Why is Joel dragging Ellie across the country as the cure in the first place? I know that sounds like an obvious question to answer, but hear me out: none of the animals we see in the game ever appear to be infected. The horses they ride are fine, the rabbits and deer Ellie hunts are fine, and the herd of giraffes (the fuck are giraffes doing in Utah?) are fine. We never even hear about infected animals; there aren't even any infected dogs to fight. And it's been twenty years since the outbreak. That's more than enough time for a house cat or whatever to turn.
What's making them immune, and why haven't the Fireflies tried developing a cure from the animals? That's how vaccines are developed in the real world, aren't they? (OK, not entirely comparable, but comparable enough.) If they did, why isn't this addressed in plot?