I hear patients quite often comment in my Scripps Ranch dental office that they received the flu shot, yet they ended up getting the flu. First, discuss your concerns with your physician and realize that I am not an expert in the field. However, I had several immunology courses and am using my memory to recall the facts. I am not going to go into extreme detail.
The flu virus is a sequence of genetic material (RNA) that infects the upper respiratory tract or basically your air passage. The virus infects the cells of the respiratory tract and start to replicate. They start spilling out of these cells and infect the cells next to them. At this time the flu virus is well underway.
Because viruses are a sequence of genetic material, there are infinite number of combinations of sequences of these genetic materials that could occur in nature. Some of these combinations lead to formation of strains of the flu that could infect humans and some may infect other species. The sequences of genetic material continue to change by mutations.
For example, if one person is infected with the flu virus, that virus could mutate and infect the next person differently. Now you have a new strain. This is also why humans can be infected with bird flu and swine flu. If a pig or bird is infected, and the flu virus mutates to a form that can infect humans, the virus can cross species.
Before each flu season, scientists decide on 4-5 strains to include in the vaccine based on information gathered on current strains of flu viruses circulating and infecting people around the world.
Out of thousands of flu subtype that can infect humans, there are only 4 or 5 strains that the vaccine will protect against. This means that if the scientists guessed wrong the flu vaccine will not have any or very little protection against the flu strain. If the flu strain is in the same family, you may get some protection.
In conclusion, there are thousands of numbers of flu viruses that can infect humans. The Flu vaccine only protects against 4-5 based on scientists predictions. If you are infected with a flu strain that is not included in the vaccine, you will have none or very little protection.
Disclaimer: Follow your physicians recommendation. They are the experts in the field.