THE COVID-19 PANDEMIC is plaguing the American military. The virus has spread in aircraft carriers and infected Marines in basic training in South Carolina, as well as airmen in basic training in San Antonio. As cases have continued to rise in military communities across the nation, the Department of Defense has asked bases to stop publicly reporting their individual numbers, citing security threats.

There have been several reports of a “readiness crisis” and doubts that the military can protect its own, including a Los Angeles Times article suggesting that the Pentagon is struggling to contain infections in the active duty ranks while also helping civilians in hard-hit states and cities. As of May 5, nearly 5,000 military personnel had tested positive for Covid-19. While the Department of Defense plans to test all of its members by this summer, in a press briefing last month, Thomas McCaffery, the Assistant Secretary of Defense for Health Affairs, acknowledged that it is fair to assume that there are many more service members who have the virus but have not been tested thus far.

As a result, the military has been unable to maintain some of its core activities. The Army stopped taking new recruits at basic training for two weeks before resuming training “at reduced capacity.” Meanwhile, the Marine Corps closed the Parris Island Boot Camp to new recruits on March 30, before reopening three weeks later. The Department of Defense also delayed all military moves, halted deployments to Afghanistan, and delayed the return of troops currently deployed there. Some returning troops are faced with quarantines in under-resourced facilities.

On April 27, 10 Senate Democrats wrote to Secretary of Defense Mark Esper, arguing that the Department of Defense’s “slow and disjointed response put service members at risk and undermined readiness”.

The reduction in operations “is becoming a big issue,” said Mark Cancian, a senior adviser for the International Security Program at the Center for Strategic and International Studies (CSIS) in Washington D.C..

The military wasn’t always in such a vulnerable position. It has a long history of success in confronting infectious disease, dating back to the Revolutionary War, when George Washington inoculated his army against smallpox because his troops were more susceptible to the disease than the British. In fact, from the military’s earliest days its doctors have led research into infectious disease to keep its personnel healthy and prepared to defend the country.

But today, with better vaccinations and other health measures in place, the assumption has become that infectious diseases have been brought under control. As a result, preventive measures in military medicine related to pandemic response have not been “forefront in most folks’ minds,” said Thomas Crabtree, a retired Army colonel and surgeon who is the group medical director for AMI, a company specializing in delivering health care solutions in remote and challenging environments. Instead, in 2017 Congress outlined a plan to eliminate about 18,000 medical positions and refocus military medicine on the so-called “trauma mission” — that is, treating burns and combat injuries from conflicts in places like Afghanistan and Iraq.

Yet as Covid-19 sweeps through the various branches, some military experts are rethinking that strategy, with the medical corps struggling to keep its active duty troops healthy while providing assistance to civilians.

“Today’s crisis should be a wake-up call to rethink any effort to downsize military health care,” wrote retired Air Force Lt. Gen. Orville Wright and retired Air Force colonel Keith Zuegel in a recent opinion piece in the Military Times. “Our nation has been caught ill-prepared for this pandemic. We lack both ready stockpiles of critical equipment and trained personnel to help respond.”

“Imprudent cuts to military health care,” the authors noted later, “pose risks that reach far beyond the military and include the nation’s greater health system.”

INFECTIOUS DISEASE HAS always been a risk within the close quarters of the military rank and file. Smallpox was especially grievous during the Revolutionary War, and for every soldier who died of combat wounds during the Civil War, two more died of typhoid and other infectious diseases. “Armies are notorious petri dishes for disease outbreaks,” said Carol Byerly, a historian of military medicine and author of the “Fever of War,” a book about the influenza pandemic that spread across the globe and swept through American military camps during World War I.

The 1918 influenza pandemic was particularly traumatic for medical officers because “they couldn’t save the lives of thousands of the healthiest people in the country — young soldiers, Byerly said. “They just failed, and they couldn’t deal with it.”

American combat deaths in World War I totaled 53,402, but about 45,000 American soldiers died of the flu and related pneumonia by the end of 1918. The commanding officer of one training camp, Byerly said, killed himself after 500 young men died of influenza in one day. In all, more than 675,000 Americans (civilians and military) died of the flu in 1918.

In an effort to prevent future catastrophic infections, medical officers set up high-level infectious disease committees during World War II to monitor outbreaks. Military scientists led the way in infectious disease research and developed the first flu vaccine in 1943.

At the same time, another disease emerged as a major health risk: “Malaria almost stopped the war in the Pacific,” Byerly said. General Douglas MacArthur, realizing that he would not be able to fight a war under such a threat, briefly stopped all operations until military scientists could get an antimalaria program going.

Virtually all antimalarial drugs currently used in civilian medicine came from research during World War II at the Walter Reed Army Institute of Research. Walter Reed, after whom the national military medical center is named, was a military physician who identified the vector for yellow fever, which was a devastating problem for American troops during the Spanish American war in 1898.

“The U.S. military has this proud tradition of focus on infectious diseases,” said Dean Winslow, a retired Air Force colonel and surgeon and current professor of medicine at Stanford University.

IN RECENT YEARS, the Military Infectious Diseases Research Program has been in charge of developing vaccines and drugs for infectious illnesses likely to impact military operations. Most of this work is carried out at the Walter Reed Army Institute of Research, the Navy Medical Research Center, and the Army Medical Research Institute of Infectious Disease. Yet even as research continues today, critics have noted that preparation for responding to pandemics has not been prioritized by the current administration.

The military has dealt with epidemics in recent decades, although none became pandemics. In 2003, during the SARS outbreak, the commander of U.S. forces based in Korea quickly recognized the threat and formed a crisis action team that implemented health surveillance, screening, contact tracing, and quarantine for suspected cases. As a result, not a single case emerged among U.S. military personnel in Korea. More recently, the U.S. military deployed to West Africa in 2014 in response to the Ebola epidemic to help establish treatment units, increase laboratory testing capacity, and train health care workers.

Nonetheless, experts say, the military is not designed to respond to a national pandemic, a fact that is not always well understood by planners responding to natural disasters. It is a common assumption that “if you have problems and you don’t have capacity, you can call in the military and they’ve got the capacity to do anything anywhere in unlimited numbers,” said Tom Cullison, a retired Navy orthopedic surgeon and rear admiral who served as deputy surgeon general of the Navy. In fact, “the military is designed for combat operations overseas. They have many plans and concept plans to do this and the the size of the various parts of the military, including the health part of it, is based on that. And there’s a finite capacity there.”

The Army and Air Force reserves have been essential to the country’s response to Covid-19, but leveraging them often means taking medical workers out of one community to send them to another; the total capacity remains limited.

So even as Esper tried to reassure the public that the military medical system is up to the dual tasks, he also tempered expectations about its capacity. At a town hall meeting on March 24, Esper said that he anticipated that the military medical facilities could face shortages with personal protective equipment “like everybody else.” In addition, the field hospitals are “geared toward treating trauma patients” and not “supporting persons with infectious diseases,” Esper told NPR on March 25.

That capacity was already in the process of being reduced in 2017, when Congress mandated sweeping reforms intended to do two things: bring all military medical facilities (Army, Air Force, and Navy) under one centralized administrative structure — the Defense Health Agency — and improve medical “readiness” specifically to treat combat trauma, while starting to outsource non-trauma care to civilian facilities.

The restructuring is anticipated to eliminate an estimated 18,000 military medical jobs. Even the Uniformed Services University, which graduated doctors and nurses early this year to send them to assist in hospital ships and field hospitals is threatened by the cuts. Congress has put a pause on those cuts for now, but the plan remains.