WASHINGTON — Dr. Rochelle Walensky was stunned. Working from her home outside Boston on a Friday night in late July, the director of the Centers for Disease Control and Prevention had just learned from members of her staff that vaccinated Americans were spreading the coronavirus.

Vaccines had been the core of President Biden’s pandemic strategy from the moment he took office. But as Dr. Walensky was briefed about a cluster of breakthrough cases in Provincetown, Mass., the reality sank in. The Delta variant, which had ravaged other parts of the world, was taking hold in the United States. And being vaccinated would not, it turned out, prevent people from becoming infected with the variant or transmitting it.

It was a “heart sink” moment, Dr. Walensky recalled in a recent interview. The discovery called into question the Biden administration’s almost single-minded focus on vaccination as the path out of the pandemic. And it made Mr. Biden’s July 4 message that the nation had moved “closer than ever to declaring our independence from a deadly virus” sound naïve.

Mr. Biden took office last January with a 200-page coronavirus response strategy, promising a “full-scale wartime effort” rooted in science and competence. The C.D.C.’s July discovery marked the point at which the virus began ruthlessly exposing the challenges it would present to his management of the pandemic.

Mr. Biden and his team have gotten much right, including getting at least one dose of a vaccine into nearly 85 percent of Americans 12 and older and rolling out life-saving treatments. Those achievements have put the United States in a far better place to combat the virus than it was a year ago, with most schools and businesses open and the death rate lower because the vaccine significantly reduces the chance of illness or death, even from the highly contagious Omicron variant.

But an examination of Mr. Biden’s first year of fighting the virus — based on interviews with scores of current and former administration officials, public health experts and governors — shows how his effort to confront “one of the most formidable enemies America has ever faced,” as he recently described it, has been marked by setbacks in three key areas:

• The White House bet the pandemic would follow a straight line, and was unprepared for the sharp turns it took. The administration did not anticipate the nature and severity of variants, even after clear warning signals from the rest of the world. And it continued to focus almost single-mindedly on vaccinations even after it became clear that the shots could not always prevent the spread of disease.

• The administration lacked a sustained focus on testing, not moving to sharply increase the supply of at-home Covid tests until the fall, with Delta tearing through the country and Omicron on its way. The lack of foresight left Americans struggling to find tests that could quickly determine if they were infected.

• The president tiptoed around an organized Republican revolt over masks, mandates, vaccine passports and even the vaccine itself, as he worried that pushing certain containment measures would only worsen an already intractable cultural and political divide in the country. The nation’s precarious economic health, and the political blowback that Mr. Biden and members of his party could face if it worsened, made him all the more cautious. So rather than forcing Americans to get shots, he spent months struggling to accomplish it through persuasion.

Mr. Biden took over the task of distributing vaccines from former President Donald J. Trump, and by all accounts he brought order to a rollout that had been dysfunctional and chaotic in its first month.

But he also inherited a bureaucracy that had been battered by the Trump White House, which undermined the C.D.C., strained the government’s credibility with the public and helped foment virulent anger throughout the country over masks, social distancing and other efforts to contain the virus. Mr. Biden has been unable to bridge those divisions.

Two years into the pandemic, even as the Omicron variant has begun to recede in parts of the country, Mr. Biden is facing huge economic and political pressures. He has rejected lockdowns, school closures or other extreme measures that could help contain future mutations but drive the country back into a punishing recession. His decisions will carry a cost no matter which way he turns.

Mr. Biden has battled the virus while also trying to make headway on other priorities: a bipartisan infrastructure deal, appointments to the federal bench and far-reaching social spending legislation. In August and September, as Delta surged, the White House was consumed by a chaotic exit from America’s 20-year war in Afghanistan.

But the pandemic loomed over everything, dragging down Mr. Biden’s approval ratings as his handling of it became for many the measuring stick by which to judge his presidency. Since he was inaugurated on Jan. 20 last year, 438,110 people have died from the virus, a number that is still increasing by more than 10,000 people every week.

“You cannot fight today’s pandemic,” said Dr. Luciana Borio, a former acting chief scientist of the Food and Drug Administration who advised Mr. Biden’s transition team. “You have to prepare for what’s next.”

‘No Policy’

On March 2, officials from the C.D.C. and other agencies held a conference call to discuss creating a federal “passport” to enable airlines, restaurants and other venues to electronically verify vaccination status.

A 27-page presentation prepared for the meeting underscored how critical the issue was: “A chaotic and ineffective vaccine credential approach could hamper our pandemic response by undercutting health safety measures, slowing economic recovery and undermining public trust and confidence.”

