More than three decades ago, the Pentagon created two pills to ward off a lethal virus infecting boot-camp recruits. But defense officials abandoned the program in 1996 as too expensive. Now recruits are dying, thousands are falling ill, and the military is desperately racing to bring back a vaccine it once owned.

A top Pentagon official called it “a major screw-up,” hobbling U.S. efforts to rapidly deploy troops abroad.

The respiratory virus now infects up to 2,500 service members monthly – a staggering 1 in 10 recruits – in the nation’s eight basic-training centers, an analysis of military health-care records shows.

Since the oral vaccinations stopped, the flu-like germ, adenovirus, is associated with the deaths of at least six recruits, four within the past year, according to military records and internal reports obtained by The Seattle Times.

In addition, hundreds of bed-ridden recruits miss critical training and have to be sent through boot camp again, at a cost of millions of dollars each year. Some are dismissed permanently with medical disabilities.

The virus is expected to kill an additional six to 10 recruits before a vaccine is again available, according to a classified Defense Department briefing this year.

The virus can strike beyond military boundaries as well.

Six children of service members in the Puget Sound area were diagnosed with the virus last winter, according to doctors at Madigan Army Medical Center near Tacoma, Wash.

Most people rebound from the infection within four days, but if untreated, it can quickly turn ferocious, with fever, sore throat and labored breathing leading to severe respiratory problems such as pneumonia and even death.

Adenovirus spreads by cough or touch, thrives in confined places such as overcrowded barracks, and targets those with weakened immune systems. Overstressed recruits, trying to get in shape and adapt to the military, turn out to be ideal incubators for the virus.

Nationally, the virus has killed more than two dozen civilian children and adults in outbreaks in medical facilities in Illinois, Louisiana, Iowa, Tennessee and New York, the federal Centers for Disease Control and Prevention reports.

Military foot-dragging and high turnover of procurement officers have caused the replacement vaccine to fall behind schedule, making pills unavailable until at least 2007, possibly 2009, military health-care records show.

Dr. Margaret Ryan, a commander at the Naval Health Research Center in San Diego and an expert on the virus, calls the vaccine lapse “indefensible.”

Original vaccine manufacturer Wyeth Laboratories warned as early as 1984 that it would stop churning out pills costing $1 each unless defense officials allocated $5 million to repair a deteriorating production plant.

Wyeth executives shuttered the facility in 1996. A military health budget later gave a reason: “suppression of program to pay higher priority items.”

The Pentagon’s unwillingness to spend $5 million on health care is now costing taxpayers tens of millions of dollars to remedy.

In September 2001, plagued by boot-camp outbreaks, defense officials finally agreed to spend $35.4 million to develop a new vaccine through Barr Laboratories of Forest, Va.

Shortly afterward, Assistant Secretary of Defense William Winkenwerder Jr. ordered vaccine efforts accelerated, according to transcripts of a Feb. 19, 2002, meeting at North Island Naval Air Station in San Diego.

“This is one of the most disappointing facts and stories that I’ve learned upon coming into my position,” he said. “I don’t want to cast aspersions on anybody who had responsibility in the past, but to be blunt this is a major screw-up. “

Some military officials questioned the need to continue the program.

Few vaccinations have proved as easy or free of adverse reactions. Recruits swallow two off-white pills, which cause a mild intestinal infection that in turn creates protective antibodies against the two most virulent strains, Type 4 and 7.

Although adenovirus thrives best in barracks, the virus can prosper anywhere. Most people experience at least one attack by age 10 and recover in a few days. The germ is fatal in rare cases, particularly to children or those with weak immune systems.

The military began using the vaccine in 1971 after adenovirus blanketed military bases during the 1950s and ’60s, killing an undisclosed number of troops. The vaccine essentially vanquished the germ, military studies show.

Later, doctors ruefully noted that a newer, younger cadre of Pentagon leaders failed to understand that the latent virus was controlled – not eliminated – and that it could escape once again if vaccine restraints were loosened.

