Dangerous pathogens left unsecured at labs across Africa. Halted inspections for mpox, Ebola and other infections at airports and other checkpoints. Millions of unscreened animals shipped across borders.

The Trump administration’s pause on foreign aid has hobbled programs that prevent and snuff out outbreaks around the world, scientists say, leaving people everywhere more vulnerable to dangerous pathogens.

That includes Americans. Outbreaks that begin overseas can travel quickly: The coronavirus may have first appeared in China, for example, but it soon appeared everywhere, including the United States. When polio or dengue appears in this country, cases are usually linked to international travel.

“It’s actually in the interest of American people to keep diseases down,” said Dr. Githinji Gitahi, who heads Amref Health Africa, a large nonprofit that relies on the United States for about 25 percent of its funding.

“Diseases make their way to the U.S. even when we have our best people on it, and now we are not putting our best people on it,” he added.

In interviews, more than 30 current and former officials of the United States Agency for International Development, members of health organizations and experts in infectious diseases described a world made more perilous than it was just a few weeks ago.

Many spoke on condition of anonymity for fear of retaliation by the federal government.

The timing is dire: The Democratic Republic of Congo is experiencing the deadliest mpox outbreak in history, with cases exploding in a dozen other African countries.

The United States is home to a worsening bird flu crisis. Multiple hemorrhagic fever viruses are smoldering: Ebola in Uganda, Marburg in Tanzania, and Lassa in Nigeria and Sierra Leone.

In 2023, U.S.A.I.D. invested about $900 million to fund labs and emergency-response preparedness in more than 30 countries. The pause on foreign aid froze those programs. Even payments to grantees for work already completed are being sorted out in the courts.

Waivers issued by the State Department were intended to allow some work to continue on containing Ebola, Marburg and mpox, as well as preparedness for bird flu.

But Trump administration appointees choked payment systems and created obstacles to implementing the waivers, according to a U.S.A.I.D. memo by Nicholas Enrich, who was the agency’s acting assistant administrator for global health until Sunday.

Then last month, the Trump administration canceled about 5,800 contracts, effectively shuttering most U.S.A.I.D.-funded initiatives, including many that had received permission to continue.

“It was finally clear that we were not going to be implementing” even programs that had waivers, Mr. Enrich recalled in an interview.

The decision is likely to result in more than 28,000 new cases of infectious diseases like Ebola and Marburg, and 200,000 cases of paralytic polio each year, according to one estimate.

Secretary of State Marco Rubio “has been working diligently since being sworn in to review every dollar spent,” the State Department said in an emailed statement.

“We’ll be able to say that every program that we are out there operating serves the national interest, because it makes us safer or stronger or more prosperous,’” the statement quoted Mr. Rubio as saying.

Most U.S.A.I.D. staff members were terminated or placed on administrative leave without warning. The agency had more than 50 people dedicated to outbreak responses, the result of a Congressional push to beef up pandemic preparedness.

Now it has six. Those who were fired included the organization’s leading expert in lab diagnostics and the manager of the Ebola response. “I have no idea how six people are going to run four outbreak responses,” said one official who was let go.

Also sent home were hundreds of thousands of community health workers in Africa who were sentinels for diseases.

In early January, the Tanzanian government denied there were new cases of Marburg, a hemorrhagic fever. It was a community health worker trained through a U.S.-funded Ebola program who reported the disease a week later.

The outbreak eventually grew to include 10 cases; it is now under control, the government has said.

Even in quieter times, foreign aid helps to prevent, detect and treat diseases that can endanger Americans, including drug-resistant H.I.V., tuberculosis and malaria, and bacteria that don’t respond to available antibiotics.

Much of that work has stopped, and other organizations or countries cannot fill the gap. Compounding the loss is America’s withdrawal from the World Health Organization, which has instituted cost-cutting measures of its own.

“This is a lose-lose scenario,” said Dr. Keiji Fukuda, who has led pandemic prevention efforts at the W.H.O. and the C.D.C.

The slashing of foreign aid deprives the world of American leadership and expertise, but it also locks the United States out of global discussions, Dr. Fukuda said: “For the life of me, I cannot see the justification or the reason for this very calculated, systematic approach to pull down public health.”

Trying to Adapt

U.S.A.I.D.’s intense focus on global health security is barely a decade old, but it has mostly received bipartisan support. The first Trump administration expanded the program to 50 countries.

Much of the aid was intended to help them eventually tackle problems on their own. And to some extent, that was happening.

But confronted with a new virus or outbreak, “there’s so many things that one has to do and learn, and many countries can’t do that on their own,” said Dr. Lucille Blumberg, an infectious diseases physician and expert on emerging diseases.

U.S.A.I.D. and its partners helped countries identify the expertise, training and machinery they needed, brought together officials in various ministries and engaged farmers, businesses and families.

