They can be caused by HSV-1 or cytomegalovirus or vericella zoster. But most aphthous ulcers don't shed any virus, and the literature is quick to point to traumatic injury to the oral mucosa.  But in my case I can (rarely) feel them coming on before they break the surface, so injury to the oral mucosa is not the cause.  Maybe mine are viral, maybe they could determine that. They run in my family.