Autoimmune diseases originatede in the gut. If proteins can get into the bloodstream through holes in the wall of the intestinal villi, which are just one cell thick, they alert the immune system system. If the protein is similar to a protein found somewhere in the body, the immune cells travel there and attack them, since they have been misidentified as “other” and not self. This is an autoimmune reaction. If it gets serious, it becomes an autoimmune disease. Perhaps the spike protein is identified as “other”, and the body attacks it where it finds it. That could be just about in any tissue