Although the infection and resulting cellular disruption is systemic, the vast majority of symptoms experienced by infected patients are directly attributed to various levels of dysfunction of the motor, sensory, autonomic, cognitive and mood-influencing functions of the brain. As discussed elsewhere, the brain is uniquely susceptible to localized viral induced damage. Clinical manifestations are probably determined by the localization of the brain infection, as well as genetically and environmentally determined differences in predisposition to various neurological and neuropsychiatric symptoms. A series of simple but objective clinical tests can be applied to help document the scope and severity of primary brain dysfunction in stealth virus infected patients.

The brain also controls many of the activities of other organ systems including gastrointestinal, cardiovascular, endocrine and various immune functions. Significant direct virus-induced damage to organs, such as the bowel, liver, thyroid, adrenal, etc., can also occur. Furthermore, secondary complications of viral infection can include the induction of auto-immunity, antigen-antibody complex formation, ischemia resulting from virus-induced vascular damage, breakdown of both the physical barriers and the cellular immune clearance mechanisms operative against common bacteria. Stealth viruses can also transactivate, and be transactivated by, other viruses, including viruses present in certain human and animal live vaccines.