The Pandemic Broke the Flu

Editor’s Note: The Atlantic is making vital coverage of the coronavirus available to all readers. Find the collection here.

In November, as fall was fading, Matt Binnicker began to hunker down for a hard winter. The coronavirus had already infected an estimated 13 million people nationwide, and his team at the Mayo Clinic in Rochester, Minnesota, was now peering over the precipice of flu season, when every coughing, feverish patient would need not one diagnostic test, but two.

Determined to stay one step ahead, Binnicker’s lab had worked furiously to develop its own influenza test in order to amp up capacity. On December 1, the team began screening all patients with respiratory symptoms for both viruses.

In the two months since, thousands of tests have turned up positive for the coronavirus. But the tally for the flu has held constant. The lab has run 20,000 flu tests—10 times as many as it processed the season before—and zero have come back positive.

“It’s absolutely remarkable,” Binnicker, the Mayo Clinic’s director of clinical virology, told me. “I fully expected there to be a typical influenza season this year.”

The same baffling trend is repeating itself nationwide, and around the globe. While the coronavirus has surged, the flu and other respiratory viruses have flickered out. Since early fall, about 800,000 laboratory samples have been tested in the United States for the flu and reported to the CDC, and only 1,500 or so have come up positive—a mere 0.2 percent. This time last year, close to 100 times as many flu cases had been identified from nearly the same number of tests. By the middle of the 2019–20 flu season, positivity rates were cresting at about 25 or 30 percent, mottling federal flu-activity maps in shades of red and orange, which denote the virus’s rampant spread. Now those maps remain almost entirely green, indicating low or minimal flu activity.

This winter has, so far, been the quietest flu season in recent memory, and the perks are clear. Fewer flu cases mean fewer deaths, fewer occupied hospital beds, and fewer overtaxed health-care workers, caregivers, and laboratory employees—a welcome respite for a country still in the coronavirus’s grip. But the flu’s absence is also unsettling. Without flu cases to study, researchers have been starved of data crucial for developing vaccines and forecasting the next outbreak. Flu viruses haven’t gone extinct. They’re temporarily in hiding. And no one’s quite sure when, or how, they will return.


The flu’s recent disappearing act has left an eerie lull in labs that were fearing the worst for months. This quiet is a jarring departure, not just from typical flu seasons, but also from the crush of the coronavirus.

“We have so much COVID circulating here in Arizona,” says Erin Graf, the director of clinical microbiology at the Mayo Clinic in Arizona. “I would have thought that if people can get COVID, people can get [the] flu.” These viruses transmit in much the same way, attack similar parts of the body, and even cause similar symptoms. But Graf’s team has done about 7,000 influenza tests since November, and only one has been positive. The 40,000 coronavirus tests, however, have returned about 6,000 positives. The Seattle Flu Study, too, is still diligently screening people for the flu to ensure that it’s not flying under the radar; of the 6,000 tests the team has run, only two have come back positive. “It’s really quite extraordinary,” says Helen Chu, the head of the study and an immunologist and epidemiologist at the University of Washington.

Other respiratory viruses have fallen away as well, among them respiratory syncytial virus, parainfluenza viruses, even other coronaviruses that cause common colds—nearly all of the usual suspects behind the fevers, coughs, and sniffles that typically rear their head this time of year. On the virological scoreboard, the only pathogen that’s truly had a good year is the new coronavirus, SARS-CoV-2.

The uneasy détente with these viruses in the United States isn’t entirely unprecedented. Similar dynamics played out first in the Southern Hemisphere, where winter stretches from June to August, with countries and cities in South America, Africa, and Australia reporting vanishingly low case numbers. But even after witnessing a similar drought of viruses in the North, scientists remain unsure of the reasons behind the shift.

The drastic behavioral changes that the pandemic has forced the world to adopt have almost certainly played a role. Widespread masking, lockdowns, and other measures that helped squelch the coronavirus in countries such as Australia appear to have wiped out other respiratory viruses too. Travel bans, instated to keep people from carrying the coronavirus across international borders, cut off the conduits for other viruses to hopscotch between countries  and seed new outbreaks—a phenomenon known to ferry flu viruses between the North and the South every year.

