On Thursday, three years and 100 days after the Trump administration declared the coronavirus a public health emergency, the Biden administration will allow the emergency declaration to expire, ushering in a new era when the government will treat Covid-19 like any other respiratory ailment.

If the coronavirus pandemic was a war, the United States is about to officially enter peacetime.

But interviews with senior federal and state health officials — including the secretary of health and human services and the commissioner of the Food and Drug Administration — make clear that while the United States has greatly improved its capacity to fight Covid-19, it is not fully prepared for a radically different future variant or a new pandemic.

State health officials, tasked with tracking the coronavirus, are burned out, their departments understaffed. President Biden’s coronavirus response team will soon disband. The White House has yet to fulfill Congress’s directive to set up a new pandemic preparedness office, and key officials, including Dr. Ashish K. Jha, the coronavirus response coordinator, and Dr. Rochelle P. Walensky, the director of the Centers for Disease Control and Prevention, are stepping down or intend to do so. 

Dr. Jha and other federal health officials have spent months laying the groundwork for the end of the public health emergency, and the Biden administration has set up programs to keep vaccines free for the uninsured and to support medical research into new vaccines and therapies. But the officials say they are operating on a tight budget; Congress has refused to give the administration any new money for the pandemic response.

When asked if the country was prepared for a new pandemic, Dr. Francis S. Collins, the former director of the National Institutes of Health, simply replied, “No.” Mr. Biden’s secretary of health and human services, Xavier Becerra, paused for several seconds before answering the same question.

“It depends on the degree,” Mr. Becerra finally said, adding: “We’ve learned a lot from Covid. We’re prepared to deal with Covid — even some of the variants as they come. If it’s something totally different, avian flu, I become a little bit more concerned. If it becomes some kind of biological weapon, you know, that’s another issue altogether.”

The emergency declaration, Dr. Jha said in an interview, has given the government and the nation’s health care system the flexibility to take extraordinary measures during the crisis, like setting up hospital beds in a parking lot. Dr. Jha, who has told colleagues he intends to return to his job as dean of the Brown University School of Public Health, said those kinds of steps were no longer necessary.

But he cautioned that the virus was not going away. More than 1,000 people are still dying of Covid-19 in the United States each week, according to the C.D.C.

“Covid is going to be with us, but we know how to live with it in a way that need not cause disruption, need not put people in the hospital — or worse,” Dr. Jha said. “And we know how to monitor this virus and manage it so that if it takes a turn, if it does something different, we’re ready for that.”

In the immediate term, the end of the emergency declaration will not cause dramatic changes for Americans, though some people could face new costs for coronavirus testing. After Thursday, private insurers will no longer be required to cover up to eight at-home tests per month. Those with Medicare or private insurance may have co-pays for lab tests.

For now, vaccines will continue to be free because the government has a stockpile of them. When they move to the commercial market later this year, they will remain free for most people with insurance. For the uninsured, the Biden administration plans to spend more than $1 billion on a new program to offer free shots, though questions remain about how the initiative will work.

It is unclear when Paxlovid, the leading antiviral medication for Covid-19, will move to the commercial market. For now, it will also remain free because of the government’s stockpile, though patients may have to pick up part of the cost once the supply is depleted.

Some experts fear that policymakers and elected officials, who have already put Covid-19 in the rearview mirror, will forget about it entirely once the emergency declaration is gone.

“It’s going to be interpreted, I fear, as a ‘mission accomplished’ moment,” said Gary Edson, the president of the Covid Collaborative, a group of experts that has worked to inform the federal response, adding, “As soon as we take that view, we’ve given up all hope, all mobilization for defensive preparedness.”

The country has learned and absorbed some lessons from Covid-19. The C.D.C. now tracks the spread of the virus by examining wastewater. The Strategic National Stockpile, the nation’s medical reserve, is substantially better equipped. As of early this month, it had 352 million N95 masks, 1.3 billion gloves and 150,000 ventilators, and the administration has more than 600 million at-home coronavirus tests on hand. The branch of the Department of Health and Human Services that handles logistics, like distributing tests and vaccines, has been beefed up.

