Trump Transition Updates: Retired General Picked to Be Russia-Ukraine Envoy

Mr. Zuckerberg flew into West Palm Beach, Fla., on Tuesday evening before joining Mr. Trump at his hotel and club, Mar-a-Lago, on Wednesday, according to the people, who spoke on the condition of anonymity because they were not authorized to discuss the meeting. The two men largely exchanged pleasantries, with Mr. Zuckerberg congratulating Mr. Trump on winning the presidency.

After the early afternoon meeting, Mr. Trump and Mr. Zuckerberg planned to have dinner at Mr. Trump’s hotel later that evening, the people said.

“It’s an important time for the future of American innovation,” a Meta representative said in a statement. “Mark was grateful for the invitation to join President Trump for dinner and the opportunity to meet with members of his team about the incoming administration.”

But Mr. Zuckerberg’s overtures come as the chief executive seeks to insulate Meta — which owns Facebook, Instagram and WhatsApp — from any potential blowback from the incoming administration. Meta has long been a target of conservatives in Washington; some in Congress have called for reining in what they see as censorship of conservative viewpoints. And Mr. Trump has personally called for Mr. Zuckerberg to be jailed in retaliation for “plotting against” him during the 2020 election.

As executives at Meta recognized Mr. Trump’s potential for victory in the 2024 election, Mr. Zuckerberg has spent the past 18 months trying to repair the relationship.

Mr. Zuckerberg had at least two private phone calls with Mr. Trump over the course of the summer, according to two people with knowledge of the talks, one of which saw the tech executive wishing Mr. Trump well and “praying” for him after the assassination attempt on his life. And in an interview over the summer, Mr. Zuckerberg said Mr. Trump looked like a “badass” after pumping his fist to the crowd when he was shot at by a would-be assassin during a rally in Pennsylvania.

Other tech executives, like Elon Musk, who has stumped for the conservative movement and gave hundreds of millions of dollars to the Trump campaign, have forged a closer relationship with Mr. Trump. (Mr. Musk and Mr. Zuckerberg have developed such a tense relationship that the two spent 2023 challenging one another to a physical fight.) But executives at Meta hope that Mr. Zuckerberg can launch a new relationship with Mr. Trump by taking a softer touch with the incoming administration.

Stephen Miller, Mr. Trump’s incoming deputy chief of staff for policy, characterized the meeting a bit differently than did Meta. Mr. Miller told Fox News on Wednesday that Mr. Zuckerberg “has been very clear about his desire to be a supporter of, and a participant in, this change we’re seeing all around America and the world, with this reform movement that Donald Trump is leading.”

“It’s not fair to federal employees,” said Everett Kelley, the president of the union, which represents about 800,000 of the roughly 2.3 million civilian workers in the U.S. government. “He wants to scare employees to the point that they just quit, and don’t come to work anymore.”

Mr. Kelley said the posts could subject the workers to abuse.

In one instance last week, Mr. Musk reposted an image identifying a worker in the International Development Finance Corporation, an agency created in President-elect Donald J. Trump’s first term to support global infrastructure and health projects.

“So many fake jobs,” Mr. Musk wrote. The post says the identified worker holds the title of director of climate diversification.

The International Development Finance Corporation said in a statement that the position described in the post is “highly technical” and demands a “deep understanding of new innovations and regulations in developing economies.”

The agency added that its climate diversification portfolio is geared toward supporting American interests, including enhancing critical mineral supply chains.

Mr. Kelley argued that Mr. Musk did not know what federal workers “do every day.” Mr. Musk could not immediately be reached for comment.

Two weeks ago, Mr. Trump announced that he would appoint Mr. Musk, the billionaire chief executive of SpaceX and Tesla, and Vivek Ramaswamy, an entrepreneur and Republican presidential contender-turned-Trump acolyte, to lead a so-called Department of Government Efficiency.

Mr. Trump has said the loosely defined commission would ultimately produce a smaller government and limit bureaucracy.

Brian Hughes, a spokesman for Mr. Trump’s presidential transition team, said in a statement on Wednesday that the second Trump administration would “have a place for people serving in government who are committed to defending the rights of the American people, putting America first, and ensuring the best use of working men and women’s tax dollars.”

A push to significantly cut the federal work force could generate fierce resistance in Congress and in the courts.

Still, Ms. Sheinbaum, who earlier in the day had made clear that Mexico would impose retaliatory tariffs in response to similar measures threatened by Mr. Trump, seemed to ease tensions by saying the exchange was “excellent.”

