Ugh, it's so cliche...and why in the world would Joel be the one escorting Ellie?
Scientist: Hey this girl might be the cure to save the entire human race!
General: Roger we'll have a military convoy ready to transport her ASAP
Joel: Not so fast gentlemen!...I think I'll take it from here...
I highly doubt it would be THAT typical and cliche'. Surely ND know if that were the case we'd all have seen it coming from a mile away. In my opinion, Ellie may not be that vital a character. The story of why Joel's escorting her is a dying friend's wish, so where would this dying friend come off knowing that about Ellie? Maybe she's his daughter and he is oblivious of this, and the dying friend knew under suspicious circumstances. Again the game revolves around the character's and their development throughout the story, so it will be a deep dark secret or something.
I'm pretty sure after the 10-20 years of an apocalyptic environment a cure would be quite pointless as re-establishing life and order would be VERY difficult.
Neil Druckmann said in the IGN interview in response to Greg telling him he thinks Ellie's the cure he said, "I think when people finally see what it is, it's not this big revelation we just wanted to experience it in context and see how it all comes together."
Skip to the 3:39 mark. There is gameplay of the Infected for those who don't wanna see it yet so watch at your own risk.
even if it was a cure, would it be an antidote to an infected or a vaccine for the survivors?
Most likely a vaccine for the survivors. Well, it wouldn't be exactly a vaccine If you're immune to an infection you possess antibodies that fight off said infection, it could be that the "fireflies" are simply trying to create "herd immunity" using immune individuals in order to pass on their antibodies to people not immune, this is called passive immunity. The only problem with this form of treatment is that it isn't permanent, and immune individuals would be required to give a lot of their blood in order to keep the population immune. Provided of course it even works in the first place.
Plus, as other posters said, wouldn't the military be on the forefront of this breakthrough? And how would the "dying friend" know that Ellie was immune? Unless her mother was immune... and they suspect maternal immunity... who knows. lol. It does sound cliche, but I guess if this is how it's gonna play out, I have faith in ND to be the one to do it. I just hope the story is deeper than that.
Slightly off topic, but it REALLY rubs me up the wrong way when people confuse 'fungus' with 'virus'. A fungus is a complex organism. In fact, fungi have a very similar cellular structure to humans, and this one of the reasons it is very hard to develop anti-fungal drugs, because such substances can also harm human cells. A 'virus' on the other hand, is NOT a living organism. It's simply a piece of coated DNA designed solely to replicate itself by hijacking the genetic machinery of cells. Sorry for the rant, but many previews have confused the two terms. I've even some writers use the phrase 'fungal virus'. Urgh
Reminds me of the Infected vs Zombies debate. Yeah they are different but people know what you mean.