In the Guilty Crown Franchise, the Apocalypse Virus is a mysterious virus which broke out in Japan.
The Apocalypse Virus is a newly-discovered lethal virus which originated from a meteorite that crashed into Japan during the Lost Christmas event. This meteor was named "the rock that started it all", and the first to touch and thus get infected was Mana Ouma. This virus slowly crystallizes it's victims in a cancerous fashion, eventually killing them. The way the virus is transmitted are not fully understood, however, as soon as a person has been infected, the body will display various stages of symptoms where the crystals form on their body.
The GHQ provides the Japanese people with vaccinations to avoid infection.