A respiratory therapist checks on Adrian James, 2, who tested positive for the coronavirus disease (COVID-19) and is on a ventilator, at SSM Health Cardinal Glennon Children’s Hospital in St. Louis, Missouri, U.S., October 5, 2021.

Callaghan O’Hare | Reuters

Trisha DeGroot’s 10-year-old daughter, Rainey, returned to her Houston home after a church choir practice in September looking unwell.

Rainey was running a fever, so DeGroot had her tested for Covid-19 as a precaution. When the results came back positive, DeGroot assumed Rainey would recover quickly, like her 13-year-old son, Sam, who had caught Covid in February.

Rainey experienced abdominal pain, a bad headache, nausea and vomiting. But after about 10 days, her personality came back and she seemed to be turning the corner, DeGroot said.

Then Rainey’s condition took a turn for the worse. She had trouble eating. The abdominal pain and headaches got worse. But the family doctor couldn’t identify why Rainey was sick. A gastroenterologist told DeGroot that some children’s bodies overreact to Covid. He prescribed a medication called cyproheptadine to ease the stomach pain and help her start eating again. It didn’t work, DeGroot said.

DeGroot, who studies nursing, took her daughter to a clinic at Texas Children’s Hospital in Houston that specializes in post-Covid symptoms. Rainey was diagnosed with long Covid and dysautonomia, a failure of the autonomic nervous system, which controls the body’s basic functions, such as digestion.

Rainey’s fight

In December, Rainey became nauseated by the smell of food and said everything tasted like it was rotting, DeGroot said. She took Rainey back to Texas Children’s Hospital, where she was admitted and treated for two weeks.

Rainey was placed on a feeding tube, which is still the only way she can eat. She is now home-schooled, but she has difficulty reading and it’s hard for her to keep up, DeGroot said.

At the time of Rainey’s infection, 10-year-old children weren’t eligible for vaccination. The Food and Drug Administration would authorize the Pfizer and BioNTech vaccine for kids ages 5 to 11 in October. DeGroot, her husband, David, and Sam were all vaccinated. Her 4-year-old daughter Helen isn’t eligible yet.

“It’s absolute misery. It takes its toll on everybody, especially your child. You do not want this.”

Rainey was infected during the surge caused by the delta variant. The highly contagious omicron variant is now driving the pandemic’s largest wave of infection across the world. As new infections soar, the number of children hospitalized in the U.S. with Covid recently hit a record high.

Infectious disease experts at children’s hospitals in Atlanta, Chicago, Cleveland, Denver and Washington, D.C., all told CNBC that they are seeing more children hospitalized with Covid than during previous waves — although the number represents a lower percentage of overall cases.

Hospitalizations rise

Pediatric infectious disease specialist Dr. Roberta DeBiasi said that at omicron’s peak 67 children were hospitalized with Covid at the Children’s National Hospital in Washington, D.C. — a pandemic high and almost three times higher than the delta peak. About 45 children are currently hospitalized there, she said.

At the Comer Children’s Hospital in Chicago, 15 children are hospitalized with Covid on any given day, said Dr. Allison Bartlett, a pediatric infectious disease specialist. That’s about twice the previous peak, which occurred in September.

“The good news is in terms of the number of children who are in our intensive care unit on ventilators, that number is about the same as it was at our last peak,” Bartlett said. “Proportionally we don’t have as many super-sick kids as we did before.”

Fewer in ICU

While more children are hospitalized with Covid, due to omicron’s high level of transmissibility, they don’t appear to be getting sicker than they did with previous strains, physicians say.

More than 80 children are currently hospitalized with Covid in the Children’s Healthcare of Atlanta system, which has three hospitals, compared with 15 children on any given day during most of October and November, when delta was the dominant variant.

However, the percentage of children in the ICU — about 10% to 15% of those hospitalized — is probably slightly lower than what the hospital saw during the delta wave’s peak, said Dr. Andi Shane, head of the infectious disease division at Children’s Healthcare of Atlanta.

The FDA cleared Pfizer’s Covid shots for 12- to 15-year-olds on May 10 and 5- to 11-year-olds on Oct. 29, giving a large portion of those kids some protection against omicron. Roughly 55% of kids ages 12 to 17 and 19% of children ages 5 to 11 are fully vaccinated right now, according to the Centers for Disease Control and Prevention.

The biggest risk

Pediatric infectious disease specialists said most of the children hospitalized with Covid are unvaccinated. Shane said children with underlying conditions who are vaccinated but got breakthrough infections are having much less severe symptoms than those who are unvaccinated and they are not being hospitalized with Covid-related complications.

“The biggest risk factor at this point is being unvaccinated,” said Dr. Sean O’Leary, a pediatric infectious disease specialist at Children’s Hospital Colorado.