“I had an excellent conversation with President Donald Trump,” she wrote on social media. “We addressed Mexico’s strategy regarding the migration phenomenon, and I shared that caravans are no longer reaching the northern border as they are being addressed within Mexico.”

That update from Ms. Sheinbaum came after Mr. Trump jolted trade relations with Mexico by saying earlier in the week that he would impose a 25 percent tariff on all goods from the country unless Mexican authorities stopped migrants and drugs, such as fentanyl, from coming across the border. The proposed move raised concerns over the potential impact on Mexico’s economy, which relies on trade with the United States.

Mr. Trump also posted on social media about the conversation with Ms. Sheinbaum, calling it “wonderful” and “productive.”

“She has agreed to stop Migration through Mexico, and into the United States, effectively closing our Southern Border,” Mr. Trump said, though Ms. Sheinbaum referred only to the caravans. “We also talked about what can be done to stop the massive drug inflow into the United States, and also, U.S. consumption of these drugs,” he added.

Ms. Sheinbaum said earlier on Wednesday, “If there are U.S. tariffs, Mexico would also raise tariffs” — making clear her stance on Mexico’s potential response.

Senior officials in her government and leading figures in Mexico’s governing party, Morena, also expressed support for retaliatory tariffs. Mexico’s economy minister, Marcelo Ebrard, said that about 400,000 jobs could be lost in the United States if Mr. Trump imposed the tariffs, calling the measure a “shot in the foot” while speaking alongside Ms. Sheinbaum at a morning news conference.

Mexico’s president did not refer to tariffs, or trade tensions in general, in her post about her conversation with Mr. Trump. Instead, she said she and Mr. Trump had “discussed strengthening collaboration on security issues within the framework of our sovereignty and the campaign we are conducting in Mexico to prevent fentanyl consumption.”

Robert F. Kennedy Jr., Mr. Trump’s choice for health secretary, has said he wants the N.I.H. to focus on chronic disease and “give infectious disease a break for about eight years.” Dr. Martin Makary, the president-elect’s choice to run the Food and Drug Administration, incorrectly predicted in 2021 that the nation was “racing toward an extremely low level of infection.”

Dr. David Weldon, a Republican former congressman who is Mr. Trump’s choice to lead the Centers for Disease Control and Prevention, has espoused the debunked theory that thimerosal, a mercury compound in certain vaccines, causes autism. As a congressman, he introduced legislation that would strip the C.D.C. of its role in ensuring vaccine safety, saying the agency had a “conflict of interest” because it also promotes vaccination.

And Dr. Mehmet Oz, the talk show host who has been picked by Mr. Trump to run Medicare and Medicaid, prodded officials in the first Trump administration to give emergency authorization for the malaria drug hydroxychloroquine to treat Covid-19. The F.D.A. later revoked the authorization when studies showed the drug carried risks, including serious heart issues, to coronavirus patients.

“If the worst case scenario happens and we have a serious public health crisis, the body count is going to be enormous because these guys don’t have the skills or the will to do anything about it,” said John P. Moore, a virologist and professor at Cornell University’s Weill Cornell Medical College.

None of Mr. Trump’s picks have deep expertise in infectious disease, and each will have to be confirmed by the Senate. “At the end of the day, if they are confirmed, we are going to have to figure out a way to work with them,” said Dr. Carlos del Rio, an infectious disease expert at Emory University.

Mr. Trump’s own commitment to pandemic preparedness is unclear. During his first administration, he dismantled a White House office that had been set up by his predecessor, President Barack Obama, to deal with emerging global health threats. Last year, President Biden created a White House Office of Pandemic Preparedness, which Mr. Trump cannot abandon because Congress mandated it by legislation in 2022.

There is no way, of course, to predict the arrival of the next pandemic. At the outset of the coronavirus pandemic, experts called it the worst public health crisis in a century. But most do not believe that it will be 100 years before another one. The current outbreak of the H5N1 virus, commonly known as “bird flu,” in cattle and poultry is of particular concern.

So far, there have been no reports of human-to-human transmission of H5N1, which is far more deadly than SARS-CoV-2, the virus that causes Covid-19. But 55 people in the United States, mostly poultry and dairy workers, have already been infected. Experts fear that as more people get infected, the virus will have an opportunity to mutate in a way that could make it easily transmissible from one person to another.

