Prototype

This is fairly easy once you have the Infected Vision ability and have learned how to fly helicopters. Hijack a helicopter, fly to an infected zone (red on the map), activate your Infected Vision ability, and fly around the rooftops looking for water towers that are glowing a bright red/orange color. If you don't see any right away, just keep flying around and eventually some should spawn. Lock on and destroy them from a distance so that they do not hatch. It shouldn't take long as you will have already had to destroy some infected water towers in the story.

You can track your progress under the Statistics -> Infected page on the pause menu.