Scientists and vaccine experts have long argued that the flu vaccine is far from perfect.

Now, new may explain why that is.

And it’s because of chickens.

The majority of flu vaccines are grown in chicken eggs, a method of vaccine development that’s been used for 70 years.

The flu virus constantly mutates, making it difficult to develop a vaccine against it. Now scientists say that growing flu vaccines in eggs can cause even more mutations.

“Producing flu vaccines in eggs can be a problem because flu viruses often acquire adaptive mutations when grown in eggs… These mutations can change the antigenic properties of the virus,” Scott Hensley, PhD, an author of the study and associate professor of microbiology at the University of Pennsylvania, told Healthline.

According to the , last year’s flu vaccine was only 42 percent effective.

Even those who were vaccinated were at risk.

Hensley says this could be due to the way the vaccines were created.

“We think that last year’s vaccine effectiveness was likely decreased by an egg-adaptive mutation that was present in most H3N2 vaccine strains last year,” he said.

A Southern prelude

Influenza experts in the Northern Hemisphere often look to the Southern Hemisphere’s flu season in an attempt to guess what the flu season may bring.

Australia is just coming out of a particularly nasty flu season, with two-and-a-half times more of flu this year than in the same period last year.

The effectiveness of the 2017 influenza vaccine was estimated to be low, and the H3N2 strain was the dominant virus of the season.

A spokesperson for the CDC says it’s too early to say what this means for the United States this season, which has only just begun.

But if H3N2 dominates as it did in Australia, it could be a rough winter.

“Typically, H3N2-predominant seasons are more severe, with greater impact on the very young and the old,” a CDC spokesperson told Healthline.

Stephen Morse, PhD, a professor of epidemiology and an influenza expert at Columbia University in New York, is hesitant to make predictions, but he says Australia’s flu season isn’t encouraging.

“Our vaccine has the same composition as the one Australia had, so I’m not hopeful about that,” he told Healthline.

Time for a new method?

Morse is one of many scientists who believe it’s time to update to a more modern method of vaccine development rather than using chicken eggs.

“It was a great idea at the time, and probably has saved many lives, but we have better methods now,” he said.

Part of the problem with growing the vaccine in eggs, Morse says, is that it can take a considerable amount of time and can be an inefficient process.

“One of the biggest problems has always been the supply of suitable embryonated eggs, which have to be certified as safe for making vaccines. You need to plan long in advance just to get enough suitable eggs at the right time. It’s also time-consuming to make vaccine this way, and hard to change once the manufacturing process is started,” he said.

To add to the challenge, each egg can only grow one strain of the flu virus. To create a vaccine against three strains (H1N1, H3N2, and B) requires three eggs and only produces enough for a single dose.

Morse concedes that the dosage from one egg can sometimes be stretched using immune enhancers.

“But at basically three eggs per person that’s still a lot of eggs,” he said.

Two potential options

There have been advancements in other methods of flu vaccine development.

A CDC spokesperson told Healthline of two such options.

One is a cell-based flu vaccine that can be produced more quickly than an egg-based vaccine. It also wouldn’t require a large number of eggs to produce.

The other is a recombinant influenza vaccine, which can be produced faster than both egg-based and cell-based vaccines and doesn’t require eggs to produce.

Morse believes we are long overdue for applying modern technologies to flu vaccines. He says it’s been a long time coming to get to a point where the development of cell-based vaccines is possible.

“Vaccine development is largely driven by economics, and flu vaccines have gone through tremendous boom and bust cycles,” he said. “There’s little incentive for innovation when there are already approved existing products, even if far from optimal, because of the need to go through rigorous regulatory approval processes.”

We may have many more flu seasons ahead with an egg-based vaccine.

Simply switching methods isn’t as easy as it sounds.

“It is difficult to quickly change the process by which influenza vaccines are made since the process of making egg-grown versus other methods is very different,” Hensley said.

“We should start to increase our infrastructure to produce influenza vaccines through methods that do not rely on eggs.”