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I love this story idea and the ending, too.
One thought: One of the cool things about "bugs" is that some people can be immune for no apparent reason, not just because they were able to avoid exposure. They will either have natural immunity or not be susceptible or have some other genetic predisposition against getting ill that becomes apparent as they remain healthy while everyone else drops like flies. This kind of thing happened during the plague and other large-scale flu outbreaks. Many of those who tended to the sick simply didn't come down with the bug. The survivors of a pandemic may, in fact, be unable to be infected regardless of their contact with the infected. They just aren't susceptible.
Of course, you don't have to be completely accurate on this point since this is fiction, but to make the "immortals" that much more evil, you could have them bringing the "breeders" in and performing gruesome laboratory tests on them before killing them to try to figure out how to develop and release a variant of the bug that will eradicate the breeders without having to smoke them out and kill them one by one.
I really think you've got a good idea for some books here! Nice work.
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