Pentagon funds “were unavailable” for Wyeth in the mid-1990s so the company “was forced to end vaccine production,” said Army epidemiologist Terrence Lee of the U.S. Army Center for Health Promotion and Preventive Medicine at an April 2002 symposium.

Wyeth spokesman Douglas Petkus said the vaccine did not appear to have a “high priority” at the time.

As vaccine production came to a halt in 1996, vaccine stockpiles were rationed to extend partial protection for three more years, with the vaccine being dispensed only between September through March.

After Wyeth’s shutdown, defense officials scouted for a new manufacturer. There were no bidders for a $14.million contract offer. In the interim, the military pushed for better hygiene, such as hand washing, records show.

Other Pentagon officials, particularly in the Air Force, questioned the need to restart a costly vaccine program, according to records at the Army Surgeon General’s Office.

At Lackland Air Force Base in San Antonio, Air Force officials, acting on their own, had quietly stopped giving recruits the pills in 1987. There had been no outbreaks and scant infections since, Air Force commanders assured the Pentagon in April 1997.

As a result, defense officials adopted a wait-and-see strategy. They waited just seven weeks.

On May 22, 1997, a feverish soldier staggered into the medical clinic at Fort Jackson, S.C., the Army’s largest basic-training center. Within months, he was followed by 673 confirmed adenovirus diagnoses of Type 4, peaking at 70 hospitalizations weekly.

The outbreak was quickly detected – and deaths averted – because of the foresight of Dr. Gregory Gray, a supervisor at the Navy’s health-research center in San Diego. He was worried about what would happen when the vaccine was halted and, working in collaboration with others, had established a system to track adenovirus at boot camps.

But the military responded sluggishly after learning of the outbreak. It took seven months to ship the vaccine from its dwindling supply to Fort Jackson as the infection raged, according to records at the Army Surgeon General’s Office. The epidemic stopped once the pills were in use.

Dr. Kevin Russell, a Navy commander at the San Diego center, said, “We saw, as we feared and as we expected, adenovirus rates jump up.” Russell, who works with Ryan, says his research with Marine platoons shows that only half of infected troops seek treatment, suggesting that adenovirus has penetrated the military far deeper than suspected.

Before long, adenovirus struck another boot camp, this time at the Lackland base, starting in October 1999 during its grueling, first-time “Warrior Week.” Over the next eight months, with no pills available, 1,371 cadets ended up flooding the base hospital, Lackland records show.

The adenovirus had irrevocably “found a home in Lackland” after all, Air Force Col. Dana Bradshaw would later acknowledge.

Within three months in 2000, two recruits die of the virus.

It wasn’t long before adenovirus killed a recruit, the first one in 28 years. On May 19, 2000, a healthy 21-year-old man arrived at the Great Lakes Naval Recruit Training Center, just north of Chicago, where up to 15,000 white-clad recruits packed the shoreline installation daily.

The trainee developed a fever June 20 and sought medical treatment and returned to his barracks. When symptoms remained unabated, he revisited the clinic June 23 and was given an antibiotic for suspected bronchitis. On June 24 he was found unconscious in the barracks. He never regained consciousness and died July 3, according to case reports from the CDC.

Within three months, the virus killed another young recruit at Great Lakes. The 18-year-old had gone to the medical clinic three times complaining of respiratory difficulties, and had been given a decongestant and acetaminophen. On Sept. 18, he went back a fourth time, suffering from severe indigestion, severe weakness and a purplish rash on his legs, suggesting hemorrhaging. He died nine hours later, according to CDC records.

At the San Diego Navy research center, Ryan investigated the deaths. Her findings provided a chilling warning: The virus could quickly kill healthy people.

“Therefore, it is quite possible that undetected adenoviral illness contributed to many more recruit deaths – especially those deaths with ill-defined causes or no pathogen identified – after the vaccine was lost,” Ryan wrote this year in the American Journal of Preventive Medicine.