In the U.S., even relatively spotty masking and physical distancing seem to have made a difference. Workplaces and businesses closed; more people stayed home when they felt sick. In many places, children, who tend to be hit particularly hard by bouts of seasonal flus, stopped mingling in schools and day cares. And a vocal push for vaccinations might have bumped influenza inoculations up a notch from previous years, according to tentative CDC estimates.

[Read: Paging Dr. Hamblin: I don’t see the upside of a flu shot.]

Many of these measures have long been known to successfully combat the spread of disease. “Each year, we try to get vaccination rates up, to get sick people to stay home,” says Ibukun Akinboyo, a pediatrician and infectious-disease physician at Duke University. “This is the first year we have this many people masking, washing their hands, and being aware of their symptoms.”

The flu and the rest of the seasonal-virus cavalry might also be easier targets to quell than the new coronavirus. To most human immune systems, prepped by previous encounters or vaccination, these annual pathogens represent a cadre of familiar foes. Their recognizability, though not potent enough to prevent new infections entirely, boosts a person’s chances of mounting a successful defense when another version of these viruses return, like a layer of hardy bark that offers a tree a touch of flame resistance.

“I think that’s one of the biggest things,” says Stacey Schultz-Cherry, a virologist and immunologist at St. Jude’s Children’s Hospital, in Memphis, Tennessee. “That low-level immunity can make a huge difference.”

The coronavirus, however, was a stray spark that leaped from the wild into a population of completely susceptible humans—a fresh batch of kindling, ready to burn.

Despite their rough overlap in symptoms, flu viruses and the new coronavirus are biologically distinct in ways that might give the newcomer an edge. The coronavirus seems to transmit more readily to others, even from people without symptoms, and has been linked to more super-spreader events. Microscopic anatomical differences might make the coronavirus more likely to cling to airborne globs of spittle, or tougher to snuff out as it traverses the space among hosts. (Oddly, rhinoviruses, the main culprits behind the common cold, haven’t been stamped out to the same extent as the flu—a hardiness that could be attributed to their tough outer armor or an as-yet-unidentified quirk in how they spread among people.)

“Flu just tends to be a lot less transmissible, which means it’s easier to suppress it,” says Shweta Bansal, a disease ecologist at Georgetown University. “That’s partly why we’re getting away with an imperfect response right now.”

All these factors together might have cleared a path for the coronavirus to jostle its way to the top, at the expense of other viruses. That tussle might even be playing out directly in individual airways: People’s immune systems tend to remain on guard for a while after they’ve cleared an infection by one virus, bolstering them against immediate invasion by another. This balance of power won’t necessarily persist in the long term, though. Viruses that settle into a population may eventually learn to play nice with one another—perhaps becoming cordial roommates, setting up simultaneous infections in the same individual, even riling one another up.


For the moment, however inadvertently, the world has tamed the flu—an unexpected blip of good news in the year-long upending of normal life and a relief for overloaded hospitals and labs. But the flu’s exile isn’t built to last. Infections are still happening, perhaps many more than are being reported as people continue to shelter at home. (Even in typical years, many presumed flu cases are not actually confirmed by laboratory tests.) And where masking and distancing slacken, these and other viruses will keep trickling through.

The next outbreak is inevitable. Its timing, however, isn’t. If gatherings remain sparse, this year’s glancing blow with the flu might repeat itself this time next year. Or the flu and its comrades could resurge in the coming weeks and months. Flu seasons in the past have simmered through the fall and early winter, only to boil over in February. “We may not be out of the woods yet,” Bansal says. Or perhaps, should certain behaviors recede in the summer, an off-season outbreak could occur.

Countries that have gotten a better handle on COVID-19 will be some of the ones to watch, Schultz-Cherry says. Where the coronavirus ebbs, other viruses might start to pick back up.

