Enteroviruses live and reproduce in your intestinal tract, and humans are susceptible to more than 70 types of them. When it comes to how common they are, they're second only to "common cold" viruses.
Most enterovirus infections do not lead to disease. When they do make people sick, it's usually with either mild cold-like symptoms or with a flu-like illness including fever and muscle aches. Flu-like symptoms are common in people with chronic fatigue syndrome, and onset of chronic fatigue syndrome often comes after a flu-like illness.
A 2007 study on chronic fatigue syndrome showed a high predominance of enteroviruses in the gut, which could explain some symptoms. More research needs to be done to verify this link.
Because the bodies of people with chronic fatigue syndrome show signs of an activated immune system, scientists have long believed that many case are caused either by an active viral or bacterial infection, or by an infection that permanently altered the immune system before leaving the body.
2007 BMJ Publishing Group Ltd. and Association of Clinical Pathologists. All rights reserved. "Chronic fatigue syndrome is associated with chronic enterovirus infection of the stomach"