As you can see, the game does not identify Jakarta as the specific breakout point as the show seems to do. Indeed, the game seems to imply that reporters/researchers in The Last of Us game universe seemed to believe that the infection may have started in South America. That article also identifies “crops” as the believed source of the infection’s spread, but it doesn’t identify bread, grain, or flour specifically.
As we also previously discussed, it should also be noted that the way the Cordyceps infection spreads from person to person was changed slightly from the game to the show. Most notably, the version of the Cordyceps infection we see in the game commonly spreads via spores that the infected hosts can release after certain stages of infection (or after they are dead). It’s possible that variations of those spores are actually what spread via those tainted crop shipments in the games. Again, though, some of the details remain unknown and intentionally ambiguous. Furthermore, the fictionalized version of that infection is different enough from its real-life counterpart to make it difficult to use that real-life infection as the basis of more detailed speculation.
There’s also the matter of certain timeline differences. As you may know, HBO’s The Last of Us alters the game’s timeline by suggesting that the initial outbreak occurred in 2003 and that the “present-day” sequences occur during 2023. In the games, though, the outbreak occurs in 2013 and the “present-day” sections take place during 2033.
Interestingly, it’s also implied that the infection also takes a little longer to spread in the games than it does in the show. After all, that aforementioned sequence set in Jakarta occurs on September 24, 2003, in the events of the show. Two days later, we see that it has caused widespread destruction as far as Austin, Texas. Radios in Austin also share reports of unrest in Jakarta at that time, which seems to imply that the outbreak spread across the globe incredibly quickly.
In the game, though, that aforementioned Texas Herald article (which was dated September 26, 2013) seems to suggest that the FDA had been monitoring potentially infected crops for a little longer than that and that some companies were already recalling their products. Again, the implication seems to be that there was at least a little more awareness of the outbreak itself but that the speed at which it spread (and the violent nature of it) ultimately caught everyone by surprise.
At this time, it also doesn’t seem like the showrunners intend to rewrite the infection’s origins as they are presented in the game or suggest that the show offers an expanded version of those events that directly applies to the games. The Last of Us series co-creator Craig Mazin previously stated that they “wanted to give a little bit more of an origin story [to the Cordyceps outbreak]” and “how also that it was global, that this wasn’t just happening in America. This was the world.” Still, there are enough differences between the origins to suggest that they belong to that “parallel universe” the showrunners talked about creating. In any case, some of the most important details remain largely the same.