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The Centers for Disease Control and Prevention has long been respected for its methodical and rigorous scientific approach. Agencies in other countries have modeled themselves after the world’s most respected public health authority, and even adopted the name.

At the start of the pandemic, the CDC acted at the pace it was used to. This time, however, with a new virus moving so quickly, the country has paid a price: Testing and surveillance was delayed as the agency tried to implement legacy approaches with squeaky infrastructure. Officials were late to recommend masking, in part because it took so long for federal scientists to realize that the virus was transmitted through the air.

Now the infectious variant of Omicron is pushing the CDC into uncharted territory. Because decisions have to be made extremely quickly, the agency has released recommendations based on what was once seen as scant evidence amid growing public concern about how these guidelines affect the economy and education.

The agency’s director, Dr. Rochelle P. Walensky sometimes skipped much of the traditional scientific review process, most recently shortening the isolation period for infected Americans.

After the Trump administration’s model of intervention, President Biden took office pledging to restore the CDC’s reputation for independence and rigorous science. Dr. The challenge now for Walensky is figuring out how to get this message across to the public: Science is lacking, and that’s our best advice for now.

Change was not easy for a bureaucracy composed primarily of medical professionals.

In recent interviews, some officials at the CDC privately called the decisions demoralizing, and Dr. They were concerned about Walensky’s growing reliance on a small group of advisors and what they saw as the heavy political influence the White House had on their actions.

Yet others from outside the institution, Dr. He praised Walensky for short-circuiting a laborious process and taking a pragmatic approach to managing a national emergency, saying he was right to move forward even when the data were unclear and agency researchers were unsure. He praised Walensky.

Serving as the agency’s interim chief during the H1N1 influenza virus outbreak in 2009, Dr. Richard E. Besser said there were policy considerations that were “not the CDC’s sole purpose” in a pandemic. When policy and economics guide agency advice, I think we need a little more clarity.

As of Sunday, an average of more than 800,000 Americans are infected daily. Data collected by The New York Times. Many schools and businesses struggle to stay open; Hospitals are approaching capacity in nearly two dozen states.

At the end of December, Dr. Walensky explained that infected Americans no longer need to isolate for 10 days if they are showing symptoms, but only for five days, and that a negative test result is not required to end the isolation period.

Critics complained that the virus could spread as infected people were allowed to return to offices and schools. Many pointed out that the research to support a shorter isolation period for Omicron infections was insufficient.

But the proposal had one key advantage: It could help hospitals, businesses and schools survive the worst of the Omicron surge.

Heading the organization under President Barack Obama, Dr. Thomas R. Frieden said the isolation recommendations were “basically correct.” “The problem is, they weren’t disclosed.”

Dr. Walensky and the CDC declined requests for comment on new tensions in the agency’s decision-making. But the director has often cited rapidly evolving science as justification for suggestions that have proven confusing or unpopular.

Testifying before the Senate on Tuesday, Dr. Walensky, the agency’s new shortened isolation times It represents “rapid science-based action to address the very real possibility of staff shortages.”

It became something like a mantra for the director.

Last March, the CDC said schoolchildren could safely sit in classrooms three feet away instead of six feet, but there was virtually no research to support the recommendation. However, this move made it easier for administrators to consider opening schools.

In May, Dr. Walensky cited scientific data when he told vaccinated people that they could remove their masks and mix freely. (The ones that come with the Delta variant.)

In August, Dr. Walensky joined President Biden to support booster vaccines for all Americans long before scientists at the Food and Drug Administration or his institution had a chance to review the data on whether it was necessary.

The latest example, the isolation recommendation, has created internal turmoil over the establishment and the way it is advertised.

On the Sunday night after Christmas, Dr. Walensky called an emergency meeting of the agency’s Covid response leaders. Speaking on condition of anonymity, he said the agency would shorten the proposed isolation period and leave a negative test result as a requirement to exit isolation, according to an official familiar with the video call. Subject.

