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(1) At present, the resource is scarce and expensive. Target its use where it is most needed and will alleviate the greatest harm, in this case where the outcome of infection is potentially death: in women.
(2) Vaccination programs in general require the allocation of significant public resources. Delivery, compliance monitoring, personnel, reporting, record-keeping, ... again, targetted use is the best use of resources.
(3) Equal treatment is not the same as identical treatment. If it were, health plans would not cover pre-natal care and delivery, or Pap smears or prostate cancer screening. There is nothing wrong with "legislating a requirement on the basis of sex" if sex is a non-specious distinction. There is no legal requirement that visually impaired people be hired as school crossing guards.
Number (3) assumes mandatory vaccination -- i.e. that there is no problem with mandating it and the question is whether it is okay to mandate it for girls and not boys. It doesn't address the question of whether it should be mandatory at all. I tend to think that it should be, in the same way as blood transfusion for children who would die without it should be, or not permitting your five-year-old to go backpacking in the wilderness alone should be.
Yes, the analogy to blood transfusion is far from perfect; we have no way of knowing which girls will die of cervical cancer. But that's how risk analysis goes. Two factors: the probability of the risk materializing and the seriousness of the harm that will result if it does. It is highly probable that yer average girl will contract HPV in her lifetime. It is much less probable that a woman who has been infected by HPV will develop cervical cancer. But the outcome if she does is horrific.
Adults can balance risks for themselves. Children cannot -- and by the time they are able to, it will very likely be too late. Parents are not always allowed to act on their own risk assessments for their children, where the society's determination is that the risk of requiring that something be done (not just the risk of the vaccine itself in this case -- all the social risks associated with overriding parental choice, etc.) is outweighed by the risk to the children.
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