I've found some cool stuff
Firstly is thelastofus youtube channe - http://www.youtube.com/user/thelastofus. Something interesting to take note of is that this channel was created in July 2006, meaning ND have known about this for at least 5 and a half years, probably more.
If you look at the other video on their channel - http://www.youtube.com/watch?v=csubsCk86sw&feature=channel_video_title - take a look at the tags you'll see the word cordyceps. Take a look at the wikipedia entry for cordyceps - http://en.wikipedia.org/wiki/Cordyceps.
The main points in this article is that cordyceps is a parasitic fungus, that usually infects insects, and occasionally other fungi. "When a cordyceps fungus attacks a host, the mycelium invades and eventually replaces the host tissue, while the elongated fruiting body (ascocarp) may be cylindrical, branched, or of complex shape."
Another extremely interesting point in the article is that the fungus has the ability to manipulate the behaviour of it's host. "Cordyceps unilateralis causes ants to climb a plant and attach there before they die. This ensures the parasite's environment is at an optimal temperature and humidity and maximal distribution of the spores from the fruiting body that sprouts out of the dead insect is achieved."
Which brings me to my next video on the official last of us website - http://www.lastofus.com/. If you click on the third video, it's an ant attatching itself to a plant. Previously no-one had a clue as to what the hell this was all about. Well now we know. And we also know what this 'plague' really is. Also, if you skip to the clip of the ant just before the screen goes black and the panting and screaming starts, you'll see a small fungus like plant growing out the back of the ants head, similarly to the growth on the faces of the zombies in todays trailer.
And finally, here is a video from IGN about some teasers hidden in U3 about the last of us, partiularly a newspaper with the headline "Scientists are still struggling to understand deadly fungus". (It does go over some of the stuff I have mentioned in this post, but trust me, I figured this all out before watching this video, and theres not as much detail as I've gone into here.)
That is all.
EDIT: Just found this IGN article and video - http://uk.ps3.ign.com/articles/121/1214349p1.html. I suggest you check it out, tbh it breaks it down a lot better than I do.
EDIT 2: This is where the clip of the ant getting infected comes from. Really interesting, and kind of creepy too - http://www.youtube.com/watch?feature=player_embedded&v=XuKjBIBBAL8
Funny, I have actually seen that Ant thing before, some years ago. It's a BBC documentary if I'm not mistaken. Oh and btw kudos