Dr. Walensky said the new guidelines will be made public the next day, and officials won’t discuss it until then.

Confused, scientists scrambled to gather limited data and rewrite hundreds of pages on the agency’s website that touched on quarantine and isolation to support the recommendations.

Before issuing a new recommendation, federal researchers normally review the data, write a draft, and fine-tune it based on comments from others. There was so little evidence that the isolation was shortened—and even that was mostly based on the Delta variant—that the “science brief” that typically accompanies the guidance was reduced to a “justification” document.

Some researchers feared being left out of the decision-making process and were outraged by the agency’s public statement the next day that the change was “motivated by science.”

While some believed the new five-day cut was arbitrary, they also knew about the data suggesting that. rapid tests may miss some Omicron infectionsand therefore mostly Dr. He agreed with Walensky’s decision not to request a negative test result before ending the isolation.

However, Dr. When Walensky briefed staff on the new proposals at the emergency meeting on December 26, they were not yet ready. Over the next week, CDC scientists struggled to set up hundreds of guidance documents on the agency’s website.

About 2,000 state and city health officials, public health laboratory directors, and epidemiologists attend a weekly meeting with CDC officials.

On the call Monday, December 27, hours before the CDC released its statement, state and local officials asked agency scientists about their isolation guidance plans for the general public.

Under strict orders not to talk about the new proposals, CDC staff remained silent.

“We would have appreciated more opportunities for input,” said Scott Becker, president of the Association of Public Health Laboratories.

Dr. Walensky’s supporters said the CDC’s return was inevitable and he made the right calls. The agency is a giant full of researchers accustomed to taking their time, and the pandemic needed more urgent solutions.

Dr. “There are people at the CDC who don’t really understand this,” Frieden said.

During his tenure, he said, he was often faced with “in some ways attractive, but in some ways problematic, the ignorance of CDC staff that their advice, guidance, disclosures can have major implications.”

A few outside experts, Dr. Walensky has become a scapegoat for people who are weary and frustrated by a virus that has repeatedly retreated and soon returned in a terrifying new form.

They said that leading the CDC is difficult even at the best of times. However, Dr. Walensky took the reins in the midst of a pandemic, a politically charged climate, and a low point in agency credibility and staff morale.

And agency researchers are still working remotely — “an almost unthinkable hurdle to overcome,” said Dr. Besser.

Dr. “I’m worried about the CDC, I’m worried about the nation’s reliance on public health,” Besser said. “But I think it’s really unfair to put this on Dr. Walensky’s shoulders.”

Dr. Walensky explained the rationale for his decisions at news briefings held by the White House. But last week, he and other agency scientists responded to broad criticism of mixed messaging. gave his briefingby answering questions from reporters about isolation guidance, increased hospitalization rate between minor children and the agency’s plans fourth shot from the coronavirus vaccine.

Some experts said the briefing was a welcome step toward rebuilding confidence in the CDC and clarifying its decisions.

Dr. “It’s crucial to separate public health considerations from political considerations,” Besser said. “And by giving briefings from the CDC, the CDC will be able to get its scientists and experts on their feet.”

Some of the current conflicts at the CDC are due to the pandemic and Dr. It precedes Walensky’s leadership. Some health officials, with the institution, Dr. He noted that tensions between the National Institutes of Health, represented by Anthony S. Fauci, have increased even during previous public health crises.

In the most recent example, Dr. Fauci and Surgeon General Dr. Vivek Murthy assured on television that he would reconsider the CDC’s isolation recommendations — when the agency has no such plans — and has annoyed senior CDC scientists.

Dean of the National School of Tropical Medicine at Baylor College of Medicine, Dr. Ideally, Xavier Becerra, secretary of health and human services, should smooth things over, said Peter Hotez.

In a rare appearance, Mr. Becerra spoke to Dr. Becerra in a CNN interview last week. He defended Walensky, saying he “has a medical license and a degree in public health.” No marketing degree.”