But within weeks, public health officials began hearing a different message from the White House, where Mr. Biden and his team were wary of Republican politicians like Gov. Ron DeSantis of Florida, who railed against such passports as “completely unacceptable.”

“The policy is no policy” was the unofficial word from the White House, one federal health official recalled.

The scientists at the C.D.C. dismantled their working group, ceding to a patchwork of state and private efforts to track inoculations and the paper coronavirus vaccination record cards that can be lost or counterfeited.

By the summer, Mr. Biden’s push to get Americans vaccinated was stalling and a chorus of voices inside and outside the government was urging him to mandate the shots.

Public health experts insisted that pleading with people to get vaccinated was not enough. But most Republican governors fiercely opposed vaccine requirements, and some asserted their own considerable power to prevent schools and businesses in their states from putting them in place.

The president believed federal vaccine mandates would backfire, according to several of his advisers. He shut down the idea of requiring domestic airline passengers to be vaccinated, which Dr. Anthony S. Fauci, Mr. Biden’s chief medical adviser for the pandemic, has supported.

Even more modest initiatives drew instant attacks. In early July, when the administration announced an enhanced door-to-door outreach campaign to get Americans vaccinated, Representative Jim Jordan of Ohio, a Trump ally and a frequent Biden critic, was among the many Republicans who pounced.

“The Biden Administration wants to knock on your door to see if you’re vaccinated,” he tweeted. “What’s next? Knocking on your door to see if you own a gun?”

The Arrival of Delta

Throughout the spring, Mr. Biden was relentlessly hopeful, even as ominous signs loomed.

Scientists, including some in the federal government, warned that the world was caught in a sprint between vaccines and variants — and the virus was winning. In India, the newly arrived Delta variant pushed Covid cases from 10,000 per day in February to 414,000 in a single day in May. Weeks later, Delta cases spiked across England, too.

But the president and his team thought the United States would be spared Delta’s ravages, Dr. Fauci said, because the “vaccine push would be able to, for the most part, nullify a Delta surge.” At the White House, Jeffrey D. Zients, Mr. Biden’s pandemic czar, was counting on it.

“The important thing was that the vaccines worked,” he recalled in an interview.

In mid-May, Dr. Walensky added to the sense of optimism with an announcement that caught much of the country by surprise: Vaccinated Americans could take their masks off with little to no risk of spreading the virus, she said.

Mr. Biden, Mr. Zients and others in the White House were ecstatic, even as they worried the public would be confused by the sudden change. Being able to drop masks indoors could mean a huge economic boost, a psychological reprieve for the public and an opportunity to ease the fierce cultural battles over Covid.

But three weeks after Mr. Biden declared on July 4 that the country was “emerging from the darkness,” the outbreak in Provincetown forced Dr. Walensky to confront a painful truth: Her decision about masks had been wrong. Vaccinated people could transmit the virus to others, after all.

Now she had some fast decisions to make. She did not want to “put masks on all of America again” based on a single outbreak, she recalled in an interview. But soon, outbreak investigations in Texas and elsewhere confirmed the findings.

A July 27 internal assessment at the Department of Health and Human Services delivered grim news: Deaths were up 45 percent from the previous week, hospitalizations were up 46 percent and cases had increased by 440 percent since June 19, when they had reached a low.

Later that day, Dr. Walensky reversed herself, telling Americans they should resume wearing masks in areas where case counts were high.

A highly respected infectious disease expert, Dr. Walensky had been brought on by Mr. Biden to restore faith in an agency that had been battered by his predecessor. But the new guidance, which essentially left it to local health officials to determine where masking was required, based on ever-changing data, only confused the public further.

Most governors and many mayors had abandoned mask mandates by then, and showed little appetite to reinstate them.

And still looming over the Biden team was the question of vaccination mandates. With vaccine uptake stalled and the more contagious Delta variant now a serious concern, Dr. Fauci had concluded that the voluntary measures his boss favored would not be enough.

His private message to the president: “No way were we going to get people vaccinated unless we mandate.”

The president agreed in September, after meeting in the Oval Office with four business leaders who told him they had successfully required all of their employees to get vaccinated. One of them, Greg Adams, the chief executive of the Kaiser Permanente health system, told the president about an unvaccinated colleague who had died of Covid, saying he wished he had required vaccines sooner.

On the Sunday before Labor Day — two weeks after the F.D.A. gave formal approval to the Pfizer vaccine — Mr. Biden was ready to go beyond pleading with people. He wanted a meeting with his Covid team, planned for the next day, to happen sooner.