“As Donald Trump gets ready to return to the White House on Jan. 20, he must be prepared to tackle one issue immediately: the possibility that the spreading avian flu might mutate to enable human-to-human transmission,” Dr. David Kessler, who ran the Biden administration’s Covid vaccine distribution initiative, wrote in a New York Times guest essay.

In an interview on Wednesday, Dr. Kessler said he was particularly concerned that longtime officials at agencies like the C.D.C., N.I.H. and F.D.A. would leave their agencies, depriving the Trump administration of their deep expertise.

“We’re not going to get though four years without infectious disease, of that you can be sure,” Dr. Kessler said. “The one thing I’ve learned is it never comes at you from where you’re expecting. But it will come at you. The most important thing is, on this they need expertise. There is no learning on the job.”

Dr. Paul A. Offit, an infectious disease expert and pediatrician at Children’s Hospital of Philadelphia, said he was particularly worried about another coronavirus with pandemic potential. The world has experienced three within the past 20 years. SARS (severe acute respiratory syndrome), erupted in China in 2002. MERS (Middle East respiratory syndrome), spread from camels to people in the Arabian Peninsula in 2012. Covid-19 emerged in 2019 in China.

Dr. Offit said cutting the N.I.H. budget for infectious disease research, as Mr. Kennedy has suggested, would be shortsighted. He noted that research into the mRNA technology that enabled the quick production of coronavirus vaccines had begun more than 20 years before the pandemic, with N.I.H. funding. The scientists who pioneered the work, Dr. Katalin Karikó and Dr. Drew Weissman, won a 2023 Nobel Prize.

Dr. del Rio said he agreed with Mr. Kennedy that more research is needed into chronic disease — but not at the expense of infectious disease. “This dichotomy between infectious disease and chronic disease is a false dichotomy,” he said.

Researchers, public health officials and scientists employed by the government have been reluctant to speak about the president-elect’s selections. Dr. Francis Collins, the former head of the National Institutes of Health, who continues to work as a researcher in his genetics lab, and who called Dr. Bhattacharya a “fringe epidemiologist,” declined to comment.

Dr. Bhattacharya is one of three lead authors of the Great Barrington Declaration, a manifesto issued in the fall of 2020, before Covid vaccines were available. The manifesto contended that the coronavirus should be allowed to spread among young healthy people who were “at minimal risk of death,” while prevention efforts were targeted to older people and the vulnerable.

The goal, the authors said, was to “minimize mortality and social harm until we reach herd immunity,” the point at which a virus cannot spread easily from person to person because most people are immune. Public health leaders dismissed it as dangerous and a recipe for millions of American deaths.

Instead, experts including Dr. Anthony S. Fauci, the now-retired head of the Institute for Allergy and Infectious Diseases that is part of N.I.H., argued that vaccination was the safest path to containing the deadly pathogen. Dr. Fauci predicted that it would take until the end of 2021, after a successful vaccination campaign, for the nation to reach herd immunity.

In the end, both sides were wrong. Coronavirus deaths in the United States hit a second spike at the end of 2021 and into early 2022, when the Omicron variant raced through the population. In the years since then, a number of public health experts have acknowledged that perhaps the lockdowns and masking and school closures went on for too long.

“I would agree that the mitigation strategies were probably wrong and they were probably there for too long,” said Dr. del Rio, the Emory University infectious disease doctor, referring to the masking and lockdowns that Dr. Bhattacharya opposed. “But the Great Barrington Declaration was also wrong and we need to accept that.

“Clearly during Covid we all made mistakes," he added, “and one thing we need to learn is to all be humble so that we don’t make them again.”

After that call and a Republican win in Iowa on Wednesday, Republicans held a 220 to 214 advantage in the House with only one race left to be determined, in the 13th Congressional District in California. Though Republicans have won more than the 218 seats necessary to control the House, Mr. Trump wants two House members to serve in his administration and a third, Matt Gaetz, resigned his seat this month.

In the last uncalled House race, in California’s Central Valley, the Democratic challenger, Adam Gray, nudged past Representative John Duarte, a Republican, for the first time on Tuesday. Mr. Gray had a 182-vote lead in the latest count.

While Ms. Steel had a large war chest and strong party backing in the 45th Congressional District, Mr. Tran, a first-time political candidate, won in part by attacking her shifting positions on abortion.

During her time in Congress, Ms. Steel was twice a co-sponsor of the Life at Conception Act, a bill that amounted to a nationwide abortion ban. She later withdrew her support from the bill, but Mr. Tran seized on Ms. Steel’s earlier position to paint her as having extreme views on reproductive rights.

