There were no signs of abating on Monday as many people went on their first trips in almost two years, and Dr. Fauci raised the possibility of a vaccine requirement for air travel.
More than 2,400 flights were canceled Monday as the highly transmissible Omicron variant is sending daily caseloads in parts of the United States soaring to levels higher than last winter's peak.
The problem was limited to a small percentage of flights, and was threatening to extend into the holiday week.
Dr. Fauci said on MSNBC on Monday that making vaccinations a requirement will encourage more people to get them. If you want to do that with domestic flights, that should be considered.
Airlines canceled thousands of flights over the holiday weekend as the Omicron variant hit flight crews. More than 3,500 flights were grounded globally and 2,300 in the US during the Christmas holiday weekend. More than 1,700 flights were canceled worldwide on Sunday.
Several airlines acknowledged that the current wave of coronaviruses contributed to the current groundings. A spokesman for the airline said that they had seen an increase in sick calls.
Six percent of Delta Air Lines flights, five percent of United Airlines flights, and two percent of American Airlines flights were canceled on Sunday.
Dan Landson, a Southwest spokesman, said that Southwest Airlines canceled 68 flights because of weather. He said in an email that there had been no operational issues related to Covid.
The stock prices of United, Delta, American and Southwest were lower on Monday.
The situation at airports is worse because of the increase in travelers this year, with roughly two million people passing through screening each day last week. The numbers on Christmas Eve and Christmas Day were much higher than last year, and some figures even exceeded those of the same days two years ago, when virtually no Americans were aware of a virus beginning to circulate halfway around the world.
The worst of the cancellation may be over in the US. Delta had expected to cancel about 200 flights on Sunday, less than the 300 it had predicted a day earlier, according to a spokeswoman. There are only 40 canceled on Monday.
On a Sunday, airlines expect a lot of travel. The Omicron variant, which is responsible for more than 70 percent of the new coronaviruses in the United States, has helped push daily case averages in the United States above 200,000 for the first time in nearly a year.
An airline trade group wants the CDC to shorten the recommended isolation period for fully vaccine-vaccinated employees who test positive to a maximum of five days.
The C.D.C. would alleviate some of the staffing pressures and set up airlines to help millions of travelers returning from their holidays, said a spokesman for JetBlue.
The flight attendants union believes that public health professionals should make the decisions about the recommended isolation times.
Some of the delays had nothing to do with the Pandemic. Alaska Airlines instituted an extensive program to keep crews healthy and even had members of its management team who are trained to be crew members step in.
On Saturday and Sunday, there were only a few cancellation related to crew exposure to the coronaviruses. It had canceled 170 flights because of the cold and snowy weather in the Pacific Northwest, which affected its hub, Seattle-Tacoma International Airport.
The Metropolitan Transportation Authority is dealing with an increase in positive cases among its staff. On Monday, the subway was running on a normal schedule, with scattered exceptions, according to the senior vice president for subways.