Still, an estimated seven million immunocompromised American adults remain especially at risk from Covid-19. Key monoclonal antibody treatments that were once critical to protecting that population are no longer cleared for use by the F.D.A. because they are ineffective against current variants. The administration is relying heavily on Paxlovid, which can reduce the severity of Covid-19.

“We need an effective monoclonal against current variants,” Dr. David A. Kessler, who left the Biden administration in January after overseeing its vaccination and treatment program. “We need a more durable vaccine. And we should never rely on just one highly effective oral antiviral.”

All told, more than 1.1 million people in the United States have died of Covid-19 — more than the number killed during both world wars. But while the military builds warships and fighter jets in peacetime, public health has long been caught in what experts call a cycle of panic and neglect.

The Covid Crisis Group, a panel of experts led by Philip D. Zelikow, a University of Virginia historian who ran the commission that investigated the Sept. 11 attacks, says Congress and policymakers must view infectious disease threats through a national security lens. The group spent two years investigating the pandemic response and recently published its findings in a book, “Lessons From the Covid War.”

Top federal health officials said the military readiness analogy was apt.

“What if we funded public health the way we funded the military?” asked Dr. Nirav D. Shah, the principal deputy director of the C.D.C. “We’d have a system that would have built-in flexibilities, in the same way that the military can respond very flexibly.”

Instead, Biden administration officials say they are scrounging for money for pandemic preparedness. One concern is that the end of the emergency will lessen the economic incentives for pharmaceutical companies to develop new drugs, treatments and vaccines because there will no longer be a guaranteed government buyer.

“One of the most important parts of Warp Speed and the whole pandemic response was reducing uncertainty for industry by putting the money up from the government,” Dr. Robert M. Califf, the F.D.A. commissioner, said in an interview, referring to Operation Warp Speed, the Trump administration’s vaccine initiative. “Because what you’re essentially asking industry to do now is to make the investment and take the risk.”

To encourage innovation, the Biden administration intends to spend $5 billion on a new initiative, called Project Next Gen, to develop a new generation of Covid-19 vaccines and treatments. Officials have said little about how that money will be spent. The Biden administration could not persuade Congress to pay for the program, said Dawn O’Connell, the top emergency preparedness official at the Department of Health and Human Services.

“We requested and requested and requested supplemental funds to be able to do Next Gen,” she said. When the money was not forthcoming from Congress, federal health officials decided to use unspent coronavirus response funds.

For now, federal regulators are settling for a more incremental strategy — redesigning annual Covid booster shots to target newer variants of Omicron. A reformulated shot will most likely roll out by early September.

With the end of the public health emergency, local and federal health officials will have less visibility into who has Covid-19 and where the virus is spreading. The C.D.C. and local health departments have used that information to guide communities about mask wearing and other precautions.

But when the emergency expires, laboratories will no longer be required to report the results of coronavirus tests to the government. Last week, the C.D.C. announced that it would no longer track community levels of Covid-19 or the percentage of tests that come back positive.

Instead, agency officials said they would rely on wastewater samples and hospital data as metrics for monitoring the virus. Hospitals will still be required to report coronavirus cases when the emergency ends, though not in as much detail as before.

After Dr. Jha leaves, leadership of the federal Covid response may function more as a committee effort among agency chiefs, with Ms. O’Connell as a central coordinator. Ms. O’Connell said last week that she had talked with White House officials about the new pandemic preparedness office but did not know of plans for its leadership.

“We’re just waiting to see where it lands,” she said.

In recent weeks, Dr. Jha has talked to leading virologists to gauge the likelihood of another Omicron-like variant. One of those scientists, Dr. Dan H. Barouch, the director of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center, said in an interview that he told Dr. Jha that the way the coronavirus mutates meant it was nearly impossible to offer more than a “gut” prediction, which he put at around 20 percent in the next two years.

Mr. Becerra insists that, whatever is coming, his department is prepared.

“At the end of any major war, you don’t just let down your guard completely,” he said. “Because while it may seem like it’s over, there could easily be a flare-up. So we may be exiting the public health emergency, but we haven’t left the public health threat.”