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Honestly I think the vaccine is a good thing overall. The downside is that they don't yet know the long-term effects. But HPV doesn't just effect the reproductive system. My dad's throat cancer was caused by HPV, it's the most-common cause for non-drinkers and non-smokers. (Although radon's up there too.)
As for comparison's to the flu vaccine, HPV doesn't mutate as fast as the flu does. And every year they're only guessing at which strain of the flu will be the most common as compared to HPV where they've isolated the major strains that cause cancer.
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