WASHINGTON — The outbreak of the respiratory virus began in China and was quickly spread around the world by air travelers, who ran high fevers. In the United States, it was first detected in Chicago, and 47 days later the World Health Organization declared a pandemic. By then it was too late: 110 million Americans were expected to become ill, leading to 7.7 million hospitalized and 586,000 dead.

That scenario, code-named “Crimson Contagion” and imagining an influenza pandemic, was simulated by the Trump administration’s Department of Health and Human Services in a series of exercises that ran from last January to August.

The simulation’s sobering results — contained in a draft report dated October 2019 that has not previously been reported — drove home just how underfunded, underprepared and uncoordinated the federal government would be for a life-or-death battle with a virus for which no treatment existed.

The draft report, marked “not to be disclosed,” laid out in stark detail repeated cases of “confusion” in the exercise. Federal agencies jockeyed over who was in charge. State officials and hospitals struggled to figure out what kind of equipment was stockpiled or available. Cities and states went their own way on school closings.

Many of the potentially deadly consequences of a failure to address the shortcomings are now playing out in all-too-real fashion across the country. And it was hardly the first warning for the nation’s leaders. Three times over the past four years the U.S. government, across two administrations, had grappled in depth with what a pandemic would look like, identifying likely shortcomings and in some cases recommending specific action.

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In 2016 the Obama administration produced a comprehensive report on the lessons learned by the government from battling Ebola. In January 2017 outgoing Obama administration officials ran an extensive exercise on responding to a pandemic for incoming senior officials of the Trump administration.

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The full story of the Trump administration’s response to the coronavirus is still playing out. Government officials, health professionals, journalists and historians will spend years looking back on the muddled messages and missed opportunities of the past three months, as President Donald Trump moved from dismissing the coronavirus as a few cases that would soon be “under control” to his revisionist announcement Monday that he had known all along that a pandemic was on the way.

What the scenario makes clear, however, is that his own administration had already modeled a similar pandemic and understood its potential trajectory.

The White House defended its record, saying it responded to the 2019 exercise with an executive order to improve the availability and quality of flu vaccines, and that it moved early this year to increase funding for the Health and Human Service Department’s program that focuses on global pandemic threats.

“Any suggestion that President Trump did not take the threat of COVID-19 seriously is false,” said Judd Deere, a White House spokesman.

But officials have declined to say why the administration was so slow to roll out broad testing, or move faster, as the simulations all indicated it should, to urge social distancing and school closings.

Asked at his news briefing Thursday about the government’s preparedness, Trump responded, “Nobody knew there would be a pandemic or epidemic of this proportion. Nobody has ever seen anything like this before.”

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The work done over the past five years, however, demonstrates that the government had considerable knowledge about the risks of a pandemic and accurately predicted the very types of problems Trump is now scrambling belatedly to address.

“Crimson Contagion,” the exercise conducted last year in Washington and 12 states including New York and Illinois, showed that federal agencies under Trump continued the Obama-era effort to think ahead about a pandemic.

But the planning and thinking happened many layers down in the bureaucracy. The knowledge and sense of urgency about the peril appear never to have gotten sufficient attention at the highest level of the executive branch or from Congress, leaving the nation with funding shortfalls, equipment shortages and disorganization within and among various branches and levels of government.

The October 2019 report in particular documents that officials at the Homeland Security and Health and Human Services departments and even the White House’s National Security Council were aware of the potential for a respiratory virus outbreak originating in China to spread quickly to the U.S. and overwhelm the nation.

“Nobody ever thought of numbers like this,’’ Trump said Wednesday, at a news conference.

In fact, they had.

From Ebola, lessons learned

As early as the George W. Bush administration, homeland security and health officials focused on big gaps in the U.S. 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.

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The Centers for Disease Control and Prevention estimates that ultimately there were about 60.8 million cases in the U.S., 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 U.S.

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 U.S. 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 U.S. 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 Kirchhoff identified were early warning signals of what has unfolded in the past three months.

His report concluded that the U.S. assumed more capability on the part of the World Health Organization than the agency actually had.

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The U.S. 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 Obama ordered.

While the U.S. rapidly developed a way to screen air passengers coming into the U.S. — borrowing from intelligence tools developed after 9/11 to track possible terrorists — Kirchhoff found deficiencies in even measuring how fast the virus was spreading.

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

The money helped fund a little-known agency inside the Health and Human Services Department 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 Thomas Duncan, a Liberian citizen, became the first person diagnosed with Ebola on U.S. territory in September 2014, errors resulted in the infection of two nurses and fear of a wider spread in the U.S. (Duncan died, but the two nurses recovered.)

What is striking in reading 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.”

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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 bench mark 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, Obama’s homeland security adviser.

Getting the Trump team’s attention

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

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She asked Tom Bossert, who was preparing to come in as 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,” Monaco said. “There is no vaccine, and you would get issues like nursing homes being particularly vulnerable, shortages of ventilators.”

Monaco was impressed by how seriously 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 the leaders at the table — Tillerson, Kelly and Perry among them — had been fired or moved on.

In 2018, Trump’s then-national security adviser, John Bolton, ousted 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, 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, Bolton lashed out at critics who said the shift had reflected disinterest in pandemic threats.

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“Claims streamlining NSC structures impaired our nation’s bio defense are false. Global health remained a top NSC priority,” Bolton wrote.

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, director of 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 U.S., Trump submitted a 2021 budget proposal that calls for a $693.3 million reduction in funding for the Centers for Disease Control, or about 9%, 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 Health and Human Services Department 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 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.

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“He recognized early that we have a big problem and we needed much bigger budgets to prepare,’’ said Richard Danzig, secretary of the Navy in the Clinton administration, who had worked with 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 U.S., 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 the U.S., with some developing respiratory symptoms and fevers en route.

A 52-year-old male 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 U.S. started.

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

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In the fictional pandemic, as the virus spread quickly across the U.S., the CDC 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 schoolchildren. The CDC recommended that states delay school openings — the exercise took place toward the end of 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 U.S. 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 Health and Human Services Department, another scenario playing out now.

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But the problems were larger than bureaucratic snags. The U.S., organizers realized, did not have the means to quickly manufacture more essential medical equipment, supplies and medicines, from antiviral medications to 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 on Capitol Hill last Thursday, as lawmakers peppered Health and Human Services Department officials with questions that sounded almost as if they had read the script from the fictional exercise, reflecting the shortage of respirators and protective gear.

Sen. Mitt Romney, R-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,” Romney added, making a point, apparently unknown to him, that the administration’s own simulation had made clear five months earlier.

(Anika Varty / The Seattle Times)

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