What will happen when humans and the flu reunite is unclear. Every skipped flu season adds to the pool of people who haven’t yet been infected, including very young children who may have never experienced these viruses at all—saplings in a fiery virus’s woody playground. Even among adults, immunity is expected to wane over time: Without an annual reminder, certain bodies might forget what it’s like to fight the flu and lower their guard. “Susceptibility is increasing in the population,” Bansal says. People with no or reduced immunity “are like fuel for the flu fire. The more fuel is available, the easier it can be for an outbreak to happen.”

The flu that returns also won’t necessarily be the same flu that left. Flu viruses are natural shape-shifters, capable of mutating and swapping segments of their genomes at extraordinarily high rates, making it easy for them to pepper themselves throughout the population on a near-annual basis. The next flu that hits might be weaker or stronger; it might be a strain that’s familiar to our immune systems—or foreign enough to wreak substantial havoc.

During typical years, those possibilities are a little easier to forecast, thanks to a well-oiled network of influenza-surveillance centers scattered across the globe. This time of year, scores of researchers would typically be buried under piles of virus-laden samples, trying to identify the most prevalent flu strains, including new versions that might have emerged. But the low visibility of this year’s flu viruses has left the usual data sets more sparsely populated than usual, which could “create some challenges” for virologists and vaccinologists, Schultz-Cherry says.

Florian Krammer, a virologist and flu expert at the Icahn School of Medicine at Mount Sinai, puts forth two possibilities for how flu strains might be busying themselves. “One is good, one is bad,” he told me. In one scenario, the stark lack of flu transmission this year could end up throttling the circulating strains—possibly even taking one out of commission entirely. “What if we just lose one of the lineages?” he said. “That would be awesome.”

Alternatively, a branch on the flu family tree could quietly split in two, leaving scientists scrambling to catch up to the spread in the fall.

[Read: Why it’s so hard to forecast the flu.]

The fogginess of the flu forecast could also make it challenging to design an on-point vaccine, Krammer said. Twice a year, the World Health Organization convenes a meeting to recommend vaccine ingredients to countries in the North and the South, based on data cultivated from global flu surveillance, to help ensure that the most troublesome strains will be covered. The Northern Hemisphere’s meeting will take place later this month; in the United States, the FDA will make the final call about what goes into this year’s forthcoming vaccine.

“I believe that they will still get it right,” Krammer said of the vaccine prognosticators. But this year, the risks of a stumble are a bit higher. At Mount Sinai, which runs its own virus surveillance program, only eight flu patients have been catalogued in recent months—an extraordinarily small fraction of the 1,000 to 1,500 known cases who typically flood the hospital this time of year.

None of that means disaster is imminent. Scientists might be able to make up for the year of difficult flu surveillance by pivoting to new vaccine technologies, such as those used in the RNA-based COVID-19 shots developed by Pfizer-BioNTech and Moderna. Typical flu vaccines take about half a year to concoct. “Six months is a long time for a virus that mutates pretty rapidly,” says Chu, the Seattle epidemiologist. But RNA-based vaccines are easier and faster to tweak and retool, meaning flu shots could someday be cooked up in a matter of weeks. “They’re so easy to change,” Chu says.

Some of these new vaccine technologies “are already being analyzed for influenza,” David Wentworth, a virologist who oversees the CDC influenza division’s virology, surveillance, and diagnosis branch, wrote in an email.

But some aspects of flu prevention are unlikely to change. If anything, the past year has reaffirmed that tried-and-true public-health measures work, says Seema Lakdawala, an expert in flu transmission at the University of Pittsburgh. “We have a glimpse of what could be very effective,” she told me. “I’m really hopeful that when people are sick, either they stay home and/or they put on a mask when they have to go out.”

With mask wearing and physical distancing continuing to flag across the country, Lakdawala conceded that continued enthusiasm for these public-health measures isn’t guaranteed. But she stressed that the world won’t have to maintain pandemic-level vigilance forever. As the flu and other viruses reemerge, the human population could return to its virological normal. Or perhaps it will stick with a less stringent version of its pandemic playbook, and find a new equilibrium—one in which there are fewer viral diseases to deal with each year. The past year’s events suggest that the flu is less feral than once thought. Our next steps could help us bring it to heel long term, or let it run wild again.

Leave a Reply

Your email address will not be published. Required fields are marked *