Mr. Zients called his deputy and told her to drop everything. “We’ve got 58 minutes,” he said.

Four days later — more than seven months into his presidency — Mr. Biden announced mandates for health care workers, federal contractors and the vast majority of federal workers, and a requirement that all companies with more than 100 workers require vaccination or weekly testing.

Public health experts said the mandates were appropriate and even long overdue. But the president’s prediction had been correct: The new policy fueled the growing sentiment, especially in conservative parts of the country, that the federal government had become too intrusive in too many areas of American life during the pandemic.

This month, the administration won half a victory: The Supreme Court allowed the health care mandate to stand, even as it struck down the requirement for large employers.

‘Who Is in Charge?’

“WTF?” a senior federal health official scribbled on a note one day in August.

Word had just come down that on Aug. 18, Mr. Biden would announce a plan to roll out booster shots, starting the third week of September with adults who had completed their initial shots at least eight months earlier.

Dr. Janet Woodcock, the acting F.D.A. commissioner, had not wanted the White House to announce a start date, according to two people familiar with her stance. While publicly endorsing the strategy, she privately warned that her regulators most likely could not act that fast, because they were still waiting on data from the vaccine manufacturers that they would then need to review.

Two weeks after Mr. Biden’s announcement, she and Dr. Walensky called Mr. Zients with bad news: The booster rollout plan would have to be scaled back. They were met with “a long silence,” according to one person with knowledge of the call, who spoke on the condition of anonymity.

The episode laid bare a fundamental problem. Some of the administration’s most difficult public health decisions are essentially hammered out by a handful of senior health officials who hold roughly the same status, none of whom are in charge. They are overseen by Mr. Zients, a former economic policy adviser to President Barack Obama who is known for his logistical and planning skills but has no public health expertise. No single public health expert has the role of guiding the response, running interference between various players or standing up to the White House when necessary.

“There is no formal decision-making process,” one senior federal official said, speaking on the condition of anonymity. “Who is in charge of all this?”

The weaknesses in the command structure have played out in disparate ways. In the case of the booster rollout, the White House appeared to overstep its bounds and left itself open to accusations that political considerations were coloring decision-making. More frequently, Dr. Walensky has announced changes in public health guidance without anyone fully vetting them with colleagues, leading to backtracking and revisions.

The team of “docs,” as Mr. Biden likes to call them, includes Dr. Walensky; Dr. Woodcock; Dr. Fauci, the director of the infectious disease division at the National Institutes of Health; and Dr. David Kessler, the chief science officer at the Department of Health and Human Services, whose duties include stocking the pandemic toolbox with vaccines and treatments. Mr. Biden’s health secretary, Xavier Becerra, a former California attorney general, is their boss, but several current and former White House officials said he plays a limited role in setting pandemic policy — a characterization that Mr. Becerra disputes.

Dr. Walensky’s announcement in May that fully vaccinated people need not wear a mask or physically distance from others, indoors or outdoors, was an example of uncoordinated policymaking.

Mr. Biden and Mr. Zients had indicated publicly that such a change might be coming. But some White House aides learned of the change only the night before Dr. Walensky announced it to the public, and there was no coordinated strategy in place to explain or defend it.

“It wasn’t like, ‘OK, let’s have a Zoom call tonight about the pros and the cons of the mask mandate.’ That didn’t happen,” Dr. Fauci said. Asked whether he tried to modify Dr. Walensky’s decision beforehand, he said, “You have to know the decision is being made before you modify it.”

The C.D.C.’s announcement last month that it was shortening the recommended isolation period for people with Covid was another bout of confused messaging. At first, the agency announced that people with resolving symptoms could stop isolating after five days without recommending they get a negative test first. But after that omission drew criticism from outside experts, the agency tweaked its guidance to say that if people have access to tests and want to use them, “the best approach is to use an antigen test towards the end of the five-day isolation period.”

“Whenever there was a proclamation that something had improved, and a public health measure could be eased, it was never framed clearly enough,” said Dr. Richard Besser, a former acting C.D.C. director.

Mr. Biden’s premature announcement of the booster rollout had its own repercussions, bringing what some saw as political pressure to bear on a fraught scientific debate.

Both Dr. Woodcock and Dr. Peter Marks, a top regulator who oversees the F.D.A.’s vaccine division, wanted booster shots to be offered quickly to as many Americans as possible. But two key subordinates, Marion Gruber and Dr. Philip Krause, who had regulated vaccines at the agency for decades, saw little rationale for offering the shots to younger, healthier people, and viewed the White House announcement as political arm-twisting.

