In an earlier article we mentioned here that vaccination can change a virus. It causes an environmental pressure that eventually results in a mutated virus that is able to evade the vaccine.
But the virus changes in more ways that we can imagine: it even changes when it is growing in eggs that produce the very vaccine we use to protect ourselves.
The Influenza vaccine of the 2012-13 Influenza season offered disappointingly modest protection against the main circulating strain, Influenza A(H3N2). It resulted in around 41 per cent protection for healthy adults and a mere nine per cent for seniors. These results were surprising, given that the Influenza A(H3N2) viruses causing illness were a close match for one the World Health Organization had selected for inclusion in that winter's vaccine. So, what went wrong?
 is offering an explanation for that phenomenon. It reveals that the H3N2 component that went into the vaccine wasn't exactly what the WHO's experts ordered. Tests showed the reference virus selected by the WHO would have offered good protection against the viruses they were collecting from sick Canadians. But the same tests also showed the H3N2 component in the vaccine did not supply that protection.
The vaccine virus contained several mutations that appeared to have undercut its ability to generate antibodies that would recognize and protect against the circulating H3N2 viruses, reported the study.
Most of the world's Influenza vaccine supply is still produced using a system where Influenza viruses are grown in hen's eggs. In the process, the viruses have to adapt a tiny bit to grow in these eggs.
It's been known for decades that that process has the potential to introduce mutations that weaken the protection that vaccine virus can offer. But it was only a theoretical problem. Until now. Suddenly it all changed from a theoretical problem into a real problem: It wasn't antigenic drift, it was vaccine mutation.
 Skowronski et al: Low 2012–13 Influenza Vaccine Effectiveness Associated with Mutation in the Egg-Adapted H3N2 Vaccine Strain Not Antigenic Drift in Circulating Viruses in PLos One - 2014