It’s that time of year again, and I’m not talking about the all-too-early Christmas cookies that appeared at CVS last week. Instead, it’s time for everyone’s favorite vaccine: the flu shot. The yearly Flu vaccine contains the ingredients necessary to prevent individuals from getting the flu. What is not as commonly known is that the flu vaccine actually is meant to protect against multiple strains of the virus. Scientists must make their best guess – which needs to be made as early as February— as to which strains they believe will be the most virulent that year.

According to the Boston Globe the shot is meant to protect against H1N1 and H3N2 – two A influenza strains – and a few influenza B strains. According to data that was presented at an infectious disease conference that took place in San Diego last week, the vaccine did not live up to expectations for preventing H3N2, which is one of the most dangerous strains of the flu. According to Wired the vaccine proved to be 63 percent effectiveness for influenza B and 65 percent for H1N1, it was only 38 percent affective at preventing H3N2.

The obvious question is: why are scientists having a hard time making an effective formula? The answer lies in the method in which the flu vaccine is created. According to the CDC there are three ways in which a vaccine can be created: egg based vaccines, cell-based vaccines, and recombinant flu vaccines. The first two require the use of chicken eggs – which is why when you get a shot the administrator will ask if you have an egg allergy – and the last method was approved in 2012 and there is only one FDA approved vaccine of this type. The first method is what has been traditionally used. The virus is grown inside the egg, and then killed before it goes through a purifying process leaving the virus antigen which is then purified.

However, the virus that you generally want to prevent is a human flu virus—meaning it prefers human cells. According to Wired, to solve this, two strains of flu are injected into the egg: the target and one that likes chickens. When viruses mingle, they will share genetic information. At this point, the researcher will choose one of the strains that looks like the one that prefers a human habitat. They use this new strain to inject into new eggs to generate the vaccine.

Why does this matter? This has to do with how the vaccine works in the human body. According to Wired the virus gives off a protein called hemagglutinin that is detectable to the human immune system. This is what alerts the body to the existence of the virus so that it can eradicate it. These proteins are capable of mutating, and in the case of H3N2 it mutates faster than H1N1 and other strains. The commonly used process explained earlier? Unfortunately it seems that it makes the mutation happen even more rapidly—so quickly that the body sometimes cannot detect it in time to trigger the immune system.

In practicality what this means for researchers is that there needs to be more focus in perfecting the third type of manufacturing type mentioned earlier – the recombinant vaccine process. As of yet, there has not been a method developed using this process in the massive scale that would be required to produce the number of vaccines that would be needed. As with all things in science, it is an ever evolving process in pursuit of perfection. However, while the vaccine might not be as effective as researchers would like, it is still important to get a vaccine—especially those who are at greater risk for complications. Any protection is, after all, preferable to no protection – especially against H3N2 which remains the strain that leads to the most hospitalizations.