• Danny Meyer's Union Square Hospitality Group will soon require indoor restaurant customers to show proof of having received a booster shot.
• Employees and new hires must also receive a booster shot, effective immediately.
• The announcement, which Meyer made on CNBC's "Squawk Box," comes amid the latest surge in Covid cases.

Danny Meyer, head of Union Square Hospitality Group, said Wednesday it will soon begin requiring restaurant customers to show proof of having received a Covid booster shot in order to dine indoors.

Employees and new hires must also receive a booster shot, effective immediately, Meyer announced on CNBC's "Squawk Box." 

The decision comes amid a new surge in Covid-19 cases driven by the highly contagious omicron variant. The coronavirus strain has show an ability to infect even those who have been vaccinated, but current data suggests immunized people, especially those who have received booster shots, are at far less risk of hospitalization or death.

"At this point, the science has changed," Meyer said. "What has been a little bit tougher has been watching this crushing wave of omicron sweeping through New York City and certainly through the country."

In New York, the wave is particularly pronounced, with a seven-day average of new coronavirus cases nearly doubling over the past week, according to a CNBC analysis of Johns Hopkins University data.

"Hospitality is a team sport — it's kind of like putting on a play on Broadway or playing a basketball game," the restaurateur said. "If you can't field a full healthy team, you're going to have to hit pause. ... We'll see how that goes."

Beginning Wednesday, New York City-based USHG is asking all staff members to receive a third shot of the Covid vaccine within 30 days of their eligibility, Meyer said. Indoor customers will have to meet the third-shot criteria in mid-January, he said.

USHG has a large presence in New York City and includes Gramercy Tavern and Union Square Cafe in Manhattan. It also operates Anchovy Social in Washington, D.C.

In late July, USHG said it would requiring vaccines for those dining or drinking at the bar indoors at its restaurants, as well as for its current employees and new hires. On Wednesday, Meyer said that 100% of its staff are fully vaccinated. The company had only a few workers who chose to leave instead of following the policy, he said.

"The good news was that we were able to bring almost everybody over the finish line," he said.

Meyer is also founder of Shake Shack and chairman of its board. However, he said the fast-casual burger chain will make its own decision regarding booster shots.

"Throughout this entire wave that we're now going through — while we've absolutely seen a ton of breakthrough cases throughout society, throughout New York City and even in our restaurants — so far not one of the cases that our staff members have encountered have been more than mild symptoms," said Meyer.

The Centers for Disease Control and Prevention has not yet changed its definition on what it means to be fully vaccinated against Covid. Currently, individuals are considered to be fully vaccinated either two weeks after their second dose of a two-dose series, such as the Pfizer-BioNtech vaccine, or two weeks after a single-dose vaccine, such as the Johnson & Johnson vaccine.

Last week, though, White House chief medical advisor Dr. Anthony Fauci said that a redefinition of what it means to be fully vaccinated against Covid-19 is "on the table." "There's no doubt that optimum vaccination is with a booster," he told CNBC.

Meyer is also considering if Covid testing should be part of its precautions to help keep employees and diners safe.

"We're accessing all kinds of testing for our team because we believe that the minute anybody has a symptom, that if they could do that for themselves at home, certainly we could do that at the restaurant," he said. "We think that that's going to have a great deal of effect in terms of stemming the wave."