What, exactly are you trying to replicate from the show? The miraculous super drug the powers-that-be despise? The plot premise of running from the authorities with a secret? The main character himself? All of it? Something else? Depending on what aspects you like, you can do different things for your game (fyi I know little about EP specifically, but translating plot into games can be universal).
So my immediate thought given this context would be to make the new strain/miracle drug/whatever be something that combats the existing evil virus as a counteragent. So it would provide some amount of resistance/immunity to it, but i like the idea of a (probably unknown) drawback. Something like cordyceps maybe that slowly takes over and/or controls the person like you mentioned.
This could easily be told to the players through the NPC you mentioned who has control of the new strain/drug; he can slowly become more erratic/out of control, and his actions can start to get more suspect (along with any potential physical signs).
So basic idea for a campaign would be: