Because the virus mutates, the same antibody that fits on the original virus (above), might not fit on the bottom virus (below). When this happens, the body is not able to effectively attack the virus.
drawn by William
Different or mutated strain becomes pandemic
In order to become a pandemic among humans, the current avian flu virus needs to mutate to be able to pass from human to human more efficiently. If the virus does mutate to become a pandemic, the vaccines being developed against current strains of avian flu virus may not be effective against the pandemic strain, because it will have mutated.
Also, there is the possibility that a totally different strain from the one that is being used for vaccines may become the predominant strain in an epidemic.
Resistance to drugs
Current avian flu viruses have shown resistance to several antiviral drugs: Tamiflu, rimantadine and amantadine.
Current methods of producing flu vaccines involve making the vaccine in chicken eggs. This process is very slow, and takes many months to complete. Using this production process, it would take an extremely long time to produce enough vaccine for everybody. In a pandemic, by the time enough vaccine is produced, it might be too late.