The Pentagon held an exercise for a flu pandemic 14 years ago. Here’s what was learned.

Sean D. Naylor
·National Security Correspondent

More than a decade before the coronavirus swept across the globe filling hospitals and roiling economies, the Pentagon quietly conducted an exercise to see how its secret bunker system built in case of nuclear war would stand up to a flu pandemic.

The 2006 exercise revealed just how hard it is to keep infected personnel out of a closed facility. It also underlined the limitations of massive Cold War-era bunker systems, especially for threats like a pandemic.

Built in the 1950s as an “underground Pentagon” where senior Defense Department officials and hundreds of their staffers could be moved quickly in the event of a nuclear war, Raven Rock has also served as an alternate defense headquarters in the face of what the government calls “all hazards,” a term that that has come to encompass a wide range of natural disasters, including pandemics.

The Pentagon. (Getty Images)
The Pentagon. (Getty Images)

In 2006, as the H5N1 “bird flu” virus was spreading around the world, the Defense Department held an exercise that tested its ability to continue operations from Raven Rock in the event of a pandemic, according to retired Army Col. Daniel Roper, who commanded Raven Rock Mountain Complex, sometimes known as “Site R,” from 2005 to 2007.

Raven Rock is one of several Cold War-era bunkers built to ensure continuity of government operations in case of nuclear war — there are similar facilities for other parts of government, such as Mt. Weather in Virginia, for the executive branch. Over the years, these facilities have been incorporated into the Pentagon’s plans for how to respond to other threats.

But even by 2006, it was increasingly clear that the hardened, deeply buried bunker-type bases like Raven Rock were of “diminishing value,” according to Paul McHale, a senior Pentagon official from that time.

“Any number of nation states have now developed capabilities that could potentially place in doubt the survivability of a hardened site,” he said. “That kind of facility was rapidly becoming an anachronism.”

In the case of a pandemic, “a hardened site would not, at least in my judgment, have been the proper choice” of a location to relocate key Pentagon personnel, said McHale. He added that his recommendation would be to move senior leaders and staff to a major military installation as far from the pandemic as possible, where they could be socially isolated.

In addition to “distancing from the pandemic outbreak,” a remote command-and-control site of that sort requires access to sufficient medical care and logistics support to sustain the newly arrived personnel indefinitely, “and most especially secure and reliable communications capabilities that could be quickly established at that site,” he said.

The 2006 exercise, which has not been previously reported, involved simulating a pandemic that would require moving personnel quickly into Raven Rock. “It was a fairly significant exercise,” Roper said, adding that the bird flu “was probably the most emergent challenge” during his time in command. “At some point there was an understanding that OK, this is a potential hazard, so we can’t wish it away,” he said. “Everybody was trying to figure out: How do we proactively prepare for it.”

The exercise took place the same year that the Pentaton issued a formal plan for dealing with pandemic flu. Formally titled “Department of Defense Implementation Plan for Pandemic Influenza,” the 87-page document was issued by the office headed by McHale, who was the assistant secretary of defense for homeland defense at the time. “We looked at a number of potential pandemic events,” McHale said. “Obviously we would have paid close attention to continuity of operations [and] continuity of government in the context of a pandemic outbreak.”

One of the major challenges of the mock pandemic exercise at Raven Rock was screening personnel quickly, while also ensuring no infected individuals enter a complex designed against nuclear attack, rather than mass illness. “The place wasn’t built for that,” Roper said. “Not to say it doesn’t have the capability, but that probably was not envisioned when they started bending metal and breaking rock.”

McHale said he did not recall the specific 2006 exercise at Raven Rock, but added that “the ability to establish a prescreening entry point into a given remote command-and-control center would need to have a degree of flexibility … that would be hard to put in place at a fixed and hardened site.”

After taking advice from a variety of experts and developing a set of procedures, the Raven Rock team screened a group of newly arrived personnel who were not routinely stationed at Raven Rock, to simulate what would have to be done amidst a crisis. “It was a dress rehearsal for what could be something larger,” Roper said.

But unlike the threat of nuclear attack, in which the key is to move people as quickly as possible into a bunker complex where they are considered relatively safe, in the case of a pandemic, it is essential to ensure the people entering the complex are not already infected. “The challenge is: How do you make it so the firemen aren’t burning your house down,” said Roper.

