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There have been fewer influenza cases in the United States this flu season than in any on record. About 2,000 cases have been recorded since late September, according to data from the Centers for Disease Control and Prevention. In recent years, the average number of cases over the same period was about 206,000.

As measures to stop the spread of the coronavirus were implemented around the country in March 2020, influenza quickly disappeared, and it still has not returned. The latest flu season, which normally would have run until next month, essentially never happened.

After fears that a “twindemic” could batter the country, the absence of the flu was a much needed reprieve that eased the burden on an overwhelmed health care system. But the lack of exposure to the flu could also make the population more susceptible to the virus when it returns — and experts say its return is certain.

“We do not know when it will come back in the United States, but we know it will come back,” said Sonja Olsen, an epidemiologist at the C.D.C.

Experts are less certain about what will happen when the flu does return. In the coming months — as millions of people return to public transit, restaurants, schools and offices — influenza outbreaks could be more widespread than normal, they say, or could occur at unusual times of the year. But it’s also possible that the virus that returns is less dangerous, having not had the opportunity to evolve while it was on hiatus.

“We don’t really have a clue,” said Richard Webby, a virologist at the St. Jude Children’s Research Hospital in Memphis. “We’re in uncharted territory. We haven’t had an influenza season this low, I think as long as we’ve been measuring it. So what the potential implications are is a bit unclear.”

Scientists do not yet know which public health measures were most effective in eradicating the flu this season, but if behaviors like mask-wearing and frequent hand-washing continue after the coronavirus pandemic is over, they could help to keep influenza at bay in the United States.

Much also depends on the latest flu vaccines, their effectiveness and the public’s willingness to get them. The recent drop in cases, however, has made it difficult for scientists to decide which flu strains to protect against in those vaccines. It’s harder to predict which strains will be circulating later, they say, when so few are circulating now.

What happened to the flu?

When the reality of the coronavirus pandemic set in last year, the country was still in the throes of the normal flu season, which had peaked in February. Then schools closed, travel halted and millions began working from home, and the number of new flu cases quickly dropped to historic lows, even as the coronavirus surged.

And the decline has not been because of a lack of testing. Since late September, 1.3 million specimens have been tested for influenza, more than the average of about one million in the same period in recent years.

The public’s history of exposure to influenza, scientists say, may partially explain why the flu virtually disappeared while the coronavirus continued to spread after safety measures were implemented.

“For something like Covid, where you have a fully susceptible population at the start of a pandemic, it takes a lot more work to slow the spread of the infection,” said Rachel Baker, an epidemiologist at Princeton University.

In other words — unlike with the coronavirus — the population has some natural immunity to the flu, from years of being exposed to various strains of the virus. People are susceptible to new strains of the flu each year, but less so than they are to wholly unfamiliar viruses.

The mere presence of the coronavirus may have also played a role in suppressing flu cases, said Dr. Webby, because there is often just one dominant respiratory virus in a population at a given time. “One tends to keep the other out,” he said.

And influenza was not the only virus that disappeared over the last year; there were also substantial drops in other respiratory illnesses, including the respiratory syncytial virus, or R.S.V., which is the most common cause of pneumonia in infants.

What will happen when the flu returns?

Influenza is a relatively common illness that has the potential to become deadly, especially among young children, seniors and adults with chronic health conditions. The C.D.C. estimates that the flu has killed 12,000 to 61,000 people a year since 2010.

If immunity to the flu declined during the pandemic because of the lack of exposure to the latest flu strains, more people than usual may be susceptible to the virus.

“Every year, anywhere between 20 to 30 percent of the population gets its immunity sort of boosted and stimulated by being exposed to the flu virus,” Dr. Webby said. “We are not going to have that this year.”

“Decreases in natural immunity are a concern,” Dr. Olsen said, “and lower immunity could lead to more infections and more severe disease.”

The result could mean larger and out-of-season outbreaks of the flu and of R.S.V., Dr. Baker said. In Florida, in fact, R.S.V. would normally be on the decline at this time of year, but it is currently having an uptick.

If offices and schools begin to reopen in greater numbers in the fall, as many expect, scientists will be watching closely.

“We are always concerned about influenza causing severe disease, particularly in persons at increased risk of complications,” Dr. Olsen said. “We know that school-age children are important drivers of influenza virus transmission. However, because influenza is difficult to predict, we cannot forecast the severity of next season.”

There is also a potential upside to the absence of influenza: Fewer cases usually lead to fewer mutations.

“Right now, because influenza isn’t circulating as much, it’s possible the virus has not had as much opportunity to evolve,” said Dr. Baker, “meaning our vaccines could be more effective than normal.”

Choosing the strains for the flu vaccine

Creating the influenza vaccine this year has been more difficult than in the past.

Every year, scientists evaluate the strains of influenza that are circulating around the world, and meet to decide which strains to protect against in that year’s vaccine. They look at the strains that are getting people sick, and use that information to predict which strains are most likely to infect people when flu season sets in.

“We met at the end of February to make those recommendations,” said Dr. Webby, referring to the World Health Organization panel that assesses the flu vaccine. “And it was tricky. The amount of data was orders of magnitude less than it typically is.”

Dr. Olsen, the C.D.C. epidemiologist, pointed out that the vaccine choices are based on more than just existing strains. Scientists also consider other data, including forecasts of “the likelihood of any emerging groups of influenza viruses becoming more prevalent in coming months.”

And, she said, the uncertainty around the return of influenza makes getting vaccinated against the flu more important, not less.

There’s another hard-to-predict factor that could play a significant role when the flu comes back: whether society will carry on behaviors learned in the pandemic that benefit public health. Will mask-wearing become the norm? Will employers give their employees more physical space?

The last time Americans had a chance to make those behaviors part of the culture, Dr. Baker pointed out, they did not.

“The 1918 influenza pandemic should have been something that gave us some sort of societal learning,” said Dr. Baker, but behavior did not change. “So what is the journey you are about to go on from the Covid-19 pandemic, along that axis?” she added. “Will you wear your mask, even if no one else is?”