Mr. Tran made a concerted effort to court Vietnamese Americans in Little Saigon, a large bloc of voters who have traditionally leaned Republican and are staunchly anti-Communist. But his profile as the son of war refugees from Vietnam largely inoculated him from Ms. Steel’s attempts to frame him as a Communist sympathizer. His background also gave voters the opportunity to elect the district’s first-ever Vietnamese American representative in Congress.

“This victory is a testament to the spirit and resilience of our community,” Mr. Tran said in a statement on Wednesday. “As the son of Vietnamese refugees, I understand firsthand the journey and sacrifices many families in our district have made for a better life.”

Ms. Steel, a prolific fund-raiser, collected $9.4 million this campaign cycle, outpacing the $5 million raised by Mr. Tran through Oct. 16, according to campaign finance filings.

In a concession statement on X, Ms. Steel thanked her supporters and said that she had worked “on behalf of legal immigrants and struggling families” as a congresswoman.

“Everything is God’s will and, like all journeys, this one is ending for a new one to begin,” she said.

Mr. Tran benefited from an influx of money from the Democratic Congressional Campaign Committee, and some national star power: Former President Bill Clinton came to the district to campaign for him.

Mr. Tran’s upset victory indicated a limit to the political reach of President-elect Donald J. Trump, who issued a late endorsement for Ms. Steel in the final days of the election and blasted Mr. Tran as a “Radical Left Puppet of Communist China.”

Democrats had already flipped a House seat in California when George Whitesides, the former NASA chief of staff, defeated Representative Mike Garcia. But both parties have had to wait weeks to learn the outcomes in two other close House contests. The state notably takes longer than other states to tabulate votes.

Annie Karni contributed reporting from Washington, and Orlando Mayorquín contributed from Los Angeles.

Mr. Trump has not offered details about what kind of peace agreement he envisions, though Ukrainian officials fear that he might slash aid to Ukraine and seek to cut a deal unfavorable to Kyiv with President Vladimir V. Putin of Russia.

Mr. Kellogg co-wrote a strategy paper in April that said the United States should focus on achieving a cease-fire and negotiated settlement to the conflict.

The United States “would continue to arm Ukraine and strengthen its defenses to ensure Russia will make no further advances and will not attack again after a cease-fire or peace agreement,” Mr. Kellogg wrote with Fred Fleitz for the America First Policy Institute. “Future American military aid, however, will require Ukraine to participate in peace talks with Russia,” they added.

The Biden administration has rejected calls for a cease-fire as favorable to Russia and has not used American aid to pressure Kyiv into peace talks.

The paper also said that Mr. Putin could be brought to the bargaining table with an offer by the United States and NATO, a mutual defense alliance, “to put off NATO membership for Ukraine for an extended period in exchange for a comprehensive and verifiable peace deal with security guarantees.” The alliance’s members have sent billions of dollars in aid to Ukraine during the war, and Ukraine has applied to become a member. Biden officials say Russia’s leader has shown no good-faith interest in peace talks.

It is unclear whether the paper reflected any of Mr. Trump’s views. Mr. Trump “also has a strategy to end the war that he has not fully revealed,” it said.

A Vietnam War veteran who helped to administer Iraq after the 2003 U.S. invasion of the country, Mr. Kellogg is seen as a relatively mainstream figure within Mr. Trump’s orbit. But he has also been a strong loyalist who advised Mr. Trump’s first presidential campaign in 2016 and has publicly defended Mr. Trump against charges of wrongdoing or holding dangerous views.

“He was with me right from the beginning!” Mr. Trump said in a Wednesday statement announcing the selection. He added that Mr. Kellogg would support his vision of “PEACE THROUGH STRENGTH.”

In February, Mr. Kellogg defended Mr. Trump after the then-candidate declared that he would encourage Russia to “do whatever the hell they want” to NATO members who fail to meet the alliance’s targets for national military spending.

The comment provoked shock and outrage across Europe and from the Biden administration. But Mr. Kellogg said that Mr. Trump was “onto something” by emphasizing the responsibility of NATO members to maintain strong armies.

“I don’t think it’s encouragement at all,” Mr. Kellogg said of the hypothetical green light to Russia, because “we know what he means when he says it.”

The F.B.I. said in a statement it was aware of the bomb threats and so-called swatting calls, which entail contacting law enforcement to falsely claim a dangerous person is at a particular address. Such calls are designed to create a frantic armed police response to frighten, harass and endanger someone at their home.

