As early as the George W. Bush administration, homeland security and health officials focused on big gaps in the American response to a biological attacks and the growing risk of pandemics. The first test came in April 2009, just a few months after the start of President Barack Obama's first term. A 10-year-old California girl was diagnosed with a contagious disease that would be called swine flu or H1N1, the first flu pandemic in more than 40 years.

The Centers for Disease Control and Prevention estimates that ultimately there were about 60.8 million cases in the United States, along with 274,304 hospitalizations and 12,469 deaths associated with H1N1.

The virus turned out to be less deadly than first expected. But it was a warning shot that officials in the Obama administration said they took seriously, kicking off a planning effort that escalated in early 2014, with the outbreak of Ebola in West Africa and ensuing fear that it could spread to the United States.

Ebola was less contagious than the flu, but far more deadly. It killed 11,000 people in Africa. But it could have been far worse. The United States sent nearly 3,000 troops to Africa to help keep the disease from spreading. While the containment effort was considered a success, inside the White House, officials sensed that the United States had gotten lucky — and that the response had revealed gaps in preparedness.

Christopher Kirchhoff, a national security aide who moved from the Pentagon to the White House to deal with the Ebola crisis, was given the job of putting together a "lessons learned" report, with input from across the government.

The weaknesses Mr. Kirchhoff identified were early warning signals of what has unfolded in the past three months.

His report concluded that the United States assumed more ability on the part of the World Health Organization than the agency actually had.

The United States had its own issues. There was no airplane in the U.S. fleet capable of evacuating an American doctor who was infected while treating patients in Liberia. The Pentagon was largely unprepared for the intervention that Mr. Obama ordered.

While the United States rapidly developed a way to screen air passengers coming into the country — borrowing from intelligence tools developed after the Sept. 11, 2001, attacks to track possible terrorists — Mr. Kirchhoff found deficiencies in even measuring how fast the virus was spreading.

The United States sent nearly 3,000 troops to Africa to help keep Ebola from spreading in 2014.Credit...Daniel Berehulak for The New York Times.

On the plus side, the Obama White House had created an Ebola Task Force, run by Ron Klain, Vice President Joseph R. Biden Jr.'s former chief of staff, before a single case emerged in the United States. Congress allocated $5.4 billion in emergency funding to pay for Ebola treatment and prevention efforts in the United States and West Africa.

Health workers entering a high-risk ward at an Ebola treatment center in 2014 in Monrovia, Liberia. The outbreak led the Obama administration to study U.S. preparedness for a pandemic.

The money helped fund a little-known agency inside the Department of Health and Human Services in charge of preparing for future contagious disease outbreaks, the same office that in 2019 ran the Crimson Contagion exercise and other similar events in the years since.

After a man named Thomas Duncan, a Liberian citizen, became the first person given a diagnosis of Ebola on American territory in September 2014, errors resulted in the infection of two nurses and fear of a wider spread in the United States. (Mr. Duncan died, but the two nurses recovered.)

What is striking in reading Mr. Kirchhoff's account today, however, is how few of the major faults he found in the American response resulted in action — even though the report was filled with department-by-department recommendations.

There were deficiencies "in personal protective equipment use, disinfection" and "social services for those placed under quarantine."

There was confusion over travel restrictions, and the need "for a smoother sliding scale of escalation of government response, from local authorities acting on their own to local authorities acting with some federal assistance" to the full activation of the federal government.

The report concluded that "a minimum planning benchmark might be an epidemic an order of magnitude or two more difficult than that presented by the outbreak of Ebola in West Africa, with much more significant domestic spread."

But one big change did come out of the study: The creation of a dedicated office at the National Security Council to coordinate responses and raise the alarm early.

"What I learned most is that we had to stand up a global biosecurity and health directorate, and get it enshrined for the next administration," said Lisa Monaco, Mr. Obama's homeland security adviser.

Getting the Trump Team's Attention

After Mr. Trump's election, Ms. Monaco arranged an extensive exercise for high-level incoming officials — including Rex W. Tillerson, the nominee for secretary of state; John F. Kelly, designated to become homeland security secretary; and Rick Perry, who would become energy secretary — gaming out the response to a deadly flu outbreak.

She asked Tom Bossert, who was preparing to come in as Mr. Trump's homeland security adviser, to run the event alongside her.

"We modeled a new strain of flu in the exercise precisely because it's so communicable," Ms. Monaco said. "There is no vaccine, and you would get issues like nursing homes being particularly vulnerable, shortages of ventilators."

Ms. Monaco was impressed by how seriously Mr. Bossert, her successor, appeared to take the threat, as did many of the 30 or so Trump team members who participated in the exercise, details of which were reported by Politico.

But by the time the current crisis hit, almost all of the leaders at the table — Mr. Tillerson, Mr. Kelly and Mr. Perry among them — had been fired or moved on.

