Red Death

The Red Death was the viral 'superbug' that agencies like the CDC are constantly warning about. One third of the global population was infected and around half of those of those died. The plague itself burned out fairly quickly - it was too virulent to survive long, but repeated small-scale outbreaks kept cropping up. More people died in the resulting famines, civil unrest, ethnic cleansings, revolutions, and wars that followed than from the plague itself.

In many of the survivors, it had gone lysogenic (the viral genetic material inserts itself into a host's genome - if the host is stressed and/or immunocompromised, the virus thinks its host is going to die, becomes lytic/pathogenic, starts replicating and the whole infection cycle starts over again. Those that carried the viral genes but weren't actually infectious... well... I think you can guess what happened. More progressive responses to set up quarantine camps/cities. Other nations/mobs decided that bullets and fire were cheaper.