A good example of this is an HIV vaccine trial that was halted in 2007. A recent reanalysis confirmed that not only did the vaccine fail to protect people from HIV, it actually made some people more susceptible to infection with the virus. Specifically, it increased the risk of uncircumcised men who already had antibodies to adenovirus before vaccination.
Adenovirus was the virus used to create the HIV vaccine. Although the reason why previous exposure to the virus, which causes the common cold, was associated with increased risk is unknown, there is one interesting hypothesis. The vaccination could have primed their immune system, causing an increased production of CD4+ T-Cells. Normally when fighting off an infection, that would be a good thing. However CD4 cells are the ones most susceptible to HIV. Making more of them is a bad outcome for an HIV vaccine.
As I said, coming up with new vaccines, treatments, and cures for STDs isn't easy. That's why I'm glad that so many scientists are giving it everything they're worth.
Source: http://std.about.com/b/2012/06/01/unforeseen-consequences.htm
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