Narcolepsy is an autoimmune disease sometimes triggered by flu? Fascinating. If only we could control the immune system better, we could fix so many problems.
Viral particles can not only be picked up as antigen, but they can also serve as adjuvant to aid the immune system in learning the wrong thing.
Auto-immune reactions are pretty rare. Central and peripheral tolerance are supposed to delete any cells that are close enough to matching against self. Developing allergies (eg. pollen, dog, etc.) can happen this way [1], and there is less mechanism to prevent it.
This would make it very difficult to target a specific gene to edit without having a wide blast radius.