Editor’s note: Since the publication of this story, the Navy has updated the number of sailors separated for COVID-19 vaccine refusal to 1,878. This brings the overall total of separated service members to 8,339.

The new year brought a major victory for thousands of service members who refused the COVID-19 vaccines – and the conservative lawmakers and pundits who backed them. The Pentagon was forced to repeal its coronavirus mandate by a largely-GOP-backed requirement added to the 2023 National Defense Authorization Act, signed into law by President Joe Biden in December. But many troops who balked at taking the shots still face uncertain futures.

The controversy shows how healthcare became a political football, with both the far right and some on the left objecting to mandated COVID vaccinations, mask-wearing, and other government public health responses. It also revealed how COVID disinformation spread and caught fire, stoking deepening mistrust of government among wide segments of American society.

More than 17,000 service members balked at taking the shots, citing safety fears linked to the vaccine’s speedy development and spurred by misinformation about messenger ribonucleic acid technology, as well as concern over fetal cell lines used in formulation and testing. The more the controversy raged in the news, the more troops asked to skip the shots, Military Times reporting found.

While the Pentagon lifted the vaccine mandate as ordered, officials warned that repealing it would affect military readiness, potentially putting service members at risk of serious illness. DoD officials believe the shots worked: Not a single service member has died of COVID-19 since early 2022, when more than 98% of the active duty force had been at least partially vaccinated.

“The Department will continue to promote and encourage COVID-19 vaccination for all Service members,” Austin wrote in the Jan. 10 memo repealing the mandate. “The Department has made COVID-19 vaccination as easy and convenient as possible, resulting in vaccines administered to over two million Service members and 96 percent of the force ― Active and Reserve ― being fully vaccinated.”

The now-lifted mandate’s aftermath is still playing out. Of the 17,000 service members who refused to take the vaccine, roughly half have been discharged and another thousand or so secured exemptions.

Separated troops are eligible to upgrade their discharges, or even come back into service if they want to. At the same time, Pentagon officials are still determining how to treat ― and possibly reprimand ― the remaining 7,000 troops who leaders say did not follow a lawful order.

The mandate’s end put a halt to any adverse actions against currently serving troops who had applied for exemptions, while opening the door for those involuntarily separated to apply to have their characterizations of service changed on their discharge paperwork. What it didn’t do was authorize them to automatically get their jobs back, or furnish any back pay for the time between their discharges and the mandate repeal, though some Republican lawmakers are still pushing for that legislation.

[Troops who refused COVID vaccines still could face punishment]

The Pentagon is also exploring how to handle a small number of still-serving troops who didn’t apply for waivers, but avoided dismissal during the vaccine mandate, meaning they refused a lawful order to get vaccinated.

“It’s very important that our service members follow orders when they are lawful, and there are thousands that did not,” Gil Cisneros, the Pentagon’s personnel boss, told members of the House Armed Services Committee in February. “The services are going through a process to review those cases to make a determination what needs to be done.”

In addition to separating more than 8,000 troops, the services granted roughly 1,200 permanent and temporary exemptions for the vaccine, whether for administrative reasons, including religious objection, or medical concerns.

The number of waivers was unprecedented. In August 2021, before the Pentagon first announced its forthcoming mandate, vaccine exemptions were relatively rare, and mostly given for past allergic reactions or for temporary situations, like pregnancy or an impending separation from service.

Involuntary discharges for separation were even more rare, and hadn’t happened in any significant way since the early 2000s, when the widespread side effects of the anthrax vaccine prompted a groundswell of troops to refuse it.

By the numbers

From late 2021 to early 2023, the military services discharged roughly 8,300 troops from the active and reserve components, most of whom received general discharges and were welcome to serve in uniform again if they got vaccinated.

The Air Force Department discharged a total of 834 personnel in 2022, before a July court order halted any further separations for those whose waivers had been rejected, according to data provided to Military Times.

As of Jan. 10, when the mandate repeal came down, the Air Force had more than 3,100 religious accommodation requests pending, with another 30 appeals waiting for department approval.

Overall, the Air Force approved 389 religious, administrative and medical exemptions for active duty troops.

The Army discharged 1,881 soldiers before Jan. 10, according to service data, while granting 191 exemptions out of 10,699 requests.

In the end, the Navy granted 168 medical exemptions, 153 of them temporary, as well as 50 religious accommodations. Data as of Jan. 9, the day before the mandate repeal, show 1,878 sailors were discharged.

In general, temporary medical exemptions can include while a service member is pregnant or breastfeeding, for example, or undergoing a medical issue or treatment that might negatively react with a vaccine.

[Services may be improperly denying vaccine religious waivers, IG says]

The Marine Corps tracks its data differently from the other services, spokesman Capt. Ryan Bruce told Military Times. The total number of waiver applications was not available, he said, but as of Jan. 5, the Corps had approved 420 administrative or medical exemptions to COVID-19 vaccination.

The most recent number for religious accommodations was 23, as of Nov. 23, he added.

