Man, I wish there was a enough interest to make a full game for these simulations (again, the unnatural obession is setting in).
I love these games to death, but they don't follow the natural dynamics in one key way:
More deadly strains of the same disease must compete with the less deadly strains. Humans use vaccines, but it's present in the natural environment as well. For example, if a strain of the cold sore suddenly went lethal, all of earth won't die, just that one strain will kill its people. It will be at an evolutionary disadvantage because everyone is already infected, so antibodies are in place and its fighting its own disease in competition as well.
Other then that, these games are (mostly) golden in how quickly they can spread. It's just (whether explicit or not) your disease is already among the very, very lucky that the human body cannot eradicate it completely.