What do you think the source of the infection is from ?
There is a recording in the hosptial where a guy was told to put the monkeys to sleep. He didn't want to. Then the recording continues and shows he was bitten by one of the monkeys.....
If I know right, the cordyceps got to humans via food, it said that in the newspaper in the bathroom when you get to play as Sarah.
I have acquired the grade of Master in The Last of Us story/character/game knowledge as I have played it through 9 times.
... I have no life.
WinterEdit is correct about the newspaper. It claims that the FDA (Food and Drug Administration) has expanded its list of contaminated crops. What we don't know are any details, as in if these are imported goods, if they were from the North American region and also then exported, or the big one - if this is the only starting source of the infection. Those are the kinds of questions we will never fully know the answers too.
The real life cordycep infection does have spawn points (it works on insects and spiders), I guess like a spore area in the game. The infected critter wanders toward its population to die and become another spore point. I would believe that the spores got into one ciritical location, such as seeds that were purchased and planted by farmers all across the country. Then perhaps they germinated and spread the virus throughout the fields.
If the original sources for these infections were numerous, then the game is basically attempting what occurred in the movie 'The Happening.' Skip seeing it, as some of the acting us unbearable. The plot of the movie is in short: Nature strikes out with an airborne virus that generates from any vegetation source. It does so in reaction to a gathering of people, in order to eliminate us. If the TLoU infection begins at multiples locations, then Nature almost has to be doing the same thing in the game. It's speculative though, because we aren't given the answers.
As for the monkeys, that was actually an attempt by the Fireflys to cure the infection. It makes them and Marlene even bigger a**holes, but I don't want to write out the whole thing. If you are interested, then please check out my The Last of Us lore vid http://www.youtube.com/watch?v=1p2cHgyY6cY and start watching at 1:01:26