The World Health Organization (WHO) today recommended that vaccine manufacturers completely change the three viral strains included in the vaccines for the Northern Hemisphere’s next influenza season

As expected, the WHO recommended that vaccines for the next flu season includes a new variant of the influenza virus that started to increase last fall—too late for it to be included in this winter’s flu vaccines. Using current vaccine manufacturing technology, companies need at least six months’ prep time to produce flu shots in time for immunization campaigns beginning in the late summer or early fall. 

Researchers first reported on the new flu variant—called influenza A(H3N2) subclade K—in October, after this season’s flu shots had already been manufactured and distributed to drug store and clinics. That led to a mismatch in the vaccines that went into people’s arms and the viruses circulating around them, said Danuta Skowronski MD, a flu researcher at the British Columbia Centre for Disease Control in western Canada.

Although vaccines manufactured for the Southern Hemisphere were updated slightly compared with those distributed in the US this year, subclade K also appeared too recently to be included for the upcoming flu season in countries such as Australia and South Africa, Skowronski said. Flu season in the Southern Hemisphere typically runs from April to October, with the highest number of cases and peak activity between June and September.

The WHO also recommended changing two other strains in flu shots for the fall. The recommendations include two influenza A viruses and one influenza B virus.

Flu shots more protective than expected

Many scientists and public health experts worried that the current flu shots used in the Northern Hemisphere would be useless against subclade K, which seems to spread more easily and cause more serious disease than other types of flu strains. 

But the vaccine worked better than expected, Skowronski said. 

In an interim report released earlier this month, researchers found that the latest flu vaccines in Canada reduced the risk of illness caused by influenza A(H3N2) viruses and severe enough to require an outpatient medical visit by 40%, compared with the risk faced by unvaccinated people. That’s not much lower than the effectiveness observed in previous years for A(H3N2) viruses, Skowronski said. Vaccines were 37% effective at preventing subclade K infections serious enough to require medical help, and 31% effective against the H1N1 influenza A strain.

Developing flu recommendations after the US exit from the WHO

Today’s WHO flu shot recommendations were the first since the United States, one of its largest donors and scientific contributors, left the organization January 22. In recent years, the United States has provided more than $680 million annually, according to the Department of Health and Human Services (HHS).

NPR reported yesterday that Centers for Disease Control and Prevention (CDC) scientists would virtually attend the WHO meeting, held in Istanbul, Turkey.

“The selection announced this week reflects why it is so critical for the CDC to remain engaged with WHO,” said Daniel Jernigan, MD, MPH, former head of the agency’s National Center for Emerging and Zoonotic Infectious Diseases.

“The vaccine updates reflect the importance of global collaboration in preventing infectious diseases—efforts that simply could not happen working alone,” Jernigan said. “The benefit goes both ways. CDC has access to viruses from around the globe, and WHO participating labs get access to CDC specialized testing.”

Many researchers have been concerned how the US pullout would affect flu shot manufacturing, said Andrew Pekosz, PhD, a professor at Johns Hopkins Bloomberg School of Public Health.

Yet two of the vaccine strains recommended for inclusion in next fall’s flu shots are based on viral samples from the United States—specifically Missouri and Pennsylvania—showing that US scientists remain involved in the process.

“This means we can be better protected against more recently circulating flu B viruses, especially in children,” Jernigan said. “The CDC is working collaboratively with other labs, sharing viruses, as part of a WHO-coordinated effort. The risk is if the CDC were prevented from participating, the other members of the WHO network lose out on our part of the work, and vice versa.”

Independent labs around the world collect and analyze viral samples, then submit them to “centralized resource databases that can also be called upon to grow some of these viruses,” Pekosz said. “So there is a redundant capacity that was built into the system many years ago to make sure that multiple labs were generating these vaccines, so that in case there was a problem in one of them, there would be backups that we’re also generating information.”

Skowronski noted that, “we were able to see the genetic makeup of the viruses circulating,” because of these lab networks. “There are lots of laboratories, academic centers and vaccine effectiveness networks that are still involved directly or indirectly.”

Will the FDA agree with WHO updates?

Countries rely on the WHO to make their own flu vaccine recipes, Pekosz said.

The US Food and Drug Administration (FDA), for example, has traditionally aligned its recommendations with those of the WHO, Pekosz said. The FDA recently announced that its Vaccines and Related Biological Products Advisory Committee (VRBPAC) will meet March 12 to discuss flu shot recommendations.

But predicting what the Trump administration will decide on health policy has been difficult.

“What is uncertain is whether FDA will agree with WHO on the vaccine virus updates and not add new barriers on influenza vaccine manufacturers making this this fall’s vaccine,” Jernigan said.

Over the past year, the Trump administration has shocked public health leaders in the United States and abroad by throwing out numerous public health policies, including recommendations for childhood vaccines. 

The selection announced this week reflects why it is so critical for the CDC to remain engaged with WHO.

Earlier this month, for example, the FDA refused to consider Moderna’s mRNA flu vaccine, even though it could potentially shorten the time it takes to manufacture flu shots from six months to six to eight weeks. That might allow drug makers to adjust to late-breaking changes in viral strains and still distribute shots before the end of the flu season, Pekosz said. The FDA reversed its decision on Moderna’s flu shot a week later. 

Adding to the uncertainty is Robert F. Kennedy Jr., a long-time anti-vaccine activist and current HHS secretary. Kennedy has repeatedly made false claims about the flu shot. For example, he blames the flu shot for causing his spasmodic dysphonia, a condition that makes his voice raspy, even though there’s no evidence to support that claim.

Strains recommended for the fall’s flu shots

The WHO recommended different strains, depending on how flu shots are manufactured. For example, some traditional vaccines are based on viruses grown in eggs, a process used for decades. New vaccines are made in cell cultures or use recombinant- or nucleic acid-based technology.

Specific recommendations of viral strains to include in this year’s flu shots include:

For egg-based vaccines 

• an A/Missouri/11/2025 (H1N1)pdm09-like virus;
• an A/Darwin/1454/2025 (H3N2)-like virus; and 
• a B/Tokyo/EIS13-175/2025 (B/Victoria lineage)-like virus.  

For cell culture-, recombinant protein- or nucleic acid-based vaccines  

• an A/Missouri/11/2025 (H1N1)pdm09-like virus; 
• an A/Darwin/1415/2025 (H3N2)-like virus; and 
• a B/Pennsylvania/14/2025 (B/Victoria lineage)-like virus.