In total, the service involuntarily separated 3,746 Marines before the mandate’s repeal.

Controversy stokes vaccine hesitancy

The COVID-19 pandemic and the subsequent development of a vaccine presented a unique situation for the military, an institution known for requiring a battery of inoculations, all of which can be given during initial medical workups as soon as recruits ship to training.

Before COVID, the anthrax vaccine had caused much controversy in the early 2000s, resulting in involuntary discharges for refusals and pushing DoD to rethink how it decides to make a vaccine mandatory.

In that spirit, the Pentagon rolled out its COVID-19 vaccination program on a voluntary basis in December 2020, delaying making it mandatory until the Food and Drug Administration granted fully licensed the Pfizer version of the vaccine in August 2021.

But by that point, COVID-19 vaccination had opened a fierce partisan divide, with many conservative politicos and influencers railing against it.

Soon after each of the military services published their mandatory vaccination policies, lawsuits sprang up, from troops accusing the services of wrongfully denying religious accommodation requests, or arguing that applying for one was futile because messaging from the chain of command made it clear they wouldn’t be approved.

[Air Force vaccine case will remain a class-action, appeals court rules]

Post-mandate, the numbers suggest that the vaccine awareness brought on by the fierce ideological debate over the COVID-19 vaccine might have increased overall anti-vaccine sentiment across the services.

In the Air Force, overall vaccine exemptions went up during the 18 months between the COVID-19 vaccine mandate’s announcement and repeal. In August 2021, the Air Force reported 336 total administrative vaccine waivers on file. As of Jan. 3, according to service data, that number has more than doubled: 12 in the active component, 742 in the Air National Guard and 62 in the Air Force Reserve.

Because each of the services has taken a different tack when tracking vaccine waiver requests and exemptions, it’s difficult to make apples-to-apples comparisons to the numbers before the COVID-19 vaccine mandate.

In August 2021, the Army reported 106 overall administrative exemptions, which included religious exemptions, as well as temporary waivers for soldiers on temporary duty, in the middle of a permanent change-of-station move or preparing to leave service in the next 6 months.

Post-mandate, now tracking religious waivers specifically, the Army is currently assessing five applications for other vaccines, none of them so far approved.

The Navy and Marine Corps reported in summer 2021 that they did not have any current religious accommodations, and hadn’t granted one in nearly a decade.

Currently, according to Navy data, there are no pending religious waivers for vaccines other than COVID. In the Marine Corps, Bruce said, no other religious waivers have been granted in the past two and a half years.

And, Navy spokeswoman Gloria Kwizera told Military Times, the service doesn’t have a process for requesting a permanent medical waiver for other vaccines.

“Navy Medicine does not track the number of Navy service members who request permanent medical exemption from a non-COVID-19 vaccine from their provider,” she said.

The Navy’s Bureau of Medicine and Surgery is also responsible for the Marine Corps.

Each of the military departments is responsible for governing its own vaccine exemption process, so it’s difficult to compare numbers of each type of waiver across the services.

Why they said “no”

While anti-vaccine sentiment has grown in the U.S. in recent years, reflected in localized outbreaks of polio and measles, Americans declined the COVID-19 vaccine at much higher rates than any other inoculation, members of the military included.

Historically, the kind of alternative beliefs, like anti-vaccine Jehovah’s Witnesses, that fostered opposition to vaccination were rarely found in the same demographics of people who were interested in military service, Katherine Kuzminski, a senior fellow at the Center for a New American Security, told Military Times on Feb. 8.

But as some right-wing factions take up the anti-vaccine cause, there is a question of whether they’ll bleed into more mainstream conservative values, and whether that will in turn affect a historically conservative-leaning military population.

“People who’ve been vaccine-aware have fallen, really, on the extreme,” she said.

[Is the military too ‘woke’ to recruit?]

Emails from Military Times readers overwhelmingly make the distinction between the COVID-19 vaccine and previous inoculations that have been around longer and had longer testing periods before FDA approval.

But the services don’t have a waiver category for “I’m just not sure the science is there,” so most exemption requests defaulted to religious reasons.

Another major point of contention for readers was that the Pfizer, Moderna and Johnson and Johnson vaccines were either made with or tested on human stem cells descended from fetal tissue, which is commonly procured after abortion procedures. But Catholic leaders have long said the “sin” is too far removed from the vaccine itself to violate any religious beliefs.

“The Pfizer and Moderna COVID-19 vaccines were tested using an abortion-derived cell line,” Archbishop for the military services Timothy P. Broglio said in an October 2021 statement, explaining that simply testing with those cells is not sinful, whereas he states that the Johnson & Johnson vaccine “was developed, tested, and is produced, with abortion-derived cell lines”, which makes it more problematic.

“If it were the only vaccine available, it would be morally permissible, but the faithful Catholic is to make known his or her preference for a more morally acceptable treatment,” the archbishop said.

