A woman is given a flu shot by at the medical offices of Yaffe Ruden & Associates in New York.
A woman is given a flu shot by at the medical offices of Yaffe Ruden & Associates in New York. - 
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This season’s flu has reached epidemic levels. And now, the Centers for Disease Control and Prevention are telling us to all go out and get a flu shot.

Flu is serious. It kills thousands. And we want everyone over the age of 6 months to get vaccinated,” says CDC spokesman Tom Skinner.

Great advice, if you can find some vaccine. Clinics and drug stores from New York to Texas to Illinois report they’re running out.

Every few years it seems like there’s a run on flu vaccine. If you're a skeptic, it may seem like a secret to the flu vaccine business: Every year the virus changes its structure just enough.

“Which means that every year, there is a need to make a new vaccine,” says Adel Mahmoud, a molecular biology professor at Princeton and former president of Merck Vaccines.

Mahmoud says manufacturers are cautious.

“Whatever ends up staying in their companies at the end of the season, they will have to destroy it and basically eat its cost,” he says.

At roughly $10 per dose of vaccine, companies don’t exactly want to flood the market. Donna Cary is a spokesperson for Sanofi Pasteur, one of the largest flu vaccine makers in the U.S.

“The primary driver in determining how much vaccine we are going to make in a year is how much our customers have ordered from us,” she says.

Before the season begins. So in years like this one, where deaths and hospitalizations are up and fear is growing and lots of people suddenly want shots, there’s less vaccine on the shelves.

The CDC's method to avoid the panic is to convince everyone to get a flu shot every year, so companies would want to produce more all the time.  

Princeton Prof. Mahmoud has another solution.

“Come up with a vaccine that does not have to be produced every year. Therefore you can stockpile it, like any other vaccine we have for any other disease,” he says.

Mahmoud says a such a breakthrough is possible soon. But until that day comes, manufacturers will continue relying on last year’s sales and this year’s orders.

So while you, me and our neighbors are out hunting for flu shots this week -- Sanofi Pasteur says its already pre-booking for the fall.

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Follow Dan Gorenstein at @dmgorenstein