When a virus enters your bloodstream, it releases several compounds that mount your body’s defense against infection. Interferon, interleukin, and prostaglandins are among the body’s most valuable compounds. They raise a fever, shift the metabolism, and increase blood flow to areas of the body that need it.
Frank Davidoff, of the American College of Physicians, suggests that although science hasn’t yet precisely defined their function, there is much evidence to suggest that these compounds are responsible for the aching feeling that accompanies colds and flus. More of the compounds are usually found in the bloodstream during the aching phase than before start. And when doctors inject a purified form of each compound into a patient, many of the symptoms of a virus, including fever, sweating, and aching, occur without actually causing the entire illness.
From: When do Fish Sleep?
by: David Feldman