As the pandemic engulfs the nation, recent recommendations from the Centers for Disease Control and Prevention have been as notable for what they do not say as for what they do. In a turnabout, the agency now is hewing more closely to scientific evidence, often contradicting the positions of the Trump administration.

In scientific briefs published on Tuesday, the C.D.C. described the benefits of masks to wearers, not just to those around them. Agency researchers also urged people to celebrate Thanksgiving only with others in their households or, failing that, to wear a mask with two or more layers.

Administration officials famously have disregarded evidence about the effectiveness of masks, one reason there have been at least three coronavirus outbreaks at the White House and hundreds of cases linked to President Trump’s rallies.

The guidance was only the latest in a series of newly assertive bulletins from the C.D.C. In recent weeks, agency officials have issued strict requirements for cruise lines; updated the science on coronavirus infections in children; re-evaluated the risk from airborne virus indoors; and released recommendations for labs investigating viral reinfections in patients.

Still, C.D.C. officials have not publicly announced these findings nor held news conferences to explain them, instead posting the bulletins quietly online. Word of them has often appeared first on Twitter and noted by outside experts. Dr. Robert Redfield, the agency’s director appointed by Mr. Trump, has remained largely silent despite record-breaking numbers of coronavirus cases.

In interviews, scientists at the C.D.C. and public health experts who work closely with them described the reasons for the shift: an administration distracted by the election, the explosion of coronavirus cases across the country, and the likelihood that Joseph R. Jr. Biden would defeat Mr. Trump — now a certainty.

“A weight’s been lifted off the C.D.C. that allows them to do their job again,” said Scott Becker, chief executive of the Association of Public Health Laboratories who has worked closely with C.D.C. scientists for decades.

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Credit…Elijah Nouvelage/Reuters

Under the Biden administration, the C.D.C. will be restored to its status as the premiere public health agency in the world, said Dr. Céline Gounder, a member of President-elect Biden’s advisory group on the coronavirus.

“While their role has been diminished during this current crisis, they play a very important role in all this,” she said. The new administration will rebuild public health and data infrastructure, restore C.D.C. staffing in its overseas outposts and give “control back to the C.D.C.”

Within the C.D.C., there is a palpable sense of relief and a determination to return to an apolitical identity, according to four senior scientists who spoke on condition of anonymity because they feared for their jobs.

“We couldn’t allow ourselves to be politicized at this moment in time,” said one of the scientists, who is involved in the agency’s pandemic response. “We weren’t going to spend time licking wounds and worrying about what had gone wrong in the past.”

Another senior C.D.C. scientist said, “Sometimes you just feel compelled to say, ‘I don’t care what happens, I’ve got to do this.’”

Until the pandemic, the C.D.C. was widely regarded as the world’s leading public health agency. But the muzzling of its scientists by the Trump administration and the politicization of some of its advice crippled its efforts to answer critical questions, experts say, including how schools, churches and businesses should reopen, and how Americans could best protect themselves and their families.

The turnabout began after the Trump administration meddled in the C.D.C.’s vaunted weekly bulletins, the Morbidity and Mortality Weekly Reports, according to Dr. Thomas R. Frieden, who led the agency under President Barack Obama.

Political appointees tried to revise, delay or even halt publication of the reports, sparking public outcry and condemnation at a congressional hearing. The dust-up precipitated the swift exit of Michael Caputo, a political appointee who had accused C.D.C. scientists of sedition, and Dr. Paul Alexander, a science adviser hired to help Mr. Caputo.

“The huge fight over the M.M.W.R. led to the administration backing off, and they’ve been putting out great M.M.W.R.s for the past six to eight weeks that are really important,” Dr. Frieden said.

The scientific brief on face coverings, for example, is at odds with the actions of administration officials including Mr. Trump, who rarely wears masks and has mocked Mr. Biden’s strict adherence to wearing them in public.

The bulletin also broke from the agency’s earlier watered-down view that the evidence “may convince” Americans that they should wear masks and that mask use “could prevent” an infected person from spreading the virus to others.

The C.D.C.’s recommendations for Thanksgiving gatherings arrived more than two weeks before the holiday, in itself an improvement. Until recently, much of the agency’s guidance was delayed by “the many eyes above them that needed to see things and clear things and possibly change things,” Mr. Becker said.