Three people familiar with the threats, speaking on condition of anonymity to discuss an ongoing investigation, said one of those targeted was Susie Wiles, Mr. Trump’s campaign manager whom he has tapped to serve as the White House chief of staff.

Representative Elise Stefanik of New York, Trump’s pick to be ambassador to the United Nations, was notified by the police that a bomb threat had been made against her home in Saratoga County, according to a statement from her office. She and her family were not there at the time.

Lee Zeldin, a former congressman from Long Island who is Trump’s pick to lead the Environmental Protection Agency, said the police had contacted him about a pipe bomb threat made to his home. The Zeldin family was not there at the time, he said in a statement.

Brooke Rollins, whom Mr. Trump said he would nominate to be agriculture secretary, wrote on social media that she had also been targeted and thanked the police in Fort Worth, Texas, for their response.

Howard Lutnick, Mr. Trump’s pick for commerce secretary, also received threats at his home on the Upper East Side of Manhattan on Wednesday, according to two people with knowledge of the incident. The New York Police Department said it had responded to “terroristic threats” there and had made no arrests.

Bomb threats and swatting calls are a growing problem for American law enforcement, as it has become easier to anonymously contact the authorities or leave threatening messages. Prominent public officials, schools and celebrities are often victims.

Saloni Sharma, a White House spokeswoman, said President Biden had been briefed on the threats and was in touch with the Trump transition team. Mr. Biden and his administration, she said, “unequivocally condemn threats of political violence.”

Tim Balk contributed reporting.

The group said it felt compelled to issue the notice out of uncertainty about whether the Education Department could be enlisted in a broader effort to locate undocumented immigrants under Mr. Trump’s administration, even though the advice cuts against its mission of helping students from disadvantaged backgrounds pay for higher education.

The notice effectively urged students who may themselves be in the country legally to consider forgoing federal student aid to avoid putting a relative at risk.

“This guidance may be particularly relevant to mixed-status families who would be participating in the federal aid application process for the first time,” the group advised. “NCAN understands the grave ramifications of this guidance and deeply regrets that we feel it is necessary to issue it.”

Some colleges and universities are also urging international students to be in the United States before Mr. Trump takes office on Jan. 20, sending travel advisories recommending that they make plans to cut short their winter vacations. The schools have warned that any rapid action by Mr. Trump to curtail immigration could leave students stranded if they’re not back in the country by then.

Susie Wiles, the incoming White House chief of staff, has been among those signaling in recent weeks that Mr. Trump intends make quick and purposeful use of executive orders to achieve some of his policy goals upon taking power. As a result, schools including the Massachusetts Institute of Technology and The University of Massachusetts, Amherst recently warned students that a flurry of such orders could throw visa processing into disarray or result in some students being denied entry to the United States.

Toward the end of Mr. Trump’s prior term, the Homeland Security Department began the process of more tightly restricting student visas, drawing legal challenges from a number of schools. Under those proposed rules, students from countries which were designated as state sponsors of terrorism, such as Iran, Syria or Sudan, would be eligible for only a two-year stay with the option to apply for an extension, instead of up to five years from the outset.

During his campaign this year, Mr. Trump also discussed bringing back some version of the ban on travelers from several predominantly Muslim countries that he pursued in his first term, which could upend plans for students coming back from those countries.

For health secretary, Mr. Trump chose Robert F. Kennedy Jr., a longtime vaccine skeptic with no medical or public health training who has accused drug companies of the “mass poisoning” of Americans.

Mr. Trump’s pick to lead the Centers for Disease Control and Prevention is Dr. Dave Weldon, a former congressman from Florida who raised doubts about vaccines and pushed to move most vaccine safety research from the agency.

And Mr. Trump’s choice to run the Centers for Medicare and Medicaid Services, the former television host Dr. Mehmet Oz, has scant experience in managing a large bureaucracy like the one he may now oversee; the agency is in charge of health care programs that cover more than 150 million Americans.

In Mr. Trump’s first term as president, pharmaceutical executives largely cheered his health policy nominees. They had ties to the moderate wing of the Republican Party and decades of conventional experience, including at major drug companies.

John LaMattina, who was once the top scientist at Pfizer and is now a senior partner at PureTech Health, a firm that creates biotech startups, said of those officials: “You could disagree with them, but at least there’s a certain knowledge base and they’ve given serious thought to these issues.”

He added: “We’re now seeing some people without any sort of background, and that’s worrisome.”

