In August, months before the first case of the new coronavirus was documented, some of Colorado’s top health officials gathered in a room at the state Department of Public Health and Environment to train for a pandemic.

The hypothetical scenario: A highly infectious and lethal new virus had jumped from animals to humans in China and was now being spread across the globe by travelers. A month-and-a-half after the first person infected with the virus was identified in the United States, the state is seeing a rising number of cases, and national estimates are that the virus could sicken more than 100 million people and kill more than 500,000 by the time it’s all over.

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The nationwide Crimson Contagion exercise this past summer was the kind of regular training that used to provide reassurance the nation would be ready should a pandemic ever hit our shores. The training pulled together 19 federal departments and agencies, 12 states including Colorado, 74 local health departments, 15 tribal nations and 87 hospitals. And it gave each of those entities an early — and eerily prescient — chance to practice how to respond to the situation they all now face.

But, in retrospect, the training also revealed the flawed assumptions that informed state and national preparedness for decades and have now made the United States a global epicenter for the coronavirus pandemic. The country was not prepared to scale up testing fast enough for a new virus. Its national stockpile of medical supplies wasn’t equipped to handle large requests from many states at the same time.

Colorado health leaders are now speaking more bluntly about how the nation’s pandemic planning did not anticipate the challenges of the coronavirus.

“None of this is built around the fact that we’re all going to get hit at once and there is no federal support,” said Scott Bookman, CDPHE’s incident commander for the response to COVID-19, the disease caused by the coronavirus. “The federal system has failed us here.”

There is another reason that the state and federal governments developed blind spots in pandemic planning, a simple theme that ties together many of the problems that have hindered response to the coronavirus: We were preparing for the wrong virus.

This is a transmission electron micrograph of a SARS-CoV-2 virus particle, isolated from a patient. SARS-CoV-2 is the scientific name of the coronavirus that causes COVID-19. The image was captured and color-enhanced at the NIAID Integrated Research Facility in Fort Detrick, Maryland. (Provided by the National Institute of Allergy and Infectious Diseases)

Focus on flu

Colorado’s official document for pandemic response is called the CDPHE Pandemic Influenza Plan. The draft executive orders that a special committee had prewritten for the governor to potentially sign during a pandemic all focused on influenza. Even the virus in the Crimson Contagion exercise was a hypothetical new strain of flu.

“We sort of tend to plan for what we know,” said Jennifer Nuzzo, an epidemiologist at the Johns Hopkins Center for Health Security. “And, in terms of pandemics that we’ve seen in the past century, they’ve largely involved influenza.”

The pandemics of 1918, 1957, 1968, all caused by strains of influenza, were most on officials’ minds as they developed pandemic plans in the early 2000s. Nuzzo said there’s usually three flu pandemics per century, and, by 2004, health officials had become concerned that another one was overdue. Thus kicked off what Nuzzo described as a modern high point for pandemic planning in 2004, 2005 and 2006 — all of it focused on the flu.

That paid off during the 2009 H1N1 flu pandemic. But when that pandemic wasn’t as bad as feared — and when pandemic preparedness ran smack into a worldwide shift toward tighter government budgets during the Great Recession — pandemic planning kind of stopped evolving, she said.

“I think that led to some complacency,” she said.

The nation’s strategic stockpile of medical supplies withered. And plans didn’t expand to consider how to respond to pandemics caused by different kinds of viruses — even though outbreaks of SARS and MERS had shown that coronaviruses were fully capable of causing pandemics.

Nuzzo and her colleagues have been warning for years that coronaviruses and other kinds of viruses should be considered in pandemic planning. In October, they published a report called the Global Health Security Index, which examined nations’ readiness for a pandemic. Among their findings was that countries’ pandemic plans focused heavily on the flu. Only 5% of nations had a plan in place to share genetic data or clinical specimens for viruses that weren’t influenza.

“There exists a stark disparity between the level of readiness for pandemic influenza and other potential high-impact respiratory pathogens,” Nuzzo and colleagues wrote in a different report, published in September. “It is important to more fully understand the systems that have been built for influenza and consider the extent to which they would be of value for responding to other high-impact respiratory pathogens.”

Nuzzo said many of the systems put in place to respond to a flu pandemic will work for other kinds of pandemics, as well. For instance, ventilators and critical-care capacity at hospitals are vital for both flu and coronavirus pandemics. But Nuzzo said it’s also clear that a pandemic caused by a virus other than flu is more difficult to respond to.

Take, for example, medicines and vaccines. There are already antiviral drugs that work against the flu, so they would give doctors an obvious weapon to blunt a pandemic caused by a new strain of flu. The Crimson Contagion exercise assumed as much, making its hypothetical new flu virus susceptible to drugs like Tamiflu, according to a federal report on the exercise obtained by The New York Times.

Similarly, not only are there already vaccines against the flu but there is also a flu vaccine industry, Nuzzo said. That means there’s already a research base from which to adapt a vaccine for a new flu strain and there are factories with the equipment needed to produce that new vaccine in large quantities.