“It actually doesn’t cost the U.S. government that much,” said an official with a large development organization. “But that sort of trust-building, communication, sharing evidence is a real strength that the U.S. brings to health security — and that’s gone.”

In Africa, some countries have reacted to the disappearance of aid with alarm, others with resignation. “We’re doing our best to adapt to this development,” said Dr. Muhammad Ali Pate, Nigeria’s health minister.

“The U.S. government is not responsible, ultimately, for the health and the security of Nigerian people,” he said. “At the end of the day, the responsibility is ours.”

A successful outbreak response requires coordination of myriad elements: investigators to confirm the initial report; workers trained to do testing; access to test kits; transport of samples; a lab with enough workers, running water, electricity and chemical supplies for diagnoses; and experts to interpret and act on the results.

In broad strokes, the C.D.C. provided expertise on diseases, U.S.A.I.D. funded logistics and the W.H.O. convened stakeholders, including ministries of health.

Before the aid freeze, employees from each organization often talked every day, sharing information and debating strategy. Together, they lowered response time to an outbreak from two weeks in 2014 to five days in 2022 to just 48 hours most recently.

But now, C.D.C. experts who have honed their expertise over decades are not even allowed to speak to colleagues at the W.H.O.

U.S.A.I.D. funding for sample transport, lab supplies, fuel for generators and phone plans for contact tracers has ended. Much of its investment in simple solutions to seemingly intractable problems has also stopped.

In West Africa, for example, rodents that spread Lassa fever invade homes in search of food. One program in U.S.A.I.D.’s Stop Spillover project introduced rodent-proof food containers to limit the problem, but has now shut down.

In Congo, where corruption, conflict and endless outbreaks mean that surveillance “looks like Swiss cheese even at the best of times,” the mpox response slowed because there were no health workers to transport samples, said a U.S.A.I.D. official familiar with the response.

More than 400 mpox patients were left stranded after fleeing overwhelmed clinics. Before a waiver restarted some work, the United States identified two new cases of mpox, both in people who had traveled to East Africa.

In Kenya, U.S.A.I.D. supported eight labs and community-based surveillance in 12 high-risk counties. Labs in the Marsabit, Mandera and Garissa counties — which border Ethiopia and Somalia — have run out of test kits and reagents for diseases including Rift Valley fever, yellow fever and polio, and have lost nearly half their staff.

Kenya also borders Uganda and Tanzania and is close to Congo — all battling dangerous outbreaks — and has lost more than 35,000 workers.

“These stop-work orders would mean that it increases the risk of an index case passing through unnoticed,” Dr. Gitahi said, referring to the first known case in an outbreak. His organization has terminated nearly 400 of its staff of 2,400.

Many labs in Africa store samples of pathogens that naturally occur in the environment, including several that can be weaponized. With surveillance programs shut off, the pathogens could be stolen, and a bioterrorism attack might go undetected until it was too late to counter.

Some experts worried about bad actors who may release a threat like cholera into the water, or weaponize anthrax or brucellosis, common in African animals. Others said they were concerned that even unskilled handling of these disease threats might be enough to set off a disaster.

Funding from the U.S. government helped hire and train lab workers to maintain and dispose of dangerous viruses and bacteria safely.

But now, pathogens can be moved in and out of labs with no one the wiser. “We have lost our ability to understand where pathogens are being held,” said Kaitlin Sandhaus, founder and chief executive of Global Implementation Solutions.

Her company helped 17 African labs become accredited in biosafety procedures and supported five countries in drafting laws to ensure compliance. Now the firm is shutting down.

In the future, other countries, including China, will know more about where risky pathogens are housed, Ms. Sandhaus said: “It feels very dangerous to me.”

China has already invested in building labs in Africa, where it is cheaper and easier to “work on whatever you would like without anyone else paying attention,” said one U.S.A.I.D. official.

Russia, too, is providing mobile labs to Ugandans in Mbale, on the border with Kenya, another official said.

Some African countries like Somalia have fragile health systems and persistent security threats, yet minimal capacity for tracking infections that sicken animals and people, said Abdinasir Yusuf Osman, a veterinary epidemiologist and chair of a working group in Somalia’s health ministry.

Each year Somalia exports millions of camels, cattle and other livestock, primarily to the Middle East. The nation has relied heavily on foreign aid to screen the animals for diseases, he said.

“The consequences of this funding shortfall, in my view, will be catastrophic and increase the likelihood of uncontrolled outbreaks,” Dr. Osman said.

In countries with larger economies, foreign aid has helped build relationships. Thailand is a pioneer in infectious diseases, and U.S.A.I.D. was funding a modest project on malaria elimination that boosts its surveillance capabilities.

The abrupt end to that commitment risks losing good will, said Jui Shah, who helped run the program.

“In Asia, relationships are crucial for any type of work, but especially for roles that work with surveillance and patient data,” she said. “Americans will suffer if other countries hesitate to engage with us about outbreaks.”