In 2018, Mr. Trump's national security adviser at the time, John R. Bolton, ousted Mr. Bossert and eliminated the National Security Council directorate, folding it into an office dedicated to weapons of mass destruction in what Trump officials called a logical consolidation.

Asked about that shift on March 13, Mr. Trump told a reporter that it was "a nasty question," before adding: "I don't know anything about it." Writing on Twitter the next day, Mr. Bolton lashed out at critics who said the shift had reflected disregard for pandemic threats.

"Claims that streamlining NSC structures impaired our nation's bio defense are false," Mr. Bolton tweeted. "Global health remained a top NSC priority."

In a statement, the National Security Council said it "has directors and staff whose full-time job it is to monitor, plan for, and respond to pandemics, including an infectious disease epidemiologist and a virologist."

But in testimony to Congress last week, Dr. Anthony S. Fauci, the director of the National Institute of Allergy and Infectious Diseases, suggested that ending the stand-alone directorate was ill-advised. "It would be nice if the office was still there," he said.

On Feb. 10, nearly three weeks after the first coronavirus case was diagnosed in the United States, Mr. Trump submitted a 2021 budget proposal that called for a $693.3 million reduction in funding for the C.D.C., or about 9 percent, although there was a modest increase for the division that combats global pandemics.

'Crimson Contagion'

The Crimson Contagion planning exercise run last year by the Department of Health and Human Services involved officials from 12 states and at least a dozen federal agencies. They included the Pentagon, the Department of Veterans Affairs and the National Security Council. Groups like the American Red Cross and American Nurses Association were invited to join, as were health insurance companies and major hospitals like the Mayo Clinic.

The war game-like exercise was overseen by Robert P. Kadlec, a former Air Force physician who has spent decades focused on biodefense issues. After stints on the Bush administration's Homeland Security Council and the staff of the Senate Intelligence Committee, he was appointed assistant secretary of Health and Human Services for Preparedness and Response.

"He recognized early that we have a big problem and we needed much bigger budgets to prepare," said Richard Danzig, the secretary of the Navy in the Clinton administration, who had worked with Mr. Kadlec.

The exercise played out in four separate stages, starting in January 2019.

The events were supposedly unspooling in real time — with the worst-case scenario underway as of Aug. 13, 2019 — when, according to the script, 12,100 cases had already been reported in the United States, with the largest number in Chicago, which had 1,400.

The fictional outbreak involved a pandemic flu, which the Department of Health and Human Services says was "very different than the novel coronavirus." The staged outbreak had started when a group of 35 tourists visiting China were infected and then flew home to Australia, Kuwait, Malaysia, Thailand, Britain and Spain, as well as to the United States, with some developing respiratory symptoms and fevers en route.

A 52-year-old man from Chicago, who was on the tour, had "low energy and a dry cough" upon his return home. His 17-year-old son on that same day went out to a large public event in Chicago, and the chain of illnesses in the United States started.

Many of the moments during the tabletop exercise are now chillingly familiar.

In the fictional pandemic, as the virus spread quickly across the United States, the C.D.C. issued guidelines for social distancing, and many employees were told to work from home.

But federal and state officials struggled to identify which employees were essential and what equipment was needed to effectively work from home.

There also was confusion over how to handle school children. The C.D.C. recommended that states delay school openings — the exercise took place toward the end of the summer. But some school districts decided to go ahead with the start of school while others followed the federal advice, causing the same types of confusion and discrepancies that have marked the response to the coronavirus.

The exercise from last year then went on to predict how the situation on the ground in the United States would worsen as the weeks passed.

Confusion emerged as state governments began to turn in large numbers to Washington for help to address shortages of antiviral medications, personal protective equipment and ventilators. Then states started to submit requests to different branches of the federal government, leading to bureaucratic chaos.

Friction also emerged between the Federal Emergency Management Agency, which is traditionally in charge of disaster response, and the Department of Health and Human Services, another scenario playing out now.

But the problems were larger than bureaucratic snags. The United States, the organizers realized, did not have the means to quickly manufacture more essential medical equipment, supplies or medicines, including antiviral medications, needles, syringes, N95 respirators and ventilators, the agency concluded.

Congress was briefed in December on some of these findings, including the inability to quickly replenish certain medical supplies, given that much of the product comes from overseas.

These concerns turned more urgent at a hearing last Thursday on Capitol Hill, as lawmakers peppered officials with the Department of Health and Human Services with questions that sounded almost as if they had read the script from the fictional exercise, reflecting the shortage of respirators and protective gear.

Senator Mitt Romney, Republican of Utah, said last week that he blamed Congress and prior administrations for not increasing stockpiles of this type of equipment.

"That is an area we ought to consider making an investment in," he added, making a point, apparently unknown to him, that the administration's own simulation had made clear five months earlier.

New York Times,

By David E. Sanger, Eric Lipton, Eileen Sullivan and Michael CrowleyPublished March 19, 2020Updated March 20, 2020, 9:49 a.m.