But there are other mandatory vaccines that use these same fetal-tissue-derived cell lines in their development, including chickenpox and measles-mumps-rubella (MMR), all of which most troops are required to take as part of basic training if they don’t have their vaccine record handy upon enlistment.

“I did see several soldiers who claimed ‘religious exemptions’ to the COVID-19 vaccines due to the fetal cell lines used in research,” wrote one reader, an Army sergeant and medic stationed at Fort Riley, Kansas.

“Most of these soldiers had no problem taking the MMR vaccine (which also uses fetal cell lines) in basic training so I found their newfound religion unconvincing, especially since I never saw them at chapel,” he told Military Times in an email, requesting anonymity out of concern for career repercussions.

Asked whether new vaccine awareness had prompted existing troops to seek waivers for vaccines other than COVID-19, only one Military Times reader said he had considered it.

“I do have strong religious beliefs that I think are consistent, demonstrable and should qualify. To be honest I feel the burden of having gone against them to save my career,” an Air Force captain stationed at Joint Base San Antonio told Military Times, who also requested anonymity out of concern for career repercussions.

Given the choice, the captain said he wouldn’t get the annual flu vaccine for personal reasons, but he did not specify which vaccines he would consider a waiver for and why.

“Part of the problem is that these requests, like conscientious objector requests, do not permit a gradation of understanding,” he said. So, to try to qualify under the exemption terms, troops often cited strongly held beliefs that stemmed from a personal creed but weren’t demonstrably supported by any religious tradition or guidance from religious leaders.

“Those who are opposing the vaccine didn’t do themselves any favors by trying to frame it in religious freedom language, when it actually was [that] there may have been some who were opposed to the the process by which the vaccines were developed, or they were opposed to the political process that developed the vaccine at the speed that it did,” Kuzminksi said. “There isn’t a clear avenue for them to register that complaint.”

This lines up with the many lawsuits filed against DoD by service members who opposed the vaccine, including those who sought religious exemptions.

[Could the Supreme Court strike down the military’s vaccination mandate?]

While some based their arguments on opposition to abortion, there were many complainants who cited more ambiguous beliefs, including concerns about the messenger ribonucleic acid technology in the Pfizer and Moderna products, or about what they put in their bodies in general.

“Plaintiffs’ sincerely held religious beliefs that their bodies are temples of the Holy Spirit and that they are to glorify God with their bodies lays the foundation for everything they do, consume, or inject into their bodies,” read one lawsuit, Navy SEAL 1-26 vs. Biden , filed in Florida. “From this foundation, they make studied and reasonable decisions about what is good and what is not good or may not be good for their bodies.”

Military leaders hoped they’d solved the objection problem when the Pentagon approved the use of alternative vaccine Novavax. But DoD data shows just 5,000 troops completed their vaccine series in the three months following Novavax emergency use authorization. For comparison, more than 300,000 troops were vaccinated in the three months prior to Novavax’s release.

Culture Clash

In the end, troop objections may have risen because of the Pentagon’s about face in vaccine policy, Kuzminksi said. Because the COVID-19 vaccine was voluntary for the first nine months of its availability, service members had the rare option to make an independent medical decision. The mandate took that choice away.

The result – that a small but vocal minority of troops and their allies on Capitol Hill were able to extinguish the Pentagon’s vaccine mandate – is sure to trigger similar attacks on other controversial public health or social policies.

Members of Congress have already targeted diversity, equity and inclusion programs, as well as Pentagon efforts to combat violent extremist activity and sentiment. A Senate Armed Services Committee report from July argued that “spending additional time and resources to combat exceptionally rare instances of extremism in the military is an inappropriate use of taxpayer funds,” and should be discontinued immediately.

It’s a political counteroffensive that started, or picked up momentum, in the early days of Defense Secretary Lloyd Austin’s tenure, when he ordered an anti-extremism stand-down and directed the department to beef up its screening, education and research efforts to both prevent extremism in the ranks and get a better idea of its prevalence.

In recent weeks, the move to equalize access to reproductive health care has also sparked the ire of Republicans in Congress.

[Troops can take three weeks off to travel for abortions, IVF treatment]

Following an announcement that DoD would cover travel costs for troops who have to travel out of state for a self-paid abortion, a group of senators sent a letter to the Pentagon demanding information on other procedures covered under that kind of policy, as well as whether anti-abortion commanders will be reprimanded if they attempt to deny leave under the new policy.

Congress is well within its powers to pass legislation hemming in Pentagon policy, but partisan squabbles have the potential to keep undermining the very definition of a lawful order, by empowering individual troops to push back against them based on personal belief, according to Kuzminski.

“That’s part of your oath, right? When you join, you’re setting aside your individual preferences or concerns in order to follow a lawful order,” she said. But with the COVID-19 mandate, “individuals who push back on a lawful order fundamentally saw that it worked.”

Meghann Myers is the Pentagon bureau chief at Military Times. She covers operations, policy, personnel, leadership and other issues affecting service members.

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