Unlike other parts of the government, the key Pentagon personnel who are supposed to move to Raven Rock can’t do their work from home if they feel sick. They also can’t necessarily be trusted to inform their chains of command that they feel ill. “They want to do their jobs when the nation needs it the most,” Roper said. “People are just going to say, ‘To hell with it, I’ve never missed a day of work.’”

But screening personnel entering the facility also presents complications, especially when the test results aren’t immediately available, according to Roper. “For the results of that to be valid, they essentially need to be quarantined from that point forward,” he said. “It’s not like you’ve just been vaccinated.”

Keeping them isolated isn’t easy: Raven Rock is 62 miles from the Washington area, and Pentagon personnel who are tested can’t return home while awaiting results, nor can they enter Raven Rock, or even be allowed to mingle with others who will enter the facility because they could infect others.

Therein lies the dilemma: In a crisis you want to move people quickly, but the faster the Defense Department tries to move personnel into Raven Rock or any similar facility, the more trade-offs have to be made between speed and the risks of the virus getting into Raven Rock or similar facilities, according to Roper. “You may be contaminating your own well, so to speak,” he said.

During the 2006 exercise, no sick individuals made it into the bunker complex, but in real life things might not work as efficiently, according to Roper. The facility’s personnel need to be on their guard because “no test is a hundred percent foolproof,” he cautioned.

Roper declined to speak in detail about Raven Rock’s medical facilities and whether they are equipped to handle a coronavirus outbreak. “Any place that’s got medical facilities probably isn’t ideally configured to deal with this,” he said. “They were built for different purposes.”

Making the screening, testing and entry process run anything close to smoothly will require a lot of trained personnel, and people with the right skills are likely to be in short supply. according to Roper. “All things being equal, you’d love to have an epidemiologist standing there,” he said. “But guess what, we’re probably going to run out of those guys pretty soon.”

Another challenge the Defense Department faces during a pandemic is deciding whether and when to start moving people to Raven Rock and other continuity-of-government sites. Unlike a military crisis, it may not be clear what should trigger that decision during the gradual spread of a disease, according to Roper.

A pandemic is “more complex,” he said, because no such “explicit event” has occurred. “There weren’t two ships colliding in the South China Sea or it wasn’t an aircraft accident,” he added. “It becomes deliberate decision making on when we need to up our game.”

“There is no break point that is objectively defined by the pandemic outbreak,” McHale agreed. “It’s really an informed judgment call on the part of the secretary of defense.”

Even if the Pentagon is fully functional at a given point during the pandemic, “prudent planning would require an assessment of whether or not the arc of the threat produced doubt as to the functionality of the department two, three or four weeks into the future,” he said. That analysis would have to consider whether critical capabilities would be degraded “by either the illness of the workforce or the likelihood that a limited number of personnel within the workforce might continue to spread the disease through and among the senior leaders.”

At midnight on Sunday, Defense Secretary Mark Esper raised the health protection condition level at the Pentagon to “bravo,” which signifies increased community transition. It is not clear whether any particular level would trigger an exodus of senior leaders and staff to Raven Rock or elsewhere. A Defense Department spokesperson did not respond to multiple emails seeking comment.

To date, the Defense Department has not commented publicly on any relocations plans, but in a press briefing Monday, Pentagon spokesperson Jonathan Hoffman said that Defense Secretary Mark Esper and Deputy Secretary David Norquist would, effective immediately, be “physically separated" from each other. "We are attempting to put ... a bubble around the two of them,” Hoffman said. “They and their staffs will only interact via teleconference. We’re screening people that are entering the secretary’s suite and limiting the number of people who have access as well.”

The 2006 bird flu virus killed untold thousands of birds but only a few hundred people because it was not very contagious between humans. By contrast, the coronavirus had already killed more than 6,700 people by Monday.

At the time of the Raven Rock exercise, the bird flu virus “wasn’t fully understood,” Roper said. However, he added, with reference to the coronavirus threat, “I think it was understood better than what we’re looking at right now.”

The question now — 14 years after that exercise — is whether the Pentagon has been properly preparing for the type of pandemic occurring now.

“I’m confident there are plans in place,” Roper said, based on his experience at Raven Rock. “I’m less confident that the plans can be exercised on a moment’s notice effectively.”

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