Whilst the viruses are different, they are based around the same ‘template’, so the scientists do have a starting point to work from.
There are three strains of flu, type A, type B and type C. Type A is the one that changes the most easily (this is called mutating). In February each year scientists look at the structure of the different viruses that are causing infections, and develop vaccines based on these. It is unlikely that these will change very much over the summer (as not many people get flu in summer time). The new vaccines are ready by September, in time to prepare to fight the flu over the winter! The whole process starts again the following February.
Of course this isn’t fool proof, and sometimes there will be mutations which we haven’t seen before, or had time to make a vaccine for (like swine flu).
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