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WASHINGTON — A federal judge on Wednesday lifted the temporary injunction he imposed Dec. 22 that banned the Pentagon from forcing all servicemembers to get the anthrax vaccine.

U.S. District Court Judge Emmet Sullivan’s reversal of his own order paves the way for the Pentagon to resume inoculating troops deployed to high risk areas like Iraq, Afghanistan and South Korea.

However, the injunction remains in place for the six anonymous “John Does” who filed the lawsuit in May seeking reprieve from a vaccine they said is unsafe and unapproved by the Food and Drug Administration.

Pentagon officials did not know by press deadline if or when they would resume vaccinating troops. “We’re aware of the ruling. That’s all I can say at this point,” spokesman James Turner said.

Sullivan lifted the injunction because the FDA, the agency licensing the vaccine, issued a formal rule last stating the 1970-approved vaccine is safe, effective and guards against all forms of anthrax.

Two weeks ago, Sullivan ruled he saw no proof in the government’s argument the FDA approved the vaccine to guard against inhalation anthrax, thus making it an investigative drug.

On Wednesday, while siding with the government to lift the ban, Sullivan remarked from the bench he found last week’s FDA rule “highly suspicious,” coming on the heels of his injunction. The vaccine’s safeness and effectiveness has been challenged for years in court, he said, and in spite of countless administrative hearings and battles, he questioned the rule’s timing.

“Only after the issuance of an injunction, up pops a federal rule” supporting the government’s position, a skeptical Sullivan told lawyer Shannen Coffin, a Justice Department attorney representing the Pentagon. “And you’re telling me it’s coincidental.”

“I’d stand on a stack of Bibles and tell you it’s coincidental,” Coffin told Sullivan.

“That’s an amazing coincidence,” Sullivan rebutted.

A few days after Sullivan’s injunction, the Pentagon halted its vaccination program altogether while lawyers fought the battle in court. According to Coffin, the stoppage meant roughly 1,000 troops a day were sent, unvaccinated, to the unspecified high risk countries. “Every day [the injunction is in place] is additional harm,” Coffin argued.

Mark Zaid, representing the six anonymous plaintiffs, told the judge he plans to continue the fight to stop the vaccine program; first arguing against the FDA’s rule that the vaccine is safe, and also that the Pentagon has violated the process by giving vaccines to some troops out of sequence, violating the FDA licensing guidelines. Both sides are to issue next week a proposal to Sullivan outlining the best future action.

The suit that spurred Sullivan’s initial ruling was filed March 18.

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