The marching orders from the Biden administration in November had seemed clear — large employers were to get their workers fully vaccinated by early next year, or make sure the workers were tested weekly. But a little more than a month later, the Labor Department's vaccine rule has been swept into confusion and uncertainty by legal battles, shifting deadlines and rising COVID case counts that throw the very definition of fully vaccinated into question.

The spread of the highly transmissible omicron variant has seemingly bolstered the government's argument, at the heart of its legal battle over the rule, that the virus remains a grave threat to workers. But the recent surge in cases has raised the issue of whether the government will take its requirements further — even as the original rule remains contentious — and ask employers to mandate booster shots, too. The country's testing capacity has also been strained, adding to concerns companies will be unable to meet the testing requirements.

"My clients are totally confused as, quite frankly, am I," Erin McLaughlin, a labor and employment lawyer at Buchanan, Ingersoll & Rooney, said Saturday. "My sense is that there are a lot of employers scrambling to try and put their mandate programs in place."

No company has been spared the whirlwind of changes in the last week, set off by the spike in COVID cases that have, in some instances, cut into their workforces. Then on Friday, an appeals court lifted the legal block on the vaccine rule, although appeals to the ruling were immediately filed, leaving the rule's legal status up in the air.

On Saturday, hours after the appeals court ruling, the Labor Department's Occupational Safety and Health Administration urged employers to start working to get in compliance. But OSHA gave employers leeway, pushing back full enforcement of the rule until February, recognizing that for all its best intentions the rule's rollout has been muddled.

For those struggling to meet OSHA's standards because of testing shortages, the Labor Department said Sunday that it would "consider refraining from enforcement" if the employer has shown a good-faith effort to comply.

The reaction of companies has been muddled as well. Over the weekend, some took the first steps in developing testing programs. Others remained in wait-and-see mode. And some employers went even further than what the government has so far required by mandating boosters, spurred by fears over the spread of omicron.

Adding a layer of confusion, many states and cities have created their own vaccine rules — some more stringent than the federal government's, as in New York City, where an option to test out of vaccine requirements is not allowed, while some, like Florida, have sought to undermine OSHA's rule. There is also the question of whether companies will eventually be required to mandate boosters, which would require accommodating the six-month delay between the second and third shots.

Anthony Capone, president of the technology and health care company DocGo, which sets up COVID testing programs for employers, said he had gotten a rush of inquiries from companies this weekend that are scrambling to set up their testing programs. DocGo has roughly tripled the number of daily COVID tests it conducts in the last few weeks. Capone added that he and many of the employers he works with are anticipating resistance if they mandate boosters.

"You can't really mandate booster shots yet," he said. "It hasn't been signed off on by any federal agency."

JPMorgan Chase, whose decision to require vaccines is complicated by its sprawling retail operations across the United States, declined to comment on how the court's most recent decision, along with the recent spike in cases, affects any plans to mandate vaccines. But the bank on Friday told its American employees who do not work in bank branches that "each group should assess who needs to come into the office, work priorities and who should revert to working from home on a more regular basis over the next few weeks."

Walmart, which has mandated vaccines for mainly its corporate staff, also did not have any comment on broadening that requirement. Only 66% of its roughly 1.6 million U.S. employees are vaccinated, according to data compiled by the Shift Project at the Kennedy School of Government at Harvard University.

Legal questions about the OSHA rule are far from resolved. Immediately after the U.S. District Court of Appeals for the 6th Circuit ruled Friday, several of the many plaintiffs who have challenged that rule asked the Supreme Court to intervene as part of its "emergency" docket. Appeals from the 6th Circuit are assigned for review by Justice Brett Kavanaugh, who under Supreme Court rules could in theory make a decision on his own but is more likely to refer the matter to the full Supreme Court. With the Labor Department now delaying full enforcement of its rule until Feb. 9, the justices have several weeks to ask for abbreviated briefings if they want them.

"Things are going back and forth literally in a matter of hours," said Sydney Heimbrock, an adviser on industry and government issues at Qualtrics, who works with hundreds of clients on using the company's software to track employee vaccination status. "The confusion stems from the on-again-off-again, is it a rule or isn't it a rule? The litigations, appeals, reversing decisions and making decisions."

Even the spread of omicron has not changed the position of some of the vaccine rule's most ardent opponents. The National Retail Federation, one of the trade groups challenging the administration's vaccine rule, is among those that have filed a petition with the Supreme Court. The group is in favor of vaccinations but has pushed for companies to get more time to carry out mandates. Still, even as it fights the administration's rule, the federation is also holding twice-weekly calls with members to compare notes on how to carry it out.

"There's no question that the increased number of variants like omicron certainly don't make it less dangerous," said Stephanie Martz, the group's chief administrative officer and general counsel. "The legitimate, remaining question is, is this inherent to the workplace?"

And employers face yet another uncertainty: Should they mandate boosters? And will they be required to?

The Labor Department said Sunday that its rule does not currently include booster shots, although it strongly encourages them. But the Centers for Disease Control and Prevention could change its definition of what it means to be fully vaccinated. Some state governments, including New York, have already indicated they plan to make the change.

That may take time, though, given the political considerations in messaging about boosters, affecting everything from holiday travel to the continued effort to increase overall vaccination rates. And some employers are not waiting for either the courts or public health officials. Just as the delta wave spurred the first round of vaccine mandates, the omicron variant has similarly pushed some employers to move ahead of the requirements.

The investment bank Jefferies Financial Group told employees Dec. 8 that they had to get booster shots by the end of January after sending its more than 4,000 employees to work from home as cases jumped.

"As has been the case throughout the pandemic, we are trying our best to keep us all ahead of the curve," the Jefferies' CEO, Rich Handler, and president, Brian Friedman, wrote in a memo to staff Saturday, adding that they believed health authorities would soon consider only people who have gotten boosters to be fully immunized.

But for companies with employees who may have higher levels of vaccine hesitancy — or human resources departments exhausted from dealing with a deluge of exemption requests — the process may begin more slowly. And it may only go forward if required.

United Airlines, one of the first to mandate vaccines, has started an "education campaign" on booster shots. Tyson Foods has begun to offer boosters in its offices and some production facilities. And Goldman Sachs has been providing boosters at its on-site health centers for months.

"A lot of companies are having enough of a hard time mandating the vaccine at all," said Douglas Brayley, an employment lawyer at Ropes & Gray. "And so I wonder if there's some reluctance to go back to people who they already had to cajole into getting the vaccine, 'Oh, and by the way, please get one more shot.'"

Other businesses said that while they had moved more rapidly than OSHA in initially mandating vaccines, they are more open to awaiting government guidance on third shots.

"As a company, we try to follow what we see in the science and evidence, and we have sometimes been more aggressive than what the government has mandated," said April Koh, founder and CEO of the mental health company Spring Health, which mandated vaccines for its 350 employees in August.

Spring Health's office is now closed, because of omicron's spread, but Koh said as she weighs whether or when to require boosters, it could help to have the validation of government guidance. "We would get an extra level of assurance from a mandate that this is scientifically validated."

This article originally appeared in The New York Times.