How COVID-19 Ended Flu Season Before It Started

In the third week of 2021, clinical laboratories nationwide tested 23,549 specimens for influenza. Of those, just 0.3 percent (65 tests) turned up positive — a number that is, to put it mildly, absolutely wild.

“Normally, this time of year, we’d be running 20 to 30 percent positive,” said Lynnette Brammer, the head of the Centers for Disease Control and Prevention’s Domestic Influenza Surveillance team.

Although the U.S. continues to struggle with COVID-19, it has apparently beaten the flu into submission. Since the end of September, the combined total of positive flu cases identified by both public health and clinical labs is fewer than 1,500. There are high schools with more people in them. The phenomenon is not only in the United States — worldwide, rates of influenza are nearly off-the-charts low. When you line multiple years up on the same graph, it can even look like there are no cases of flu this year. That’s how out of step we are with the norm.

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That data is mind-blowing, especially because many observers spent the fall worried about a “twindemic.” The minuscule flu season also raises a few questions: How can there be so many cases of one respiratory illness and so few of another? Why isn’t there always a tidy match between the places with the least COVID-19 and the places with the least flu, or vice versa? And, seriously, are the flu numbers really that low?

The answers are complex, even though this teeny-tiny flu season is a simple fact.

We don’t track the flu the way we track COVID-19. The average seasonal flu exists in a weird liminal space, serious enough to keep an eye on, but also not so serious that we are literally trying to count every single case. After all, most people who get sick with the flu won’t even bother to go get tested for it. They’ll have a couple bad days in bed (if they’re able to take off work) and otherwise go about life basically unchanged.

Instead, counts of flu cases come from a few different surveillance systems, including a network of around 100 public health and 300 clinical labs that participate in virologic surveillance, reporting weekly test numbers and positive cases to the CDC. There’s also a network of doctors’ offices reporting cases of “influenza-like illness,” a network of hospitals reporting lab-confirmed cases and mortality surveillance data from the National Center for Health Statistics, which pulls numbers for flu, pneumonia and other respiratory illnesses directly from death certificates. Other than the NCHS numbers, none of these networks represent truly national figures. They’re a sampling, from across the nation, and they’re reported voluntarily. This is why annual numbers of flu cases (and even deaths) are an estimate, extrapolated from the narrower picture we can see.

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All of that is to say that there were almost certainly more than 65 cases of flu in the entire United States a couple weeks ago. That number represents what was counted at the member labs — not what existed in total. And even this number is likely an undercount, experts told me, because, right now, people with the symptoms of respiratory illness are significantly more worried about COVID-19 than the flu. “If people aren’t getting tested for it, then we don’t find it,” said Janet Hamilton, executive director of the Council of State and Territorial Epidemiologists. “And the protocol isn’t to test for flu if you’re negative for COVID.” There are probably a lot of people whose fears of COVID-19 infection are assuaged by a negative test result, and who just go home and deal with whatever illness they do have without seeking any medical treatment.

That said, Hamilton and others told me there’s reason to believe actual cases of flu are, indeed, way down. The fact that we are seeing negligible flu seasons in other countries, which count their flu cases differently than we do, is part of the reason why. Also, hospitalizations for flu in the United States are also way down. “People in the hospital get properly diagnosed. So it’s a better indication of lower circulation in people,” said Adolfo García-Sastre, director of the Center for Research on Influenza Pathogenesis at the Icahn School of Medicine in New York. Between Oct. 1 and Jan. 23, there were a total 142 laboratory-confirmed flu hospitalizations in this country — 0.5 per 100,000 Americans over nearly four months. Typically, by this time of year, we’re talking dozens per 100,000 every week.

This massive shift, experts told me, is likely tied to the precautions we’ve taken to avoid catching COVID-19: mask-wearing, social distancing, obsessive cleaning of surfaces (which doesn’t do much to prevent COVID-19 but probably is preventing flu) and even keeping kids out of the classroom. “The major vector for influenza is children,” said David Topham, co-director of the New York Influenza Center of Excellence in Rochester. If they don’t get to breathe on each other like normal, they also can’t transmit as much flu. And that trick still works, even if flu isn’t the reason we’re keeping them distanced.

Influenza hasn’t been our target with all these interventions, but we’ve certainly given it a good pummelling. And that’s because flu just isn’t as transmissible as COVID-19. The R0 (pronounced R naught) — the number that quantifies the average number of people who will catch a virus from a single infected person — is significantly lower for flu than for COVID-19. “R naught is usually around 1 or 1.5 for flu. And for SARS-CoV-2 it’s between 2 and 4,” Topham said, referring to the novel coronavirus’s scientific title. “When you do masking and social distancing, you can artificially lower R naught. So that probably pushes flu down to a range of less than 1. Somebody gets infected, they infect less than another person, and then it’s not viable.”

Our strategies are working on COVID-19, as well. Just not as dramatically, because it was more likely to spread to more people to begin with.

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That doesn’t totally explain why places that have taken masking and distancing very seriously — Australia, for example — and places that have not — the U.S., say — are both experiencing a nearly nonexistent flu season. Significantly reduced international travel has probably played a role in that, Brammer said. Usually, our flu season follows that of the Southern Hemisphere. But if there wasn’t much of one there, and there wasn’t much travel to transport the virus — the flu has no way to travel.

Meanwhile, within the United States, flu rates have remained low in both the states that have instituted measures like masking mandates and those that have not. And García-Sastre said that’s probably because of a little concept you might have heard of: herd immunity. Just like you don’t need to vaccinate absolutely everyone to get a benefit in reduced disease transmission, you also probably don’t need to have the entire population wearing masks and practicing social distancing to see a benefit.

Still, scientists don’t know for certain what’s happening because the trouble with a really, really minuscule flu season is that it doesn’t leave you enough cases to make solid statistical inferences. We don’t know, for example, much about what happens when you get both the flu and COVID-19, because there haven’t been enough cases of it to do good research. We don’t really know how this bottleneck is affecting which strains of flu are circulating for the same reason. We don’t even know, for certain, that it is the masks and distancing that are squashing the flu because there are so few flu cases left to look at.

And that’s an irony that could end up affecting future flu seasons. Take the flu vaccine. Experts use data from past flu seasons to decide which strains people should be inoculated against. “It is definitely going to make the selection of viruses for next years’ vaccine more challenging. We just don’t have a lot to look at worldwide,” Brammer said. “What happens in the long term, I don’t know.”