The implications remain unclear for Americans who rely on medications or on widespread immunity from diseases that, for now, are rare. Some in the Trump administration want to speed drug approvals, potentially seeding the market with drugs of uncertain effectiveness. Mr. Kennedy has in some forums called for more independent safety reviews of established vaccines, and at other times he has demanded fewer constraints on unconventional and unproven treatments.

But Mr. Kennedy has also tapped in to veins of outrage among consumers and lawmakers, who have long vilified drug companies for setting high prices on certain drugs and reaping billions of dollars in profits rather than putting patients first.

In choosing such a vociferous critic as Mr. Kennedy, the president-elect stunned the sector, causing vaccine and biotechnology stocks to plummet temporarily.

And though Mr. Kennedy most recently said that he would not take vaccines away from Americans who want them, even a modest reduction in the number of people receiving certain shots could spook investors and translate into hundreds of millions of dollars of lost revenue. The industry is also concerned that drug approvals could be delayed if Mr. Kennedy makes good on his threats to fire drug regulators, or if they quit in droves to avoid working under his leadership.

“There was cautious optimism on Trump when he won, and that was very rapidly replaced with concern over R.F.K. Jr.,” said Brian Skorney, a drug industry analyst at the investment bank Baird.

Drug companies’ political action committees made millions of dollars in contributions to both Democrats and Republicans this election cycle, and the industry’s lobbying groups can wield considerable influence over policy and legislation.

Top pharmaceutical executives have said little publicly about Mr. Trump’s picks for health policy positions, seeking to avoid alienating the people who would regulate them. Their lobbying groups have publicly issued polite statements saying they want to work constructively with the administration.

But Derek Lowe, a longtime pharmaceutical researcher and industry commentator, has sharply criticized Mr. Kennedy on his blog, calling him “a demagogue whose positions on key public health issues like vaccination are nothing short of disastrous.”

“You really can’t engage with someone like that. There is no common ground,” Mr. Lowe said in an interview.

Drug industry officials have a long list of concerns about Mr. Kennedy, who did not return a request for comment for this article. They are particularly worried that he could seek to undermine childhood vaccines; one way would be for him to push to revise the government’s recommendations on immunizations.

Mr. Kennedy has also called for overturning legal protections that shield vaccine makers from litigation when people are seriously harmed by vaccines — a change that would upend an established compensation program and could expose the industry to costly lawsuits.

The stakes appear to be highest for companies that make vaccines. About a fifth of Merck’s revenue comes from two types of vaccines that Mr. Kennedy has targeted: a vaccine against the human papillomavirus that has averted thousands of cancer cases, and the shots that children receive to protect them against measles, mumps and rubella. (Merck declined to comment.)

Vaccine sales represent about 3 percent of the industry’s overall prescription drug revenues, according to IQVIA, an industry data provider. With some exceptions, vaccines tend to generate relatively low returns compared with profits from more expensive products used for diseases like cancer and arthritis.

Drug manufacturers also fear the effect Mr. Kennedy could have at the Food and Drug Administration. They often complain that the agency can be too onerous, but their business model is reliant on a well-staffed F.D.A. that can weed out would-be competitors that haven’t met its standards for safety and effectiveness.

Mr. Kennedy regularly lambastes the F.D.A. as “corrupt” and too close to the drug industry. He has denounced the fees the agency receives from makers of medical devices and drugs, which make up about half of its $7.2 billion annual budget.

It’s unclear how Mr. Kennedy’s views will mesh with those of Jim O’Neill, a Silicon Valley investor and former government official who would serve as his deputy if he is confirmed. Mr. O’Neill, a former top aide to the billionaire Peter Thiel, has called for approving drugs once they’ve been shown to be safe but before they have been shown to be effective. That idea goes well beyond the deregulation favored by most pharmaceutical executives.

Karoline Leavitt, a spokeswoman for Mr. Trump’s transition who will be his press secretary, described the president-elect’s choices for administration posts as “highly qualified” and reflective of “his priority to put America First.”

Although lawmakers in both parties frequently criticize the drug industry for charging high prices, Mr. Kennedy paints pharmaceutical companies in a much harsher light.

In an interview last year, Mr. Kennedy called vaccine makers “the most corrupt companies in the world” and “serial felons.” He has advanced falsehoods about the science underlying some of the industry’s most influential products, suggesting that vaccines cause autism and that H.I.V. may not be the true cause of AIDS. He has embraced an increasingly popular notion that healthy food and lifestyle changes — not pharmaceutical products — will heal sick people. Referring to drug companies, he wrote on X this year, “The sicker we get the richer and more powerful they become.”

