It's honestly irrelevant, as the second game doesn't neccessarily explains which one was the canon one, and even so it wouldn't matter much, as the outcome was the same regardless, with the only difference being the amount of people infected (a small portion vs most of the world). If you'd like my judgement about it, I'd say the first ending from the first game (where you tamper with the shuttle), because otherwise, the city in which the second game takes place would look quite different, imho.