Hospitals nationwide are preparing for a third winter with Covid — the first one that's also expected to include high levels of influenza and other respiratory illnesses that have simmered quietly in the background for the past two years.

Flu cases are already rising in parts of the U.S., according to the Centers for Disease Control and Prevention. Pediatricians, too, are seeing a growing number of children sick with respiratory syncytial virus, or RSV, and enteroviruses.

And despite a downward trend in Covid, tens of thousands of new cases are still being diagnosed every day.

The convergence of viruses is hitting health care systems as they're forced to reckon with staffing shortages that worsened during the pandemic.

"If you go around the nation and ask hospitals how busy they are, every single one of them will tell you: They’re busy," said Dr. Carlos del Rio, an executive associate dean at the Emory University School of Medicine and Grady Health System in Atlanta.

Health care workers are quitting at rates 23 percent higher than when the pandemic began, mirroring a larger nationwide trend of workers leaving their jobs, according to Health System Tracker, a joint effort between the nonprofits Peterson Center on Healthcare and Kaiser Family Foundation to monitor how well the U.S. health care system is performing.

"Nurses were on the front line, and some of them burned out and quit," said Dr. James McDeavitt, executive vice president and dean of clinical affairs at Baylor College of Medicine in Houston. "Others that were in their 50s and 60s who maybe thought they'd be working for another five years took an early retirement."

Dr. Bernard Camins, medical director for infection prevention at the Mount Sinai Health System in New York City, has noted a similar "mass exodus" of health care workers who retired early or moved to a different line of work altogether.

Now, he said, "there's a constant struggle to recruit new people."

Staffing deficits mean there is little wiggle room to accommodate any additional surges of patients, whether they're sick with Covid, flu or other illness.

"There's no excess capacity in hospitals," del Rio said. "Anything that increases the number of patients is going to tip the scales."

Despite the shortages, hospital leaders applaud health care workers who have been able to stay the course and are ready for this next phase of infectious disease.

Morale is “actually pretty good,” McDeavitt said. “We’ve moved on from early in the pandemic, wondering if we were going to get sick and potentially die.”

“I think those worries are alleviated,” McDeavitt said. “We know how to handle it now.”

Where are we now?

Reports of Covid cases have been decreasing steadily since early August. As of Oct. 6, the average number of new cases per day, based on a seven-day average, is 44,743 — the lowest it's been since April.

Covid-related hospitalizations, too, continue to tick down. As of Oct. 5, the average daily number of hospital beds used by a Covid patient was at its lowest since June, at 27,161.

But as the cold weather sets in and people increasingly gather indoors, Covid cases are expected to rise.

A recent analysis from the Mayo Clinic in Rochester, Minnesota, predicts that average Covid cases per day nationwide will increase by more than 10 percent in the coming weeks.

“We’ll see an increase in Covid cases — probably not to the extent that we saw in the winter of 2020 and winter of 2021 — but we will see a rise,” said Matthew Binnicker, director of clinical virology at the Mayo Clinic. “Most of those will be infections that lead to mild to moderate illness.”

How well do Covid boosters work?

That prediction reflects what is known so far about how the latest Covid vaccines work. While the shots may not prevent a person from getting sick following an infection, they have been shown throughout the pandemic to keep infected people out of the hospital and from dying.

“How much of a rise in the hospitalizations and deaths we will see is really going to depend on the extent to which people are getting up to date on their vaccines,” especially those at highest risk for severe illness, such as the elderly and those with weak immune systems, said Jennifer Nuzzo, director of the Pandemic Center at Brown University School of Public Health.

The vast majority of Covid cases circulating now are an omicron subvariant, BA.5. The latest version of the Covid vaccine targets BA.5, but since its debut in September, fewer than 4% of people eligible for the extra shot have received it.

The Commonwealth Fund recently predicted that more than 745,000 Covid-related hospitalizations and more than 75,000 such deaths could be avoided, if more people got the bivalent shot.

The U.S. is also seeing the beginning of what is expected to be the first rough flu season in years. While overall numbers remain low, the CDC reported an increase in positive flu tests last week.

“It’s very likely that we’re going to see influenza roaring back with a vengeance this winter,” said Dr. Dan Uslan, co-chief infection prevention officer for UCLA Health in Los Angeles.

What's happening in Australia could be a preview: The country is exiting its worst flu season in at least five years, according to the country’s Department of Health and Aged Care.

“Data from the Southern Hemisphere are not good,” Binnicker, of the Mayo Clinic, said. “We need to double down on prevention measures,” such as masking and physical distancing.

There are already signs that viruses are circulating more than they have in recent years.

Pediatricians have begun to see “high numbers of severely sick patients with respiratory illnesses,” said Dr. Sarah Combs, an emergency medicine physician at Children’s National in Washington, D.C. The illnesses are not necessarily linked to either Covid or flu.

“We are seeing child after child coming in with breathing trouble related to what would commonly be called just a cold or a sniffle,” Combs said. These are children who do not have asthma or other chronic lung diseases that would make them more susceptible to breathing problems.

“They come in having a cold and then within 24 hours they’re actually struggling to breathe,” she said.

The CDC recommends an annual flu shot for everyone aged 6 months and older. Children younger than age 9 who have never had a flu vaccine, the CDC said, should get two this year, at least four weeks apart.

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