There are multiple settings in the book because it spans a long period of time (1980 to 1993) and follows viruses all over the world. Much of the African portion of the story takes place in Kenya and Sudan, and the real centerpiece is Kitum Cave in western Kenya. The story starts and ends there although under very different circumstances. On the international level, there are also references to the Marburg virus' stint in Germany, and a monkey farm in the Philippines. Aside from these brief mentions, the true settings of the story are Africa and the United States.
The North American portion of the book takes place near Washington, D.C. Fort Detrick, the base of operations for the United States Army Medical Research Institute of Infectious Diseases (USAMRIID) is located near Frederick, Maryland, and many of the story's participants work at this installation. The other important setting is the monkey house in Reston. The fact that the potential Ebola outbreak is happening so near the capital of one of the most powerful nations on earth certainly adds to the tension of the story.