They outlined their position in an extraordinary public dissent in the British medical journal The Lancet, days after announcing that they were leaving the agency. Dr. Krause said in an interview that he saw a “dismantling of the process” of regulation.

Advisers to the C.D.C. and the F.D.A. also argued to scale back Mr. Biden’s promise, leading to months of staggered and confusing rollouts of the extra shots to various population groups. Adults were not universally eligible for a booster until late November. Some governors grew so impatient in the meantime that they cleared adults in their states to seek boosters without official federal approval.

To date, just 43 percent of fully vaccinated adults have received a booster. Data published on Friday by the C.D.C. showed boosters were reducing the number of infections from the Omicron variant and keeping infected people out of the hospital.

Ignoring Tests

By the time Omicron emerged in South Africa in late November, Dr. Fauci knew instinctively that it was going to be bad.

He was alarmed by the high number of mutations: more than 50 in all. And the variant was spreading fast. On a chart that South Africa’s researchers showed him on the rate of infection, the line went “straight up,” Dr. Fauci said.

The reason soon became clear. The vaccines continued to give robust protection against severe disease and hospitalization from Omicron, but the variant was more agile than Delta in evading the body’s defenses. Even people who had been boosted might get infected.

The revelations made it more important for everyone — including vaccinated people — to know if they were infected before being around family and friends. That highlighted the administration’s failure to ensure a supply of at-home tests that could confirm an infection in 15 minutes.

Amazon, Walmart and other national chains were soon out of stock. Long lines formed outside pharmacies as Americans tried to protect their families over the holidays. And the administration was left scrambling for a quick fix to a long-term supply problem it had mostly ignored until nearly the fall.

The administration had made a calculated bet: Unlike their strategy with vaccines and Covid treatments, officials figured they could allow demand to determine the supply of tests, with manufacturers ramping up production as needed. The Biden team allocated roughly $16.6 billion to buy vaccines and nearly $15 billion for Covid treatments over the year, but signed $3 billion worth of contracts to buy tests only in September and October.

In nine speeches about his pandemic response that Mr. Biden had delivered in May and June, he made no mention of needing tests. With caseloads low at the time, public interest in tests flagged as well.

Over the summer, workers at Abbott Labs in Maine, which made one of the only rapid tests available at the time, were told to take unsold test kits apart and trash them. Then they were laid off.

When Omicron arrived, the administration initially resisted calls to distribute free tests to the public. Natalie Quillian, a top aide to Mr. Zients, said in an interview in December that the White House felt tests should be covered by insurance, not provided free by the government. Dr. Tom Inglesby, a senior adviser in charge of testing, said the administration wanted to target free tests to places that needed them most, like schools and nursing homes.

“It’s a very, very, very expensive strategy to buy all tests for all people,” he said.

As it turned out, the bet was a bad one. By year’s end, facing a barrage of criticism, Mr. Biden pledged 500 million free tests for all Americans, followed by another 500 million a few weeks later. The first of those tests have just begun to arrive, and the bulk of them most likely will not arrive until after the administration’s own experts predict Omicron will have peaked later this month.

“Yeah,” Mr. Biden told ABC’s David Muir in a December interview, “I wish I had thought about ordering a half a billion two months ago.”

‘A Job Not Yet Finished’

As the administration heads into its second year of battling the pandemic, Omicron and Delta have proved that mutations of the virus have the potential to flood hospitals with patients, turning some into crisis zones. Tens of millions remain unvaccinated, many more lack boosters and officials are anxiously watching for signs that a retooled vaccine might be needed soon. Antiviral pills appear to be a breakthrough in treatment, but remain scarce.

Experts like Dr. Tom Frieden, the C.D.C. director under Mr. Obama, have predicted three possible scenarios ahead: that the nation reaches a kind of truce with the virus, with clusters of outbreaks; that the virus weakens to a threat more akin to a common cold; or that, in the worst case, a variant emerges that combines the contagiousness of Omicron with the virulence of Delta.

Dr. Frieden said the White House must plan for them all. Some former Biden advisers have called for the president to plan for the “new normal” — and accept that Covid-19 is here to stay.

Inside the West Wing, there is little evidence that Mr. Biden is shifting strategies. He is keeping his public health team intact as his second year begins, and continues to project a sense of optimism.

“Some people may call what’s happening now ‘the new normal,’” he said on Wednesday during a formal news conference in the East Room of the White House. “I call it a job not yet finished.”