So we'll have my scientist helping people, but working for the military or coup to look for a cure as well. They will be hell bent on going after anyone with the virus, no matter the stages and she will be quick adamant that anyone not in stage 4 lets call it still deserves to live and has a chance of survival.

Disease: (bit like leprosy and tears down the humans ability to reason properly, which quickly aggregates into aggression, rage and a lack of morality)

Stage 1 - Slight mental incapacitation, like an acid trip
Stage 2 - Higher level of mental incapacitation and sores along the open orfaces of the body (nose, mouth, ears, genitals)
Stage 3 - Mildly aggressive and the appearance of something with leprosy, black out periods and mental instability
Stage 4 - Completely loss to humanity, skill cracked and covered in open sores, teeth and eyes infected and filled with mucus and highly aggressive without reason. (Similar to an animal attacking anything in sight)

Incubation period is different for people due to immunities created through harboring the chicken pox or swine flu and surviving. Because all medical records have been destroyed in the fall out, it is impossible to tell if someone has immunity without testing which is expensive and seemingly a waste of time. Due to random incubation periods, the disease was undiscovered at its creation and spreads through air, body fluids and eating infected animals.

The big cities on the east coast was nuked, and laid to nuclear wastelands. New York City, Philadelphia, Washington. 
The government is in the Cheyanne Mountains which are located in the Mid-North US, near Canada.