• Public health officials have warned for weeks that the U.S. would face another Covid wave due to the delta variant this winter.
• The detection of omicron in at least 25 states has raised concern that the variant could lead to an additional infection wave if it proves even more contagious.
• "In the weeks to come with omicron, what we've got here might be a perfect storm," said Dr. Barbara Sattkamp Taylor, an expert on infectious disease at UT Health San Antonio,

When the first wave of Covid infections hit the U.S. in March 2020, health-care workers at Pennsylvania's largest hospital system expected the crisis to last six months at most.

More than a year-and-a-half later, University of Pittsburgh Medical Center is fighting another Covid wave, driven by the highly contagious delta variant. 

"We expected this to be a three- to six-month crisis and then we expected it to be over — instead it's 20 months," Dr. John Goldman, an infectious disease expert at UPMC Harrisburg, told CNBC. "We have been very busy since essentially March of 2020. It is very hard for people to continue that level of intensity."

Public health officials have warned for weeks that the U.S. would face another Covid wave due to delta this winter, as families gather for the holidays and people spend more time inside to escape the cold. Goldman said the medical center is facing the second-highest peak of Covid hospital admissions since last winter, driven largely by the unvaccinated. 

The University of Pittsburgh Medical Center, which has more than 40 hospitals and 8,700 beds, is close to capacity and at times is running over, Goldman said. Staffing is also tight as some health-care professionals have experienced burnout and found work elsewhere where they can make more money in a tight labor market, he said.

Goldman said the hospital system is trying to treat people as quickly and safely as possible, and is encouraging the public to test for Covid through their doctor's office instead of at emergency rooms to keep hospital beds open for severely sick patients. UPMC is also using more telemedicine appointments to treat more people without checking them into the hospital, he said.

At the start of the pandemic, the average patient was older than 65 and often a nursing home resident, according to Goldman. In the current Covid wave, the patients are younger, often between the ages of 55 and 65, he said.

"Quite honestly it's also hard to see that level of death," Goldman said. "We're used to being able to fix young, healthy people. We're not used to seeing them die."

In Minnesota, the Mayo Clinic and other hospitals took out full page ads in major state newspapers on Sunday pleading with the public to get vaccinated and wear a mask.

"We're heartbroken. We're overwhelmed," the ad said. "Our emergency departments are overfilled and we have patients in every bed. Now an ominous question looms: Will you be able to get care from your local community hospital without delay? Today, that is uncertain."

As hospitals from the Great Lakes to the Northeast battle delta, infectious disease experts are worried about the prospect of a worsening situation fueled by the heavily mutated omicron variant, now present in at least 36 states. It accounts for 3% of all cases in the U.S. and in more heavily populated states like New York and New Jersey, the Centers for Disease Control and Prevention estimates it accounts for 13% of all Covid cases, CDC Director Dr. Rochelle Walensky said Wednesday.

White House chief medical advisor Dr. Anthony Fauci  has said there's "no doubt" community spread is underway. 

"In the weeks to come with omicron, what we've got here might be a perfect storm," Dr. Barbara Sattkamp Taylor, an expert on infectious disease at UT Health San Antonio, told CNBC. We have "a more infectious variant along with the upcoming holiday travel. And so we're concerned about what we're going to see later this month and early in January."

'Twin threats'

Information on omicron remains limited, but preliminary studies and real-time reporting from southern Africa, where omicron was first identified, as well as in Europe, suggests the variant is significantly more contagious than any other Covid strain. World Health officials said Wednesday the number of cases in the U.K. is doubling every two days or less. People infected with omicron have mostly reported mild symptoms so far, but scientists and public health officials caution it could take weeks to determine whether the variant causes more or less severe disease.

The UDC is advising that delta remains the primary threat to public health this winter, though omicron infections are increasing. Delta represented about 97% of Covid samples and omicron made up about 3% samples analyzed by CDC during the week ended Dec. 11. The week prior, omicron represented less than 1% of samples.

The U.S. is reporting nearly 120,000 new cases per day, based on a seven-day average of data compiled by Johns Hopkins University. Its rate is flat over the past week but up 25% from before Thanksgiving

About 68,000 Americans are hospitalized with Covid-19, according to a seven-day average of U.S. Department of Health and Human Services data through Tuesday, up 21% over the past two weeks. Though rising, that is still lower than the delta wave's peak when more than 100,000 patients were hospitalized in early September.

"Delta continues to drive cases across the country, especially in those who are unvaccinated," the CDC's Walensky said during a White House Covid update on Dec. 4

However, the United Kingdom is already sounding the alarm over omicron. Britain's chief medical officers issued a level 4 Covid alert on Sunday, a step below the highest threat level, warning that omicron hospitalizations are already occurring and "are very likely to increase rapidly." 

The nation's Health Security Agency said last week that omicron is showing a significant transmission advantage over delta. Health Secretary Sajid Javid told British lawmakers the variant could explode to more than 1 million cases in the U.K. by the new year, describing the simultaneous circulation of delta and omicron as "twin threats" to public health.

Walensky does not believe the U.S. is facing the same urgency. "I don't expect we will be on the same time horizon as the U.K. and we're continuing to follow cases and we'll look at that carefully," she said during a White House Covid update on Friday.

However, Dr. Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, believes omicron will likely overtake delta in the U.S. soon. "It's just a matter of time before omicron becomes the dominant variant here, and I think that could happen relatively quickly," Osterholm told CNBC in an interview last week.

Most Covid patients unvaccinated

As public health officials grapple with the implications of omicron, hospitals in Michigan are already battling a wave of delta infections. Dr. Darryl Elmouchi, president of Spectrum Health West Michigan, said the system's 14 hospitals have suffered "far and away the worst surge" in recent months. 

Michigan has the highest rate of Covid hospitalizations in the country, adjusted for population, with a seven-day average of more than 4,700 patients, a CNBC analysis of HHS data shows.

The combination of Covid patients and those with more typical health problems have pushed intensive-care units to about 140% capacity for more than a month, Elmouchi said.

The vast majority of those currently hospitalized with Covid across the system are unvaccinated. Spectrum Health hospital admissions peaked in November 2020 before a surge in fatalities in December. Elmouchi expects this winter to worsen.

"We are absolutely and sadly on track to follow the same but worse this fall," Elmouchi said. "We are projecting December deaths to be at absolute peak levels."

In Pennsylvania, Goldman said Covid patients admitted to the University of Pittsburgh Medical Center are also largely unvaccinated. UPMC Altoona in central Pennsylvania, where only about 45% of the population is fully vaccinated, has the highest number of Covid positive admissions in the system, he said.

Pennsylvania has the fourth-highest number of hospitalizations nationwide, also adjusted for population, with an average of more than 5,000 Covid patients in the hospital every day over the last week, according to HHS data.

Goldman estimated that 80% to 90% of the hospital system's Covid patients are unvaccinated, and up to 95% of those treated in intensive-care units are not immunized against the virus. He said some patients who are unvaccinated simply don't trust the vaccine or think the shots are too new, while others believe there is some kind of conspiracy involving the vaccine.

"There are people who have gotten a lot of disinformation," Goldman said. "I unfortunately don't know how you convince someone who believes in conspiracy theories that conspiracy theories don't exist. My experience has been that's really difficult."

The urgency of boosters

Though the current surge is driven by the delta variant, Elmouchi said the emergence of omicron increases the urgency of booster vaccination efforts. 

"As hard as it's been to convince so many to get a regular course of vaccination, I think we're going to be in a new phase where we're going to have to try to convince everybody to get a booster," he said, adding that "if history over the past six to 12 months is any indication, that's not going to be easy."

Since the CDC approved booster shots, only a small fraction of Spectrum Health Covid admissions – 19 patients out of thousands who have entered one of their hospitals – had received a booster dose more than two weeks before being admitted, Elmouchi said.

Boosters have become a major focus of public health officials as protection provided by the vaccines wears off over time and many people received their first shots more than six months ago. What's more, the omicron variant is able to significantly evade protection from Pfizer and BioNTech's two-dose vaccine, according to preliminary data from the companies and South African scientists.

The journal Science, in a study published last month before the detection of omicron, found the protection against infection provided by Pfizer and BioNTech's vaccine dropped from 86% in February to 43% in October. However, Pfizer's vice president of vaccine clinical research, John Perez, told a CDC advisory committee last month that the booster dose provides 95% protection against symptomatic infection in people 16 and older.

However, the initial two-dose vaccination series still provides protection against severe illness. Goldman said fully vaccinated people who do have severe breakthrough infections are normally elderly, often between 75 and 80 years of age, or they have multiple medical problems or suppressed immune systems. Most fully vaccinated patients who get infected show very mild symptoms, he said.

"The vast majority of vaccinated patients never make it to the hospital because their symptoms are so mild, and I think a lot of vaccinated patients never get tested because they think that they have mild allergies or a slight viral illness," Goldman said.

Initial lab studies also indicate that boosters protect against omicron. Pfizer and BioNTech released preliminary lab data last week that indicates a booster shot provides similar virus-fighting power against the variant as the first two doses against the original strain of the virus.

'We need people to do their part'

With more than 60 million people still unvaccinated in the U.S., Osterholm in Minnesota emphasized that the U.S. needs to get more first shots in people's arms as well. He said the public also needs to understand that masking and social distancing remain crucial tools in the fight against Covid.

"There are many states in this country where bars are full, restaurants are full — all the social events before the pandemic are going on now and this is a real challenge," Osterholm said.

Some European nations are reintroducing restrictions in an effort to fight delta and to prevent omicron from spiraling out of control. England is urging people to work from home, mandating masks in most indoor public spaces, and requiring proof of two vaccine doses before entering nightclubs and large events.

Germany has barred the unvaccinated from all nonessential businesses, France is closing nightclubs for four weeks and Austria is in the middle of a nationwide lockdown.

In the U.S., President Joe Biden has ruled out lockdowns, relying instead on efforts to get more people vaccinated and ramp up testing as the country heads into winter.

Taylor, the infectious disease expert at UT Health in San Antonio, said the U.S. is also seeing more flu infections this year, after the flu season was virtually eliminated in 2020 due to the strict social distancing rules implemented to control Covid.

"Hospitals are already at capacity almost every winter because of flu and other seasonal illnesses. So if we add even a small increase in Covid on top of that, it would be really, really concerning," Taylor said.

Goldman is also worried that a surge of delta infections combined with the flu season will lead to sharp increase in hospital admissions this winter. He asked the public to show understanding as health-care workers do their best to treat the influx of patients.

"When people have to wait, they tend to be shorter with us," Goldman said. "And we need the public to understand we're all working very hard. And then what we really need to get through this is for people to do their part, and I consider doing that part to be vaccinated."