Thousands of flights canceled again as snowstorms and omicron wreak havoc

Rolling flight cancellations continued into the new year as more than 2,100 flights to, from and within the U.S. were canceled on Monday.

The cancellations came as a winter storm slammed into the mid-Atlantic and staffing issues linked to the spread of the omicron variant of COVID-19 continued to plague U.S. carriers. Preemptive cancellations were extended into Wednesday, underscoring the likely longevity of the disruptions that have been near-constant since Christmas Eve.

More than 20 million Americans were under winter storm warnings Monday, with snowfall totals of as much as 8 to 10 inches forecast across the Appalachians — including in Washington, D.C. Strong winds and rain were expected in the Carolinas and Georgia, as well.

The weather, coupled with ongoing staffing shortages caused by pilots, flight attendants and other front-line airline workers testing positive for COVID-19 meant the first business week of the new year began with significant impacts to air travel, even as airlines raced to manage residual disruptions from the holiday travel week.

Southwest Airlines canceled 479 flights — or 13% of its scheduled operations for the day — as of 11 a.m. ET, according to flight-tracking service FlightAware. JetBlue canceled 144 flights (14%).

SkyWest, a regional airline that operates flights for the major U.S. airlines, including United out of Denver, canceled 274 flights (11%).

Delta Air Lines canceled 125 flights (4%), while United Airlines cut 113 (5%). Both airlines, along with JetBlue, were the most impacted by the initial staffing shortages starting on Christmas Eve.

Fellow mainline carrier American Airlines, on the other hand, appeared to have a somewhat smoother operation on Monday with 70 cancellations (2%). Alaska Airlines, which saw its operations severely hampered by two storms in Seattle last week, canceled 75 flights on Monday (11%).

Although the mainline operations appeared to be coping fairly well on Monday, the regional airlines that operate flights on behalf of the major carriers appeared to be having a more difficult time.

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Aside from SkyWest, Republic — which flies for American, Delta and United — saw the most impact on Monday. The regional airline canceled 165 flights, 15% of its scheduled operations for the day. Endeavor Air, a Delta subsidiary, cut 132 flights (15%), while PSA Airlines, a wholly-owned American Airlines subsidiary, canceled 104 flights (13%). Mesa, which flies for American and United, canceled 92 flights (18%).

Smaller regional carriers weren't spared: CommutAir and Air Wisconsin, which both fly for United, canceled 47 (19%) and 35 (15%) flights, respectively. Envoy Air and Piedmont, both American Airlines regional operators, cut 32 (3%) and 27 (8%) of their flights, respectively.

America's low-cost carriers also saw cancellations on Monday — potentially a more difficult situation for stranded passengers, due to the smaller networks and higher reliance of point-to-point flying among the low-costs.

Allegiant, which has been plagued by cancellations in recent days, canceled 68 flights (13%). Spirit Airlines canceled 55 flights (6%) on Monday, while Frontier canceled 24 (4%). Breeze, the new startup by JetBlue founder David Neeleman, canceled 14 flights (32%).

Several airlines have confirmed that a large number of cancellations have resulted from flight crews testing positive for COVID-19 as the omicron variant spreads across the U.S.

At least at one airline, albeit one seeing less impact from the current case counts, the majority of the sick calls were from pilots.

Between Dec. 24 and Dec. 31, pilot staffing was the cause of between 80% and 90% of American Airlines' flight cancellations, Capt. Dennis Tajer, a spokesman for the Allied Pilots Association, told TPG on Saturday. APA is the union representing American's pilots.

"American builds the schedule for a sunny day, not for weather events or COVID disruptions," Tajer said.

American said on Sunday that a significant portion of its cancellations were due to the weather, and that the number of COVID-related sick calls is "consistent with what we have seen over the past few days."

Many of the cancellations are being carried out proactively, airlines have said — typically several hours to several days before a flight is scheduled to depart — a strategic decision airlines make to try and minimize disruptions that have the potential to be greater.

JetBlue said last week Thursday that it was cutting flights through Jan. 13 in an effort to give customers more time to plan alternatives.

Related: Here's what to do if your flight is delayed or canceled

"Like many businesses and organizations, we have seen a surge in the number of sick calls from omicron," the airline said in a statement provided by a spokesperson. "We entered the holiday season with the highest staffing levels we've had since the pandemic began and are using all resources available to cover our staffing needs."

The spokesperson said that JetBlue was cutting about 1,280 flights between Dec. 30 and Jan. 13 — an average of 85 flights per day.

On Monday, the Centers for Disease Control and Prevention (CDC) shortened the time that people who test positive for COVID-19 must isolate, lowering it from ten days to five, which could alleviate pressure on industries with large numbers of staff out on sick leave. The lobbying organization for U.S airlines, Airlines for America, late last month asked the CDC to revise the guidance, arguing that the longer period was demonstrably unnecessary and could lead to operational disruptions. Delta and JetBlue also separately made similar requests to the CDC, which has led to some criticism and skepticism surrounding the guidelines.

Related: What do the CDC's new isolation and quarantine recommendations mean for travel?

Despite the shortened isolation period, however, the rapid and expansive spread of the omicron variant has the potential to drag out the disruption to air travel.

"The nationwide spike in Omicron cases has had a direct impact on our flight crews and the people who run our operation," United Airlines said in a statement Sunday. "As a result, we've unfortunately had to cancel some flights and are notifying impacted customers in advance of them coming to the airport. We're sorry for the disruption and are working hard to rebook as many people as possible and get them on their way during the holidays."

Ethan Klapper contributed to this report.