None of that exists for the new coronavirus, she said. Research that had begun on a vaccine for the SARS virus – which was a coronavirus similar to the current one — petered out shortly after its epidemic did. Without a virus actively menacing the globe, there was no market for private industry to continue developing a vaccine, Nuzzo said.

So, while a vaccine for a new strain of flu could be ready in as little as six to eight months, Nuzzo and other experts have said a vaccine for the new coronavirus could take as long as 18 months. And then companies will need to scale up their capacity to produce that vaccine in large enough quantities to meet global demand.

“It’s a very different timeline to get to immunity than we have with influenza,” she said.

DENVER, CO – MARCH 14: Ralen Johnson is testing samples for COVID-19 at Colorado Department of Public Health and Environment Laboratory Services Division in Denver, Colorado on Saturday. March 14, 2020. (Pool photo by Hyoung Chang/The Denver Post)

Testing for a new virus

Perhaps the biggest hindrance caused by the nation’s and Colorado’s focus on influenza in prior planning has been testing.

Flu tests are plentiful, with results returned quickly, all across the country. Even if they can’t automatically identify new types of flu, they serve as a vital early warning signal to the presence of a dangerous new strain.

“We better know what normal looks like, so when something abnormal happens like a pandemic strain, we can better differentiate,” Nuzzo said.

But screening for the new coronavirus — which required the U.S. Centers for Disease Control and Prevention to develop a whole new test — has been a constant struggle in the United States. Dr. Anthony Fauci, the head of the National Institute of Allergy and Infectious Diseases, has said it was “a failing” for the federal government not to get the test more widely distributed early on.

Neither the state’s nor the federal government’s reports on the Crimson Contagion exercise suggest the training focused much on testing. Colorado’s pandemic plan calls on the state lab, which Bookman also oversees, to increase testing capacity and provide support for other labs to do the same.

But Bookman said the system is not designed for CDPHE’s lab to bear the entire burden of testing in a pandemic.

“It has never been the role of public health to do mass sample collection,” he said. “It’s just never been our job. We’re doing everything we can to rise to the circumstance. … But it’s never been a part of our work at this scale.”

Hospitals have begun to pick up more testing for their own patients, and private labs have begun to gear up to analyze samples from the general public — though widespread testing is still far off. But Bookman said the new challenge has become finding health care workers — and the equipment needed to protect them — who can collect testing samples.

“That is the single biggest bottleneck in the system,” he said.

State workers on March 23, 2020, prepare to distribute medical supplies received from the Strategic National Stockpile for use during the coronavirus pandemic. (Provided by the Colorado Department of Public Health and Environment)

Seeking federal help

Apart from the focus on flu, there are other ways Colorado’s and the nation’s pandemic response plans failed to prepare for the current situation. And the Crimson Contagion exercise laid them bare: A lack of coordination between local, state and federal governments for supplies and funding.

“States experienced multiple challenges requesting resources from the federal government due to a lack of standardized, well-understood, and properly executed resource request processes,” the federal after-action report on the exercise concluded.

Colorado’s after-action report, which CDPHE provided to The Colorado Sun, reveals a similar confusion over requesting aid from the federal government and coordinating local efforts. The process for requesting help from other states was unclear. The report says an understanding of what’s available from the Strategic National Stockpile “needs to be improved.”

“It was clear that resource ordering and sharing is an unfamiliar subject,” Colorado’s report states. “No one was quite sure where to look for statewide resources.”

Colorado has already emptied its state cache of medical supplies to send out to local hospitals and public health agencies, Bookman said. It makes no sense to hold them in a warehouse when they could be distributed now to where they will be needed.

But Bookman said the support from the federal government to replenish those supplies has not arrived — as Colorado competes against other states for resources that are distributed in uneven fashion. According to the state Health Department, Colorado has received about 99,000 N95 masks, 230,000 surgical masks, 43,000 face shields, 43,000 surgical gowns and 108,000 gloves from the Strategic National Stockpile — projected to be enough for about two days’ worth of operations at Colorado hospitals. Bookman said the state’s request was “multiple orders of magnitude greater than what they sent us.”

“We’re working under the assumption that they are going to send us what they can when they can,” he said.

Defenders of the federal government’s response say it is unfair to expect the Strategic National Stockpile to provide for the needs of all 50 states at the same time. It was designed as a stopgap solution in times of local crisis, not a nationwide storehouse.

“The Strategic National Stockpile is not designed to be the sole solution to these problems,” Greg Burel, who directed the stockpile program for more than 12 years, told NBC News.

But that underscores the point that Nuzzo and others are making: State and federal governments may have been prepared for a pandemic — just not this one. And it’s why Bookman says the state and local governments, health care providers and everyday Coloradans must work together to make sure the state can squeeze the most out of what it has available.

“I think what we are learning in the state of Colorado and across the nation today is that a lot of our plans assume there would be surge capacity and assistance coming in from other areas,” Bookman said. “What we are realizing is that when a pandemic hits everybody all at once, those planning assumptions are no longer true.”

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