the beginning of May, word leaked that the daily meetings of the task force itself would be ended, though Mr. Trump, who had not been told, backpedaled after the coverage caused an uproar.

On testing, Mr. Trump shifted from stressing that the nation was already doing more than any other country to deriding its importance. By June the president was regularly making nonsensical statements like, “If we stop testing right now, we’d have very few cases, if any.”

But during the middle weeks of April the president’s decision to largely walk away from an active leadership role — and give many states permission to believe the worst of the crisis was behind them — came abruptly into public view.

On April 10, Mr. Trump declared that, in his role as something akin to a “wartime president,” it would be his decision about whether to reopen the country. “That’s my metrics,” he told reporters, pointing to his own head. “I would say without question it’s the biggest decision I’ve ever had to make.”

Three days later, he reiterated his responsibility. “When somebody is the president of the United States, the authority is total and that’s the way it’s got to be,” he said.

The next day, Dr. Birx and Dr. Fauci presented Mr. Trump with a plan for issuing guidelines to start reopening the country at the end of the month. Developed largely by Dr. Birx and held closely by her until being presented to the president — most task force members did not see them beforehand — the guidelines laid out broad, voluntary standards for states considering how fast to come out of the lockdown.

In political terms, the document’s message was that responsibility for dealing with the pandemic was shifting from Mr. Trump to the states.

On April 16, when Mr. Trump publicly announced the guidelines, he made the message to the governors explicit.

“You’re going to call your own shots,” he said.

Birx’s Influence

Inside the White House, Dr. Birx was the chief evangelist for the idea that the threat from the virus was fading.

Unlike Dr. Fauci, Dr. Birx is a strong believer in models that forecast the course of an outbreak. Dr. Fauci has cautioned that “models are only models” and that real-world outcomes depend on how people respond to calls for changes in behavior — to stay home, for example, or wear masks in public — sacrifices that required a sense of shared national responsibility.

In his decades of responding to outbreaks, Dr. Fauci, a voracious reader of political histories, learned to rely on reports from the ground. Late at night in his home office this spring, Dr. Fauci, who declined to comment for this article, dialed health officials in New Orleans, New York and Chicago, where he heard desperation unrecognizable in the more sanguine White House meetings.

Dr. Fauci had his own critics, who said he relied on anecdotes and experience rather than data, and who felt he was not sufficiently attuned to the devastating economic and social consequences of a national lockdown.

As the pandemic worsened, Dr. Fauci’s darker view of the circumstances was countered by the reassurances ostensibly offered by Dr. Birx’s data.

A renowned AIDS researcher who holds the title of “ambassador” as the State Department’s special representative for global health diplomacy, she had assembled a team of analysts who worked late nights in the White House complex, feeding her a constant stream of updated data, packaged in PowerPoint slides emailed to senior officials each day.

There were warnings that the models she studied might not be accurate, especially in predicting the course of the virus against a backdrop of evolving political, economic and social factors. Among the models Dr. Birx relied on most was one produced by researchers at the University of Washington. But when Mr. Hassett reviewed its performance by looking back on its predictions from three weeks earlier, it turned out to be hit or miss.

The authors of the University of Washington model spoke to Dr. Birx or members of her team almost daily, they said, and often cautioned that their work was only supposed to offer a snapshot based on key assumptions, like people continuing to abide by social distancing until June 1.

“We made clear that to get the epidemic under control and bring it down to effectively zero transmission required the social distancing mandates to be in place,” said Christopher J. L. Murray, the director of the modeling program. “April 22 — somewhere around that period. That’s when the tone shifted. They started to ask questions about what will be the trajectory and where with the lifting of mandates?”

Some state officials were also alarmed by the administration’s use of the University of Washington model.

Colorado health officials wrote to the administration on April 9, pleading that the White House not use the model to allocate supplies to the state, saying its predictions were rosier than the grim reality they were encountering. (When those concerns were relayed to her, Dr. Birx replied that decisions on allocating equipment were based on factors beyond the one model.)

Dr. Birx declined to be interviewed. A task force official said that she had only used the University of Washington model in a limited way and that the White House used “real data, not modeled data, to understand the pandemic in the United States.”

The official said the White House “immediately reacted to the early signs of community spread” by working with governors in the affected states.

But despite the outside warnings and evidence by early May that new infections, while down, remained higher than anticipated, the White House never fundamentally re-examined the course it had set in mid-April.

Dr. Fauci, a friend of Dr. Birx’s for 30 years, would describe her as more political than him, a “different species.” More pessimistic by nature, Dr. Fauci privately warned that the virus was going to be difficult to control, often commenting that he was the “skunk at the garden party.”

By contrast, Dr. Birx regularly delivered what the new team was hoping for.

“All metros are stabilizing,” she would tell them, describing the virus as having hit its “peak” around mid-April. The New York area accounted for half of the total cases in the country, she said. The slope was heading in the right direction. “We’re behind the worst of it.” She endorsed the idea that the death counts and hospitalization numbers could be inflated.

For Dr. Birx, Italy’s experience was a particularly telling — and positive — comparison. She routinely told colleagues that the United States was on the same trajectory as Italy, which had huge spikes before infections and deaths flattened to close to zero.

“She said we were basically going to track Italy,” one senior adviser later recalled.

Dr. Birx would roam the halls of the White House, talking to Mr. Kushner, Ms. Hicks and others, sometimes passing out diagrams to bolster her case. “We’ve hit our peak,” she would say, and that message would find its way back to Mr. Trump.

