Did you get your flu shot? I didn't really want to (I hate needles) but as an infectious disease physician at NewYork-Presbyterian Hospital, it would be exceedingly poor form if I opted out. My job requires it, and I recommend the vaccine to just about every patient, every day. The shot doesn't actually hurt, and if you look at the terrifying data—influenza kills between 3,000 and 50,000 Americans every year—it seems insane not to get immunized. Annual vaccination reduces your chance of dying from the virus by more than 40 percent! But on Wednesday, the Centers for Disease Control announced that this year's vaccine kinda sucks. To be specific, it's less than 50 percent effective against the predominant strain of circulating virus. So what went wrong?

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It turns out the whole thing is a big guessing game. Influenza vaccines are produced in eggs, and take approximately six months to manufacture, which means scientists start making the flu vaccine in February or March, way before they know which strain is going to be the most problematic. The decision of which strains to include in the vaccine is based upon global surveillance of viruses circulating at the end of the prior influenza season. Scientists are making a guess, but it's an educated guess.

The flu shot you got (or will get) covers three or four strains of influenza. The one I received covers three strains (two of influenza A, and one of influenza B), but at the hospital across the street, Memorial Sloan Kettering, they administer one that covers four strains: two A and two B. It's debatable which one is better.

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This general strategy of vaccine development usually works, but if the virus mutates, or an unexpected strain emerges, you won't be protected. This is not to stay you shouldn't get a flu shot—YOU DEFINITELY SHOULD—but when you do, you really have no idea how much protection it's going to afford you.

You see, most studies have overestimated the true efficacy of the flu vaccine. The numbers most frequently quoted are between 70 and 90 percent, but a comprehensive review over nine flu seasons indicates that in adults aged 18 to 64, vaccine efficacy was really only 59 percent, with a range of 16 to 76 percent. One study found that the effectiveness of the vaccine during the 2004-2005 was only around 10 percent; two years later, during the 2006-2007 season, that number jumped to 52 percent. This year, the predominant strain of influenza is called H3N2, and preliminary studies indicate the vaccine is a good match for only 48 percent of H3N2 strains. (Influenza A and B are are further subdivided by the characteristics of two proteins called hemagglutinin and neuraminidase; H3N2 refers to subtle variations in these two proteins.)

That is to say, this year's shot is performing worse than average, but not much worse. And on the spectrum of underperforming shots, it's still nowhere near the floor.

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This relatively poor match—let's be honest, less than 50 percent isn't great—is because of something called antigenic drift, which means the virus has mutated ever so slightly, just enough to evade the antibodies that were generated after you got your flu shot. The vaccine makers accurately predicted H3N2, but they were unable to predict this subtle drift.

"One thing to understand about flu," CDC Director Dr. Tom Frieden said in a phone conference Thursday, "is that it is unpredictable. Every season is different, with different flu viruses spreading and causing illness. Unfortunately, about half of the H3N2 viruses that we've analyzed this season are different from the H3N2 virus that's included in this year's flu vaccine. They're different enough that we're concerned that protection from H3N2 viruses may be lower than we usually see."

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Influenza virus is remarkable for its high rate of mutation, which is why you have to get vaccinated every single year. It's also why I've been instructed to use two drugs to treat patients with this flu season: Tamiflu and Relenza. The virus might be able to alter its structure to evade one of these drugs, but probably not both. Let's keep our fingers crossed this strategy works.

The last thing to consider is that we're still very early into flu season. H3N2 is the predominant strain now, but another strain may emerge in early 2015, one that is covered by the vaccine. I receive a weekly virology report about the infections that are spreading in our city and our hospital and it rarely stays the same from one week to the next. Viruses, like vaccines, are unpredictable. We really don't know what the flu season is going to look like three months from now or if the latest vaccine is actually a dud. So if you haven't yet gotten your shot, don't let the latest news deter you. It's still worth it.

Matt McCarthy is author of the forthcoming book The Real Doctor Will See You Shortly. He is not related to Jenny McCarthy, but he is on Twitter.

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Image by Sam Woolley