We're missing out on a better way to make flu vaccines

Every year, the World Health Organization makes a gamble: which flu viruses will dominate? They get two chances (one for each hemisphere) and this year, the WHO seems to have gotten it right twice. But vaccine effectiveness was still only 10 percent in Australia.

It's going to be a tough flu season—and we have eggs to blame.

Just because the shot is only 10 percent effective, that doesn't mean it's 90 percent useless. The percentage indicates how much the shot reduces your risk of getting the disease, but it doesn't reflect how much it can help you ward off the most severe symptoms. Even a mismatched vaccine gives your body some advantage when faced with the influenza virus, so getting the shot helps you regardless.

It's important to remember that an ineffective vaccine year actually makes it more crucial for everyone to get the shot. We prevent the spread of viruses through herd immunity, which relies on a certain percentage of people getting vaccinated. For shots that are highly effective, the percent of people who need to get it is lower because inoculated individuals are so unlikely to contract the disease. But vaccines that aren't very effective require more recipients to reduce the risk of spreading.

But if we picked the right flu strains for this year's vaccine, why isn't it more effective?

The vast majority of flu shots in the U.S. are grown inside egg cells. Eggs provide a great home for replicating viruses and are easy to work with, so they've been used for decades. People with egg allergies have to get a different shot, but other than that small subpopulation, we used to think that the vaccines we produced this way were perfectly acceptable.

But recent research suggests that viruses grown in eggs undergo a crucial change that makes the resulting vaccines less effective.

Our bodies identify the flu based primarily on a key part of the virus called hemagglutinin. HA is an antigen, which is the bit of the virus that our immune cells are able to bind to. A vaccine essentially trains your immune system to recognize specific antigens by growing a virus inside living cells, then inactivating the virus and collecting the antigens. If you later contract a virus with antigens just like those in the shot, your immune systems is already prepared to fight off the infection. But if the antigens differ, you have to ramp up your defense much further, allowing the virus key time to take over your body.

When the H3N2 strain of flu grows inside eggs, its HA mutates to allow the virus to replicate better in its new environment. That means laboratories are producing a flu vaccine based on a mutated version of the virus. When we later go look at the circulating flu and compare it to the reference used for the vaccine, we might think that we called it right. But the reality is that the virus that labs start with isn't the same virus that ultimately goes into the shot. Even when we seem to predict the right strains, the vaccine often ends up only 40-60 percent effective. This could help explain why.

Not all flu strains mutate the same way in egg cells. The problem is that H3N2 is often the predominant strain. Australia had an awful flu season, and it looks like it was because of mutations in the H3N2 strain used for the vaccine.

An update from the Centers for Disease Control last week found that the majority of the circulating viruses in the U.S. matched with the reference viruses. Most years, we would think that was good news. This year, given that most viruses are H3N2, we know it could make for a particularly ineffective vaccine.

This is also the first year that we could have had an alternative. People with egg allergies get a different shot, one grow in animal cells instead of eggs, that doesn’t seem to get these problematic mutations. For the 2016-17 flu season, the U.S. had a cell-based vaccine that had initially been in eggs, so it had the same issues as the standard vaccine. But this year, the cell-based vaccine was only ever grown in animal cells. That might make it more effective than any egg-originating vaccine, though we won’t be sure until we get more analytical data toward the end of the season.

In the future, though, this could be a much better method of creating vaccines. It’s actually faster, too. Eggs have to be gathered fresh each season, but animal cells can just be frozen during the off-season and thawed as needed.

Even though this technology has been around for a while, pharmaceutical companies have been hesitant to make the switch. It’s expensive to make such a fundamental change to manufacturing, and there wasn’t evidence that the cell-based shot was any more effective—or in-demand—than the egg-based one. In fact, egg vaccines were so popular that it was difficult to study the small subset of people who got cell-based shots instead. But if it turns out that the non-egg option is simply a better vaccine, pharma companies might be motivated to change their methods.

You knew it was coming.

Even though this year’s vaccine might be only 10 percent effective, it can still help your body prepare for the virus to some degree. Eggs don’t create such drastic changes that the antigen is completely unrecognizable, and every little bit of preparation helps.

This is doubly true if you work with children or the elderly, or are yourself a school-age kid or elderly. Those two populations are at the greatest risk for having serious complications from influenza—and let’s not forget that tens of thousands of people die from the flu every year. It’s easy to pass along a virus that you don’t realize you have, and it’s your responsibility as a healthy adult to do your best to limit the spread.

It already looks like an early flu season, so get to your closest pharmacy and get the shot today. Don’t wait until it’s too late.