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A flu shot is a vaccine to prevent or lessen the effects of infection with the influenza virus. New vaccines are made available every year via the health care and disease control branches of one's government, like the CDC in the United States. Generally these vaccines are pasteurized versions of the original viruses themselves. The body then creates antibodies from these templates that it circulates indefinitely.
 Fun with flu
Flu shots are also a great topic to bring up in arguments with idiots who don't believe in evolution because it's precisely due to evolution that the CDC releases a new round of flu vaccines yearly. One could call a creationist a hypocrite if said creationist has had more than one flu vaccine. This is generally not a good idea since most idiots would rather forgo reasonable medicine (like flu shots) than be called a hypocrite so this argument is best to be used as a last resort... or as mockery. Be warned—you will be charged with gotcha arguments if this is used on more than one quack. Doonesbury sums this up quite well, although the exact context of the comic was about bacteria and their resistance.
Usually, vaccines are highly effective. Vaccination against influenza, however, is slightly more complicated. The prevalence of the virus and its many strains (as well as seasonal variants) make vaccination quite tricky - there really is no cure for the common cold. A Cochrane Collaboration review concluded the effectiveness of vaccination against flu in healthy adults is small.