• JetBlue will cut about 1,280 flights from Dec. 30 through Jan. 13.
• Airlines have canceled thousands of flights since Christmas Eve due to bad weather and a wave of Covid-19 among flight crews.
• JetBlue said the schedule cuts will help avoid last-minute cancellations.

JetBlue Airways will cut more than 1,280 flights from Thursday through mid-January in anticipation of more Covid-19 infections among pilots and flight attendants, while cancellations continued to climb around the country.

New York-based JetBlue and other airlines, including United Airlines, Delta Air Lines and American Airlines, have canceled more than 8,000 flights since Christmas Eve, according to airline data firm FlightAware, as carriers were hit with bad weather and a surge in sick calls from crews.

The disruptions cap another rocky year for travel as airlines at times struggled to ramp up flying to meet a resurgence in demand after a paltry 2020.

More than 1,100 flights were scrubbed nationwide on Thursday, according to FlightAware. JetBlue canceled 175 flights or 17% of its schedule. United, meanwhile, canceled 192 flights, or 9% of its mainline schedule, while regional airline SkyWest dropped 198, or 8%. Seattle-based Alaska Airlines canceled 95 flights, 14% of what it planned to fly.

Delta said it scrapped 250 out of its 4,179 scheduled mainline and regional departures on Thursday because of weather and the omicron variant of Covid. It plans to cancel between 200 and 300 through the weekend.

Delta, United and others have offered staff extra pay to pick up shifts to mitigate the disruptions.

"This past week has been one of our most difficult operating periods during the pandemic," three JetBlue department leaders wrote Tuesday in a note to staff, which was seen by CNBC. "The exponential growth in Omicron cases over just a couple of days is at a level that no one could reasonably prepare for."

The planned flight cuts are slightly below 10% of JetBlue's daily schedules.

CEO Robin Hayes told CNBC's "Closing Bell" on Thursday that the cancellations aim to avoid last-minute changes on passengers.

"The worst type of cancellation as we all know is that cancellation that happens at the airport," Hayes said.

Sick calls across the industry have come from both pilots and flight attendants. The Association of Flight Attendants-CWA, which represents some 50,000 cabin crew members at United, Spirit and others, said cases among flight attendants have spiked and that some airlines are on track to have the highest monthly totals of positive tests since the pandemic began, though a spokeswoman declined to specify which carriers.

The Transportation Department noted that travelers are owed refunds if their airline cancels flights or significantly changes the schedule and passengers opt against taking an alternative flight.

"The Department is monitoring airlines' actions and reviewing complaints that it receives against them to ensure that consumers' rights are not violated," a DOT spokesperson said in an emailed statement. "The Department will act if airlines fail to comply with the applicable law."

CDC loosens isolation guidelines

The Centers for Disease Control and Prevention on Monday cut its recommended isolation time to five days from 10 for individuals who have tested positive for Covid but are asymptomatic.

JetBlue had followed Delta last week in urging the CDC to halve its guidance on isolation for breakthrough Covid cases to five days, warning about staffing shortages and flight disruptions as omicron was rapidly spreading. Other airlines followed suit.

JetBlue updated its leave policies after the CDC's announcement to allow staff to return to work if they are symptom-free after five days.

The JetBlue department heads said in the staff note that they are hopeful that the new guidelines would help bring back staff faster but added, "we know that Omicron cases have yet to peak in the Northeast (and won't for at least another week or two) where the vast majority of our Crewmembers are based."

The AFA, the largest U.S. flight attendants union, had urged the CDC against making the change and said stronger protocols are needed, like a negative test, to return to work and 10 days of isolation for unvaccinated workers who test positive.

"We believe this is the wrong move for aviation as it accepts that infectious people will be put back on the job or flying as passengers on our planes," AFA's international president, Sara Nelson, wrote to airline CEOs on Wednesday. "While our union did not—and does not—support the updated guidance, we stand ready to work together with airlines to implement the new rules in a way that will protect workers and provide clarity and confidence for our passengers."

JetBlue shares fell 1% on Thursday, closing at $14.24, a bigger percentage drop than other carriers. Southwest Airlines and American, which had relatively few cancellations on Thursday added 1.3% to $42.72 and 0.1% to $18.07, respectively.