Second Plague

The Second Plague was a viral epidemic that struck the continent of Africa in late 2006 and whiped out almost all of its population.

An outbreak of a virus called L-11 struck Africa and caused the deaths of 96% of the continent's population over the course of three months. By 2012, the continent had become practically uninhabited and plans were mained to divide Africa between the rest of the world. The plans were met with resistance by the remaining people living on the continent.

Reference

 * Assassin's Creed