COVID helped to kill off a flu strain. Here's how that will affect influenza vaccines in the future.

This fall’s flu shot will be designed to protect you from just three strains of the influenza virus, instead of the usual four, according to the U.S. Food and Drug Administration (FDA). That’s because an entire branch of the influenza family tree has died out, and experts say that's likely due, at least in part, to the COVID pandemic and the precautions many people were taking. Here’s what to know about the now “extinct” Yamagata influenza B virus, what happened to it and how its disappearance will affect next year’s flu vaccines.

What happened to the Yamagata strain of flu?

In the years leading up to the pandemic, Dr. Arnold Monto, a professor emeritus of epidemiology at the University of Michigan and member of the FDA's vaccine committee, tells Yahoo Life that scientists got a clue that Yamagata might be on the decline because “it wasn’t diversifying the way that B Victoria did," which is another lineage of influenza B. "Victoria was doing all the weird, wonderful things that flu viruses do," says Monto, "but that wasn’t happening with B Yamagata."

Then the COVID pandemic hit, and scientists stopped seeing Yamagata in samples taken from patients with flu altogether. “None at all — extinction,” says Monto.

It’s impossible to say for sure what caused the death of the Yamagata strain, according to Monto and Dr. Pedro Piedra, a professor of molecular virology, microbiology and pediatrics at Baylor College of Medicine. But they and most virologists consider the various methods to slow the spread of COVID, like masking and social distancing, a major factor.

One reason that might have led to the extinction of Yamagata is that influenza B almost exclusively infects humans, Piedra tells Yahoo Life, while influenza infects animals. “For viruses to stay alive, they need a host,” he explains. “So imagine for influenza B Yamagata, all of a sudden the ability to transmit is not possible, because the host is now protecting themselves through non-pharmacological interventions,” such as avoiding close contact with other people to slow the spread of COVID.

The Victoria B strain was more prevalent than Yamagata before the pandemic and managed to hang on, but “the year prior to the pandemic, there was less Yamagata circulating, so that when it took a hit, that hit was more dramatic,” Piedra explains. Influenza A, meanwhile, had plenty of animal hosts to sustain it while humans hid out.

Why this matters

Each year, scientists have to guess which subtypes of influenza viruses they think will be most actively circulating in order to formulate the most protective vaccine possible. That’s a serious challenge because viruses are constantly recombining and mutating.

There are four broad types of influenza: A, B, C and D. But types C and D rarely appear and generally cause only mild illnesses. For this reason, the CDC and the World Health Organization don’t consider them to be public health threats.

Strains of influenza A and B, on the other hand, circle the globe seasonally. More than 130 subtypes of influenza A have been discovered in nature, according to the CDC, while influenza B has been divided into just two groups, known as lineages: B Victoria and B Yamagata. But vaccine makers can’t yet include more than four types of the flu virus in a given vaccine due to technological limitations. Since 2014, therefore, the vaccine has been made to protect against two strains of influenza A — H1N1 and H3N2 — and two strains of influenza B, Victoria and Yamagata.

But with the disappearance of Yamagata, the U.S. and much of the world will use a shot based on just three strains of flu — or a trivalent vaccine — instead of a quadrivalent vaccine, which is designed to protect against four strains.

Making a vaccine based on fewer flu strains could improve vaccine-making capacity globally, research suggests. “It gives you a little more leeway,” Piedra says.

It means that making the vaccine won’t take quite as long, so scientists may have a little longer to pick the flu strains the vaccine is designed to block — a decision that typically happens in May. Or, as Piedra explains: “You will have the vaccine a little earlier, to be sure that everyone who wants to be is vaccinated. If the vaccine comes in late, it’s much harder to vaccinate everyone and have broad coverage.”

How trivalent flu vaccines be as protective?

Yes, say both Monto and Piedra. There’s no evidence that Yamagata B is still around, so the vaccine will be tailored to the strains that are circulating. “As a matter of principle, you don’t want to vaccinate people with something that you don’t need,” says Monto.

It’s also worth noting that it's not impossible for the B Yamagata strain to reemerge, says Piedra. But he adds that there’s no reason to vaccinate against it now and no immediate cause for concern that it will come back. Also, according to Monto, there's a good reason to leave it out of the vaccine recipe. In the U.S., flu shots contain an inactivated — virology-speak for “dead” — bit of virus that’s incapable of causing infection. But the nasal spray form uses what’s called a live attenuated influenza vaccine, meaning it contains weakened, live viruses.

This version of the virus is generally too weak to cause illness, but "the concern there was about not wanting to bring back something that was gone” by including B Yamagata in these vaccines, Monto says. So come the fall, the flu shot and nasal spray will protect against three subtypes instead.