Evolutionarily, this process increases a sick person's chances of survival. Like any good military operation, the magnitude of the response is generally well-regulated and determined by the intensity and duration of the threat. The degree of muscle catabolism and protein loss is related to the height and duration of the fever caused by the infection. Unfortunately, there is no evidence that controlling a fever with acetaminophen or ibuprofen decreases this loss of hard-earned muscle. Your muscles have many good reasons to ache when you have an infection.
Skeletal muscle is the main source of catabolized protein, but heart muscle contributes as well.
Skeletal muscle biopsies done in feverish people and laboratory animals during acute infections demonstrate microscopic evidence of muscle damage. The same chemicals that initiate muscle breakdown during infection also inhibit effective muscle building and repair, making it virtually impossible to build muscle during any infection more serious than a cold. Unfortunately, you can't even lose body fat while you are sick, as fat metabolism is impaired during infections. So any weight loss during a febrile illness is generally lean muscle mass. During a febrile or systemic illness, athletes should be wary of stressing muscles that are actively being broken down to fuel the body's defenses.