Before I go on, there will be spoilers from here on in, just saying it again.
I managed to find the recordings in the final act. On one of them, a doctor (in a rather self-satisfied tone) talks about how the cure that might be found through Ellie as comparable to the discovery of penicillin. Why not Insulin, or the polio vaccine, or cancer drugs?
Penicillin is a drug that was found because a petri dish was left on a counter, the dish grew a MOLD, which killed the bacteria present. At first I though, "How ironic, penicillin is a lifesaver, it came from a mold, mold is very similar to fungus, (I think they're one and the same, correct me if wrong) now Cordyceps fungus has brought down humanity."
I thought ND was being clever, then, I remembered, overuse of penicillin is a health-care crisis, many diseases are growing resistant to the drug. Forcing the use of more powerful penicillin. Wouldn't it be possible that some fool tried to craft a new penicillin, they used a Cordyceps variation or it became contaminated, and it caused the disease? Huh.
The discovery of penicillin was accidental, the petri dish was almost thrown out, and it turned out to be a universal life-saver. I think the cure for humanity won't happen because someone actively sought it. It'll be an accident. In the opening credits, a voice says something like "Look to the light." Fungus and mold love the damp, and a lot of them like the dark places, the cure might happen due to some kind of light, not sunlight, obviously, but another variety, gamma rays, ultra-violet light (I'm no physicist, wiki-answers people) the answer is often right in front of people. A couple hours in a tanning bed might fix people right up.
Naughty Dog has made an amazing game, it's a game where you're encouraged to notice the details. The trophy list supports this.
What do you guys think?