In a recent interview with PSU, when asked in regards to whether this entry would see the end of the franchise, executive producer Ken Rosman decided to respond "A virus can keep spreading if its not contained." Indeed, Mr. Rosman.
The virus referenced above being a plot point central to the series. Prototype 2 will see the introduction of a new protagonist bent on stopping the Blacklight virus from spreading. James Heller takes over from last game's anti-hero Alex Mercer for the duration of the game.
Prototype 2 will see a release in April 2012.