After the two highly publicized Navy deaths, the Institute of Medicine, an independent advisory committee of civilian doctors in Washington, D.C., began to investigate the abandonment of the adenovirus vaccine. In a scathing report, the doctors pointed to seven adenovirus epidemics at bases that could have been prevented had the vaccine been properly funded.

Their November 2000 report said the military’s procurement system proved “incapable” of securing adenovirus vaccine, and its $14.million contract offer was “clearly not sufficient.” It called for “extreme urgency.”

Spurred by the report and the rising infection rates, the Defense Department signed the $35.4.million contract with Barr in September 2001.

However, the vaccine will not be finished until at least 2007, with a “potential push out” date of 2009, Alan Liss, Barr’s senior director of biotechnology, said. Although the new vaccine is a mirror of the old formula, he said the drugmaker still must adhere to a lengthy clinical-trial process.

The military has closely held information about four of the six deaths associated with adenovirus. The Seattle Times learned of the four deaths, each of which occurred in the past year, when it obtained an internal March 31 report by the U.S. Army Medical Research and Materiel Command at Fort Detrick, Md.

“Within the past six months, four military recruits died from suspected adenovirus infection,” the report said. “This accentuates the urgent need to quickly develop the adenovirus vaccines.”

Another report by the Armed Forces Epidemiological Board in February gave scant details about three of the four deaths: the death of a Marine recruit in San Diego on Sept. 3, 2003; the death of an Army recruit at Fort Sill, Okla., on Nov. 3; and the Dec. 3 death of an Army recruit who had just returned home from Fort Leonard Wood, Mo.

When contacted for this story, the military would not provide names of the recruits or information on the fourth death.

At Madigan Army Medical Center near Tacoma, Dr. Andrew Wiesen, chief of epidemiology and disease control, is trying to keep the potentially fatal adenovirus from spreading within his hospital and leapfrogging into the community. He tests all young patients exhibiting respiratory-disease symptoms at Madigan, which sees about 3,000 patients a day.

Wiesen, a lieutenant colonel, detects four to six cases of severe pediatric adenovirus each year, usually in children of current or former service members living in the Fort Lewis area.

By segregating infected patients and treating symptoms aggressively, doctors manage to keep the isolated cases from sparking outbreaks.

Researchers have never linked a major civilian outbreak to exposures by infected military personnel, although some military doctors fear that has been the case, according to records at the Army Surgeon General’s Office.

Military and public-health professionals are deeply concerned about one of the virus’ most deadly strains: Ad7d2. This strain flared up in the civilian world in June 1996, just months after the military began limiting the vaccine pills in boot camps to the winter months. The outbreak killed seven children and infected six others at a pediatric chronic-care facility in Houma, La.

In November 1998, the Ad7d2 strain killed eight children and infected 23 others in a long-term pediatric care center in Chicago.

The Chicago center was just miles away from the Great Lakes naval base that had been hit the year before with an Ad7d2 outbreak that infected 396 recruits, CDC records show.

The germ spread rapidly child to child, carried by nurses who didn’t wash their hands or who had become ill themselves, a CDC investigation found.

In Iowa, four children at a pediatric chronic-care facility died from Ad7d2 in October 2000. Sixteen others were infected.

Gray, who had set up the boot-camp tracking system for the germ, now is spearheading the nation’s most ambitious civilian studies of adenovirus, at the University of Iowa. He has a $2.8.million grant from the National Institute of Allergy and Infectious Diseases to collect adenovirus samples over three years. Doctors at Children’s Hospital & Regional Medical Center in Seattle will submit a proposal to participate in the study.

Gray said he thinks the Ad7d2 strain has become prevalent nationally. The 15-city study targets high-risk populations, including young children, transplant patients and military recruits.

At Madigan, Wiesen suspects the study will confirm that adenovirus is a largely unrecognized civilian problem.

“Nobody routinely tests for adenovirus because it looks like other respiratory diseases,” he said. “If you don’t test, you’ll never know it’s a problem.”