Dr. Birx began using versions of the phrase “putting out the embers,” wording that was later picked up by the press secretary, Kayleigh McEnany, and by Mr. Trump himself.

By the middle of May, the task force believed that another resurgence was not likely until the fall, senior administration officials said.

The New York region appeared well on its way to driving new infections down to levels it could handle — it was the one area of the country that did resemble the Italian model. But the models and analysis embraced by the West Wing failed to account for the weakening adherence to the lockdowns across the country that began even before Mr. Trump started urging governors to “liberate” their residents from the methodical guidelines his own government had established.

Later, it was clear that states that rushed to reopen before meeting the criteria in the guidelines — like Arizona, Texas and Alabama — would have among the worst surges in new cases.

Dr. Birx’s belief that the United States would mirror Italy turned out to be disastrously wrong. The Italians had been almost entirely compliant with stay-at-home orders and social distancing, squelching new infections to negligible levels before the country slowly reopened. Americans, by contrast, began backing away by late April from what social distancing efforts they had been making, egged on by Mr. Trump.

The difference was critical. As communities across the United States raced to reopen, the daily number of new cases barely dropped below 20,000 in early May. The virus was still circulating across the country.

Italy’s recovery curve, it turned out, looked nothing like the American one.

The Consequences

The real-world consequences of Mr. Trump’s abdication of responsibility rippled across the country.

During a briefing on April 20, Mr. Trump mocked Gov. Larry Hogan of Maryland, a fellow Republican, for the state’s inability to find enough testing. Dr. Birx displayed maps with dozens of dots indicating labs that could help.

“He really didn’t know about the federal laboratories,” Mr. Trump told reporters with mock astonishment. “He didn’t know about it.”

But when Frances B. Phillips, the state’s deputy health secretary, reached out to one of those dots — a National Institutes of Health facility in Maryland — she was told that they were suffering from the same shortages as state labs and were not in a position to help.

“It was clear that we were on our own and we need to develop our own strategy, which is very unlike the kind of federal response in the past public health emergencies,” Ms. Phillips recalled.

In California, Mr. Newsom had already experienced firsthand the complexities of getting help from Washington.

After offering to help acquire 350,000 testing swabs during an early morning conversation with one of Mr. Newsom’s advisers, Mr. Kushner made it clear that the federal help would hinge on the governor doing him a favor.

“The governor of California, Gavin Newsom, had to call Donald Trump, and ask him for the swabs” recalled the adviser, Bob Kocher, an Obama-era White House health care official.

Mr. Newsom made the call as requested and then praised Mr. Trump that same day during a news conference where he announced the commitment, giving Mr. Trump credit for the “substantial increase in supply” headed to California.

Mayor Francis X. Suarez of Miami, a Republican, said that the White House approach had only one focus: reopening businesses, instead of anticipating how cities and states should respond if cases surged again.

“It was all predicated on reduction, open, reduction, open more, reduction, open,” he said. “There was never what happens if there is an increase after you reopen?”

Other nations had moved aggressively to employ an array of techniques that Mr. Trump never mobilized on a federal level, including national testing strategies and contact tracing to track down and isolate people who had interacted with newly diagnosed patients.

“These things were done in Germany, in Italy, in Greece, Vietnam, in Singapore, in New Zealand and in China,” said Andy Slavitt, a former federal health care official who had been advising the White House.

“They were not secret,” he said. “Not mysterious. And these were not all wealthy countries. They just took accountability for getting it done. But we did not do that here. There was zero chance here that we would ever have been in a situation where we would be dealing with ‘embers.’”

A New Surge

By early June, it was clear that the White House had gotten it wrong.

In task force meetings, officials discussed a spike in cases across the South and whether any bumps in caseloads were caused by crowded protests over the killing of George Floyd. They briefly considered if it was a fleeting side effect of Memorial Day gatherings.

They soon realized there was more at play.

Digging into new data from Dr. Birx, they concluded the virus was in fact spreading with invisible ferocity during the weeks in May when states were opening up with Mr. Trump’s encouragement and many were all but declaring victory.

With the benefit of hindsight, the head of the Centers for Disease Control and Prevention, Dr. Robert R. Redfield, acknowledged this week in a conversation with the Journal of the American Medical Association that administration officials — himself included — severely underestimated infections in April and May. He estimated they were missing as many as 10 cases each day for every one they were confirming.

The number of new cases has now surged far higher than the previous peak of more than 36,000 a day in mid-April. On Thursday, there were more than 75,000 confirmed new cases, a record.

Mr. Trump’s disdain for testing continues to affect the country. By the middle of June, lines stretched for blocks in Phoenix and in Austin, Texas. And getting results could take a week to 10 days, officials in Texas said — effectively inviting the virus to spread uncontrollably.

Dr. Mandy K. Cohen, the top health official in North Carolina, contacted the Trump administration after a surge in June, asking the government to quickly open 100 new testing sites in her state, in addition to the 13 it was then operating.

“We will keep those 13 open for another month — you are welcome,” Dr. Cohen said, mocking the response she received.

It was a devastating situation, said Mayor Steve Adler of Austin, who watched as the Covid-19 cases at intensive care units at area hospitals jumped from three in mid-May to 185 by early July. Mr. Adler had a simple plea for the White House.

“When we were trying to get people to wear masks, they would point to the president and say, well, not something that we need to do,” he said.

Mr. Suarez expressed similar frustrations with Mr. Trump’s dismissive approach to mask wearing. “People follow leaders,” he said, before rephrasing his remarks. “People follow the people who are supposed to be leaders.”