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Experts say getting vaccinated is still the best way to reduce your odds of getting the flu. Getty Images
  • The flu vaccine for the 2018–2019 season was only 29 percent effective.
  • The main reason for the vaccine’s ineffectiveness was a strain of H3N2 flu that developed in the spring.
  • The effectiveness is difficult to predict because the flu virus constantly mutates, so scientists have to develop a new vaccine every year.
  • The flu vaccine still prevents hundreds of thousands of illnesses every year and increases a region’s “herd immunity.
  • The CDC and other experts still recommend you get the flu vaccine every year.

Getting vaccinated can help protect you from contracting the flu.

But it’s not a guarantee you won’t get sick.

That’s because the flu is “smart,” Dr. Kathleen Neuzil, director of the Center for Vaccine Development at the University of Maryland School of Medicine, told Healthline.

The virus’s ability to rapidly mutate means a vaccine developed for one strain won’t work against a strain that develops later.

That’s exactly what happened during the 2018–19 flu season.

Epidemiologists anticipated the H1N1 strain would be dominant during the U.S. flu season that ended this spring, so the vaccine that was developed and distributed targeted H1N1.

Initially the scientists’ prediction played out as expected. But later in the season, the H3N2 strain of flu began spreading.

“Unfortunately, the development of the next season’s influenza vaccine, containing three to four strains, requires a six-plus month lead time,” Dr. Jack Springer, assistant professor of emergency medicine at the Zucker School of Medicine at Hofstra-Northwell in New York, told Healthline.

The flu shot developed in February 2018 for the 2018–19 season contained a H1N1 vaccine but not one for H3N2.

“The 2018–19 influenza season was a moderate severity season with two waves of influenza A activity of similar magnitude during the season,” the Centers for Disease Control and Prevention (CDC) reported in its Morbidity and Mortality Weekly Report on June 21. “H1N1 predominated from October 2018 to mid-February 2019, and H3N2 activity increased from mid-February through mid-May.”

With no effective vaccine available to combat H3N2, the overall effectiveness of the flu vaccine fell to 29 percent, the CDC reported.

By contrast, vaccine effectiveness was estimated at 49 percent during the period that H1N1 was dominant. Once H3N2 began spreading, effectiveness plunged to 9 percent.

Springer explains that even though the flu shot wasn’t preventive for H3N2, it still had a “nonspecific effect that acts on similar flu viruses to greatly limit severity.”

While the CDC numbers sounds dire, the effectiveness of the flu vaccine still fell solidly in the middle when viewed historically, according to Neuzil. Vaccine effectiveness rates in recent years have been as low as 19 percent and as high as 52 percent, she says.

“Influenza keeps you on your toes,” Neuzil said.

She points out that while the measles vaccine in use today has remained fundamentally unchanged for years, a new flu vaccine must be developed every year.

“It’s predictably unpredictable,” she said of influenza. She adds the low vaccine effectiveness in 2018–19 wasn’t unusual.

Neuzil says the time needed to develop, test, and distribute a new vaccine makes it unlikely that public health officials can respond to an emerging flu strain in time to make a difference.

Antiviral drugs such as Tamiflu are “effective and probably underused” against the flu, Neuzil says. Ultimately, however, “We need a better flu vaccine that could be cross-protective from season to season.”

Current flu vaccines identify proteins on the surface of the influenza virus and provoke a response by the immune system.

“We know that attacking these proteins can prevent the flu, but they are constantly changing,” Neuzil said. “We’re looking for other parts of the virus where we can prevent the flu with antibodies that don’t change as much.”

Among the biotechnology firms working on novel therapies to prevent and treat influenza is San Diego-based Cidara Therapeutics.

The company is developing a hybrid drug dubbed CB-012. It targets an enzyme on the surface of the influenza virus critical for reproduction as well as a bi-specific immunotherapy to prompt the immune system to attack the virus.

“If the virus mutates (to counter the therapy), it cannot reproduce,” Jeff Stein, PhD, the company’s president and CEO, told Healthline.

CB-012 has been shown to reduce viral load and provide long-lasting prevention of flu transmission in animal testing.

Cidara is currently laying the groundwork for bringing the therapy to clinical trials as the first step toward Food and Drug Administration review.

“It could be good for both flu treatment and prevention,” Dr. Taylor Sandison, Cidara’s chief medical officer, told Healthline.

Experts note that even in years with relatively low vaccine effectiveness, the flu shot prevents hundreds of thousands of flu infections — both among people who get the flu shot and the population that avoids getting infected by people who have been vaccinated.

“That’s still 30 percent of people who were not spreading the flu to anyone else,” Neuzil said.

“The vaccine prevents significant morbidity and mortality in tens of thousands of lives annually, if not more,” Springer added. “I put my arm out as early as I can each season.”

“First of all, accept the fact that no vaccine is 100 percent effective,” Dr. David Cutler, health sciences assistant clinical professor at the David Geffen School of Medicine at UCLA and chairman of the Santa Monica Family Physicians medical group, told Healthline.

“Secondly, there are many factors which can influence the likelihood of getting the flu. Individual behavior like hand-washing, the rate of vaccination in your community, and the people you are exposed to will all have profound effects on your likelihood of getting the flu in any year,” Cutler said.

The H3N2 strain may have been especially virulent because it arrived so late, regardless of whether a vaccine had been available, Cutler notes.

“Late in the flu season, people can get more lax about their behavior, making transmission of flu more likely,” he said.

So, while vaccine effectiveness may vary from year to year, Cutler and other experts maintain that “the single most important thing you can do to prevent the flu is get a flu vaccine.”