“His view of our world seems to be that everything is a conspiracy,” said Brad Loncar, a former biotech investor who now runs BiotechTV, an industry media company. “If you really know our industry, it’s made up of well-intentioned, smart people, and it’s one of the most innovative sectors of our entire economy.”

Pharmaceutical officials were relieved by Mr. Trump’s pick to lead the F.D.A., Dr. Martin Makary, who has a contrarian bent but has been aligned with scientific consensus on vaccine safety and is not seen as a threat to unwind the status quo.

Drug companies hope to have an ally in Vivek Ramaswamy, who made his fortune as a biotechnology executive and has been named to lead a government efficiency effort alongside Elon Musk. Mr. Ramaswamy has been critical of what he describes as regulatory red tape that slows new drug approvals.

And Mr. O’Neill, the president-elect’s choice for deputy health secretary, has close ties to some biotechnology and medical technology companies, though he is less well-connected to major industry players.

Bracing for the potential of public attacks and new proposals that could hurt their bottom lines, drug companies are said to be reaching out to contacts close to Mr. Trump in hopes of influencing the incoming administration. Some are also considering new ways to defend their businesses from government initiatives they consider detrimental.

“There’s no playbook for dealing with these disruptive figures like Kennedy,” said Sam Geduldig, managing partner of the right-leaning lobbying firm CGCN Group.

Other lobbyists said they are instructing pharmaceutical clients not to hit the panic button yet. Once Congress returns after the Thanksgiving break, Mr. Kennedy is expected to make the rounds on Capitol Hill.

He could face trouble winning the support he needs from Senate Republicans to be confirmed because of his record on vaccines, his past support for abortion rights and his ideas about overhauling the food system.

Drug industry officials have long regarded Mr. Trump as a wild card, just as likely to be a boon as a foe.

In 2020, the Trump administration’s Operation Warp Speed worked closely with drug makers and poured billions of dollars into producing highly effective Covid shots in record time, saving countless lives. Mr. Trump’s pandemic-era health secretary, Alex Azar, spoke with admiration that year about “our partners in the private sector.”

But this year, Mr. Trump spoke little about Operation Warp Speed.

With some exceptions, the drug industry has been in something of a slump since the heights of the pandemic, when it enjoyed a boost in its public image and investors eager to get in on huge gains poured money into drug stocks.

But trust in vaccines and public health institutions has eroded at the same time as the bubble in the biotech markets has deflated. Among major Covid vaccine makers, Moderna’s stock price is down tenfold, and Pfizer’s stock price has fallen by half, from their high-water marks in 2021. An index of smaller biotechnology stocks is down by close to half.

Drug company officials still see opportunities to benefit from Mr. Trump’s win.

The industry is looking forward to Mr. Trump replacing Lina Khan, the chair of the Federal Trade Commission, as he is expected to do. She has been aggressive in taking on big business, including pharma.

The industry is also hopeful that Trump could help reverse its worst policy defeat in recent memory. Under the 2022 Inflation Reduction Act, President Biden’s signature policy achievement, Democratic lawmakers empowered Medicare to directly negotiate the prices of certain prescription drugs — cutting into manufacturers’ profits and raising the specter of similar price cuts in the commercial market. Republicans in Congress have said that they want to repeal the negotiation program.

“Together, Jay and RFK Jr. will restore the NIH to a Gold Standard of Medical Research as they examine the underlying causes of, and solutions to, America’s biggest health challenges, including our Crisis of Chronic Illness and Disease,” Mr. Trump wrote on social media, referring to Robert F. Kennedy Jr., his choice to lead the N.I.H.’s parent agency, the Department of Health and Human Services.

If confirmed by the Senate, Dr. Bhattacharya would lead the world’s premier medical research agency, with a $48 billion budget and 27 separate institutes and centers, each with its own research agenda, focusing on different diseases like cancer and diabetes. Dr. Bhattacharya, who is not a practicing physician, has called for overhauling the N.I.H. and limiting the power of civil servants who, he believes, played too prominent a role in shaping federal policy during the pandemic.

He is the latest in a series of Trump health picks who came to prominence during the coronavirus pandemic and who hold views on medicine and public health that are at times outside the mainstream. The president-elect’s health choices, experts agree, suggest a shake-up is coming to the nation’s public health and biomedical establishment.

Dr. Bhattacharya is one of three lead authors of the Great Barrington Declaration, a manifesto issued in 2020 that contended that the virus should be allowed to spread among young healthy people who were “at minimal risk of death” and could thus develop natural immunity, while prevention efforts were targeted to older people and the vulnerable.

