The government has an interest in vaccinating its population. Do citizens have a right against their being vaccinated? Citizens have a right against the government not to be made to do what violates their conscience. But, of course, this has limits, for one's conscience is fallible and given to error. If the population of citizens who, out of a (false) religious belief do not believe they should have vaccinations, is small enough so as not to jeopardize the "herd immunity," the government should not force these citizens to be immunized.
Still, one's moral rights do not entitle one to put others in an unnecessarily high risk of harm. This is why the blind do not have a right to drive on public roads. The more serious the disease is, the more the government should play a role in mandating vaccinations which are known to be effective and are known to have a small risk of negative side-effects. This is for the common good. The less serious the disease is, the less the government should play a role in mandating vaccinations (though the government still might have an interest in providing evidence for the cost/benefits of these vaccinations).
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