“But the Thanksgiving and mask thing sort of made me realize, OK, we’re getting a little bit ahead of it, like we used to,” he added.

Other C.D.C. documents in recent weeks have also taken an uncompromising tone. The Trump administration blocked a C.D.C. order to keep cruise ships docked until February, but in late October, the agency’s scientists outlined strict new rules for the industry, including requiring cruise ships to have C.D.C. approval for the laboratories and tests they use.

(Nonetheless, one of the first ships to resume cruising in the Caribbean now hosts a coronavirus outbreak.)

Also in October, Dr. Michael Beach, a senior C.D.C. scientist, told a House subcommittee that the agency’s guidance on schools — written under pressure from the White House — did not reflect the latest science on risks of children becoming infected with and transmitting the coronavirus.

The current version, updated a week later, said, “The body of evidence is growing that children of all ages are susceptible to SARS-CoV-2 infection and, contrary to early reports, might play a role in transmission.”

The C.D.C. also acknowledged in October, months after the World Health Organization had done so, that the coronavirus could be airborne in poorly ventilated indoor settings. And it laid out sensible, science-based steps that public health laboratories should take to confirm suspected reinfections with the virus.

Credit…Taylor Glascock for The New York Times

But none of these reports have been accompanied by briefings by agency scientists — a mainstay of the C.D.C.’s response to previous infectious disease outbreaks.

The mask advice, for example, might have been missed if news organizations had not caught wind of its arrival and reported it — squandering an opportunity for federal scientists to explain how the science has evolved and what it means to the public, several experts said.

“Here’s a situation now where there’s enough data to recommend it scientifically, and it might help change the behavior of some people, if you were seeing the normal reinforcers of public health and political leaders supporting each other,” said Dr. Richard Besser, who served as interim chief of the C.D.C. during the H1N1 virus outbreak of 2009.

The continuing absence of public health messaging from government agencies is dangerous, given the uncontrolled spread of the coronavirus and the approaching holidays, he and others said.

Dr. Carlos del Rio, an infectious disease expert at Emory University in Atlanta, said he had advised his friends at the C.D.C., including Dr. Redfield, to “do the right thing.”

“I told Redfield, ‘You start doing press briefings, you step up — and if they fire you, they fire you,’” Dr. del Rio recalled. “There’s a total vacuum in the coronavirus response at this point in time.”

Dr. Redfield did not respond to a request for comment.

The silence has also frustrated scientists inside the agency. The directors of the C.D.C.’s 10 centers “meet together every week, and what are they talking about? And why aren’t they collectively figuring out what’s best for the agency?” one irate C.D.C. scientist asked.

While counterparts at the Food and Drug Administration drew a line in the sand, declaring that they would shepherd vaccines for the coronavirus with independence and transparency, C.D.C. officials have not spoken up against the administration’s interference.

“We didn’t see anyone publicly fall on their sword for C.D.C., and that may have been what was needed,” a senior C.D.C. researcher said.

These scientists were worried that the past year may have permanently tarnished the C.D.C.’s credibility and the respect of its partners at the state and international levels. Several said they were considering leaving their posts because the institutional problems that intensified during the pandemic might not resolve even with a new director at the helm.

(A recent employee survey for the first time asked C.D.C. employees whether they were considering leaving the agency, and whether their job satisfaction had changed during the pandemic.)

The scientists were also anxious about how the next few weeks will unfold. The nation is facing record numbers of infections and hospitalizations, and record numbers of deaths may soon follow.

Whether the C.D.C. can adequately respond will depend on whether administration officials resume meddling with the agency or remain distracted during the lame-duck period.

Already at least one Trump appointee has vacated a key position. Tammy Beckham, a close aide to the administration’s testing czar, Adm. Brett P. Giroir, oversaw supply and distribution of testing supplies but moved last week to the F.D.A.

Dr. Beckham was succeeded by a veteran agency scientist, Dr. Michael Iademarco. Some within the agency saw it as a sign that pressure from the administration may ease even before Mr. Biden takes office.

“This is not about a Republican or a Democrat,” one senior scientist said. “This is about public health. The pandemic is not partisan.”