Through a connection with a Stanford colleague, Dr. Scott Atlas, who was advising Mr. Trump during his first term, Dr. Bhattacharya presented his views to Alex M. Azar II, Mr. Trump’s health secretary. The condemnation from the public health establishment was swift. Dr. Bhattacharya and his fellow authors were promptly dismissed as cranks whose “fringe” policy prescriptions would lead to millions of unnecessary deaths.

Dr. Bhattacharya also became a go-to witness in court cases challenging federal and state Covid policies. He joined a group of plaintiffs in suing the Biden administration over what he called “Covid censorship,” arguing that the administration violated the First Amendment in working with social media companies to tamp down on Covid misinformation.

He also argued against mask mandates for schoolchildren in Florida and Tennessee. Judges in both states dismissed him as unqualified to make medical pronouncements on the matter.

“His demeanor and tone while testifying suggest that he is advancing a personal agenda,” Judge Waverly D. Crenshaw Jr. of the U.S. District Court for the Middle District of Tennessee wrote in 2021, adding that he was “simply unwilling to trust Dr. Bhattacharya.”

More recently, amid widespread recognition of the economic and mental health harms caused by lockdowns and school closures, Dr. Bhattacharya’s views have been getting a second look, to the consternation of his critics, who have accused those entertaining his ideas of “sane-washing” him.

Perhaps the most notable reflection has come from Dr. Francis Collins, the former director of the National Institutes of Health. In 2020, Dr. Collins called Dr. Bhattacharya and his co-authors “fringe epidemiologists.” Last year, Dr. Collins suggested that he and other policymakers might have been too narrowly focused on public health goals — saving lives at any cost — and not attuned enough to balancing health needs with economic ones.

“I think a lot of us involved in trying to make those recommendations had that mind-set — and that was really unfortunate, it’s another mistake we made,” Dr. Collins said in December 2023, at a conversation hosted by Braver Angels, a group that addresses political polarization. He did not address Dr. Bhattacharya or the Great Barrington Declaration specifically.

But Dr. Bhattacharya still provokes extremely strong feelings. Dr. Jonathan Howard, an associate professor of neurology and psychiatry at NYU Langone Health, who treated patients at Bellevue Hospital at the height of the pandemic, has assailed Dr. Bhattacharya in a book, “We Want Them Infected.”

Dr. Howard said Dr. Bhattacharya “bungled basic facts” about the pandemic. In March 2020, for example, Dr. Bhattacharya suggested in a Wall Street Journal opinion essay that the pandemic was not as deadly as it was being made out to be, and that the death toll might top out at 40,000 Americans; in the end, 1.2 million died.

Dr. Bhattacharya responded on social media by calling Dr. Howard “unhinged” and his book “inane,” advising him to “take an epidemiology class if you don’t want to keep embarrassing yourself.”

The Great Barrington Declaration grew out of a meeting in Great Barrington, Mass., convened by the American Institute for Economic Research, a think tank dedicated to free-market principles. Its authors, who included doctors, scientists and epidemiologists, wrote that they had “grave concerns about the damaging physical and mental health impacts of the prevailing Covid-19 policies.” They called their approach “Focused Protection.”

Alarmed and angry, 80 experts published a manifesto of their own, the John Snow Memorandum (named after the 19th-century English epidemiologist), saying that the declaration’s approach would endanger Americans who had underlying conditions that put them at high risk from severe Covid-19 — at least one-third of U.S. citizens, by most estimates — and result in perhaps a half-million deaths.

“I think it’s wrong, I think it’s unsafe, I think it invites people to act in ways that have the potential to do an enormous amount of harm,” Dr. Rochelle P. Walensky, a Harvard infectious disease specialist, said at the time. Dr. Walensky later became director of the Centers for Disease Control and Prevention when President Biden took office.

Last month, Dr. Bhattacharya hosted a forum on pandemic policy at Stanford, saying he had hoped to bring together people of different views who would “talk to each other in a civil way.” But the forum itself became the target of attacks — a development that Stanford’s president, Jonathan Levin, called “dispiriting.”

One of Dr. Bhattacharya’s Stanford colleagues, Dr. Pantea Javidan of the Department of Psychiatry and Behavioral Sciences, was quoted in The San Jose Mercury News as saying the symposium gave “a platform for discredited figures who continually promote dangerous, scientifically unsupported or thoroughly debunked approaches to Covid.”