Acho que você está falando da trilogia Idlewild . É 2 décadas depois do que você o coloca - publicado pela primeira vez em 2003.
Idlewild : It is a not-too-distant future in our all-too-recognizable world. It is the late twenty-first century and a deadly virus has seeped into human kind's genetic make-up. Eighteen years later and ten individuals are about to come of age. One of them, a young man, is suddenly startled awake. He has no memory. His surroundings mean nothing to him. All he knows for certain is that someone is trying to kill him. Unsure who he can trust, he is reacquainted with his companions, all of whom are being trained at a special establishment run by the elusive Maestro. As he tries to uncover the identity of his would-be killer, it becomes clear that more - so much more - than just his life is at stake . . .
EdenBorn : A bitter and disillusioned Halloween has chosen to exile himself but his peers seek to repopulate the Earth and rebuild civilization. They are mankind's last, best and perhaps only hope. However an ideological split has divided them into two very different societies: one looks to resurrect the human race, the other to improve humanity via genetic manipulation. So a new generation of children is born, but as they mature it becomes clear that all is not well. Someone - or something - is moving against them, even as Black Ep, the plague that claimed billions of lives, returns in search of new victims. The survivors must work together, but to save the future Halloween must first let go of the past...