CDC Director Dr. Rochelle Walensky told reporters earlier this month that unvaccinated 12- to 15-year-olds are 11 times more likely to end up in the hospital with Covid than vaccinated children in the same age group. However, kids under 5 are particularly vulnerable right now because they are not yet eligible for vaccination.

“Sadly, we are seeing the rates of hospitalizations increasing for children zero to 4, children who are not yet currently eligible for Covid-19 vaccination,” Walensky told reporters.

‘Such a contagious variant’

O’Leary, who is also vice chair of the American Academy of Pediatrics’ committee on infectious diseases, said about a third of the children in his hospital with the virus were admitted for other things, but the other two-thirds of them need hospital care because of Covid.

“Yes, we’re going to see more kids hospitalized with other things that also have Covid, because this is such a contagious variant and infection is so common right now. But we are also very much seeing a lot of kids hospitalized with Covid,” O’Leary said.

An average of roughly 5,100 kids, from infants to 17-year-olds, were hospitalized with Covid as of Jan. 20, according to a seven-day average of data from the Department of Health and Human Services, up 26% over the past two weeks.

‘Absolute misery’

Obesity and asthma

Bartlett said many of the children hospitalized with Covid at Comer in Chicago are also obese.

Dr. Camille Sabella, an infectious disease specialist at Cleveland Clinic Children’s, said severe asthma is another major risk factor. Sabella said the children’s hospital has between 15 and 20 pediatric patients infected with Covid on any given day, compared with less than five in September and October. He estimated that about 70% of them are hospitalized because of Covid.

The CDC found that two-thirds of children hospitalized with Covid had one or more underlying health issues, with obesity the most common condition, according to a study of pediatric patients at six hospitals during July and August when the delta variant was predominant.

“Everyone is at risk from Covid. You do not know what Covid will do to you in the window of infection or in the long term of having Covid — you just don’t know.”

O’Leary and DeBiasi said about a third of children hospitalized because of Covid ultimately need intensive care and oxygen support due to respiratory failure.

‘We haven’t even scratched the surface’

104-degree fever

Janelle Bardon’s daughter, Taylor, was a healthy 17-year-old in Louisville, Kentucky, until she caught Covid in the summer of 2020. Taylor had no underlying health conditions and played field hockey. She lost her senses of taste and smell after infection but had no other symptoms and tested negative four weeks later, Bardon said.

When Taylor went back to field hockey, she felt short of breath and dizzy and struggled with endurance. Bardon, a registered nurse with 20 years of experience, took Taylor to a cardiologist, who found that she had second-degree heart block, or irregular heart rhythm.

Taylor’s condition deteriorated during a family trip to Disney World that fall. She developed a 104-degree fever, a sunburn-like rash and a terrible sore throat and could barely walk, Bardon said. Taylor had symptoms similar to hypovolemic shock, in which the heart rate is high, blood pressure is low and oxygen delivery to organs drops.

MISC-C and long Covid

‘Lifelong illness’

“Now she’s stuck with a lifelong illness,” Bardon said. Taylor will have to take either colchicine, an anti-inflammatory pill normally used to treat gout, or anakinra injections, which are used to treat rheumatoid arthritis, Bardon said.

O’Leary, the pediatrician in Colorado, said MIS-C usually develops two to six weeks after infection, which would suggest a wave of cases in the coming weeks. However, O’Leary said it is too early to determine the omicron variant’s association with MIS-C.

The CDC, in a recent study, found that vaccination with two Pfizer doses was 91% effective at protecting adolescents 12 to 18 against MIS-C. Taylor was vaccinated last summer.

Megean Naughton’s family came down with Covid after her husband, Patrick, a firefighter, was infected in the summer of 2020. Her daughter Zoe, who is now 14, was sick in bed for four weeks. 

“She recovered, and she was well for about five months. And then one day she got sick and then she literally could not stand up,” said Naughton, a stay-at-home mom of five children. Zoe was a healthy child who played lacrosse before Covid, Naughton said.

‘Everyone is at risk’

Zoe was in bed for five months, and Naughton had to take her out of school on a medical withdrawal. Zoe was hospitalized for four days after experiencing dehydration and severe migraines, Naughton said.

Naughton scheduled a telehealth appointment with Norton Children’s Hospital in Louisville, Kentucky, which runs a specialized clinic for kids experiencing lingering Covid symptoms. That’s when Zoe was diagnosed with long Covid, Naughton said.

Zoe missed the entire second semester of eighth grade and is now in physical rehabilitation. She still experiences dizziness and severe headaches and is constantly in pain, Naughton said.

“Everyone is at risk from Covid,” Naughton said. “You do not know what Covid will do to you in the window of infection or in the long term of having Covid — you just don’t know.”

— CNBC’s Nate Rattner contributed to this report