People that suffer from viral infections like the flu will eventually receive a low to moderate fever. As the condition progresses and intensifies, chills may accompany the increase in body temperature. As discussed, the hypothalamus gland controls the release of pyrogens associated with creating fever symptoms.
If left untreated, the bacterial infection progresses into the paroxysmal stage of the disease. During this stage, the hypothalamus will step-up the production of pyrogens. It does so in an attempt to kill off the bacteria. This elevation in pyrogens results in a higher fever. Many infected individuals also associate this with a bout of the flu.
Along with this increase in body temperature come sudden chills. These chills can wrap the entire body. You may be lying warm in bed, and experience chills. The hypothalamus increases the body-temperature set-point. Your body notices the lag and sends chills over your skin and through the muscular system.