Evolution is not driven in this manner. Mutations appear spontaneously. If several versions of a disease are thwarted by a vaccine, a mutation that is not affected by the vaccine may rise to become dominant. But the mutation was not caused by the vaccine. It was there already and would have been obscure unless the other versions failed.
In the end, despite the mutation, the vaccine did more good than harm.
Again, not claiming this is "Science". Just my layman's understanding of it.
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