The first data on how well the flu vaccine is working this season in America has just been published — and it helps explain why everyone appears to be sick right now.

The study, from the Centers for Disease Control and Prevention’s Morbidity and Mortality Weekly Report, tracked flu cases among 1,700 children and adults across the US. They found the flu shot was 36 percent effective overall, meaning it reduced a person’s risk of getting sick with flu and going to a doctor’s office by about a third.

But the vaccine’s effectiveness against H3N2, the most commonly circulating strain this flu season, was much lower: 25 percent. And this finding squares with an earlier report from Canada, which found the flu vaccine was only 17 percent effective against H3N2.

“The evidence is mounting, from Australia and now from Canada, that the vaccine protection is low [this year],” said Danuta Skowronski, the lead author on the Canadian study and an influenza epidemiologist at the British Columbia Center for Disease Control.

In a good year, the flu shot’s effectiveness hovers between 50 and 70 percent. But in years when the H3N2 type of flu virus circulates — as it is this year — the vaccine tends to be less protective.

To understand why the shot appears to be underperforming this year, you need to understand how the flu vaccine is made — a production process that involves eggs.

Whenever H3N2 is the dominant flu strain, vaccines don’t work as well

There are four species of influenza viruses — A, B, C, and D — and seasonal flu is caused by influenza A and B. Every year, different strains of these viruses circulate.

To formulate the flu vaccine, public health agencies essentially make early educated guesses on which strains will make the rounds. And that’s not easy.

In February, long before flu season begins in the US, the World Health Organization offers a prediction, based on surveillance and laboratory and clinical studies. Then each country uses that prediction to approve vaccines in its jurisdiction. (In the US, the Food and Drug Administration makes the final call.)

The potential for error here can dramatically alter the effectiveness of the flu shot in a given season. If vaccine makers prepare for one combination of viruses and different ones end up circulating widely, the vaccine won’t work that well.

But there’s another thing that researchers have recently come to realize also alters the vaccine’s effectiveness: Whenever H3N2, a strain of the influenza A virus, is the dominant flu type in circulation, the vaccine doesn’t perform as well.

Edward Belongia, a senior epidemiologist at the Marshfield Clinic Research Institute in Wisconsin who has studied flu vaccine effectiveness, found that the combined vaccine effectiveness during H3N2 seasons was 33 percent. The flu shot’s effectiveness rose to 54 percent during influenza type B seasons, and 67 percent during H1N1 seasons. (This year’s shot is also preventing illness from other flu types more effectively than H3N2, according to the CDC. The vaccine’s effectiveness rose to 67 percent against H1N1 and 42 percent against influenza B viruses.)

Part of the reason has to do with ... eggs

There are a couple of reasons why it’s harder to vaccinate against H3N2. For one, the virus mutates as it moves through the population at a faster rate than other flu viruses — making it even harder to design a shot that matches the circulating virus.

One other reason the flu vaccine tends to underperform in H3N2 years has to do with ... eggs. To produce the vaccines, manufacturers need to grow a lot of flu virus — and they discovered long ago that flu virus grows extremely effectively in eggs. So viruses are injected into fertilized hen’s eggs, incubated for several days while they replicate, then harvested from the eggs, killed (or inactivated), and purified to go into vaccines.

“It’s an antiquated process, but it’s time-honored,” Anthony Fauci, the head of the NIH’s infectious diseases division, explained. While flu vaccines developed with more modern (cell-based and recombinant) methods of production have been licensed in the US, it’s not yet clear they are more protective against flu than the egg-based vaccines.

Plus, no other cell system comes close to growing the flu virus as cheaply or efficiently as eggs, and the industry has invested a lot in the egg-production infrastructure. So, Fauci explained, “We are stuck in the [egg-based] way, and it’s tough to transition to a more modern technology.”

But lately, researchers have found that there are problems with the egg-based approach that specifically relate to H3N2.

“In the process of adapting virus to grow in eggs, that seems to introduce further changes to the [H3N2] virus, which may impair the effectiveness of the vaccine,” Belongia said. In other words, while growing the flu virus for vaccines, H3N2 mutates to adapt to the eggs, which seems to result in a vaccine mismatch.

Skowronski, whose research helped uncover the egg problem, thinks scientists will discover other reasons the flu vaccine sometimes underperforms. “I don’t think [egg-based production methods] tell the whole story,” she said, noting how complicated flu viruses — and our responses to them — are.

But eggs certainly tell an underappreciated part of the story. And while scientists pursue the holy grail of a universal flu vaccine, they should also try to understand how our current production methods hamper the vaccines we have now.