“How will cooperation with the United States on counterterrorism develop in the view of these new constraints? I would argue the space will contract,” said Aaron David Miller, a former State Department Middle East expert who is now at the Woodrow Wilson International Center for Scholars.

Some U.S. officials and analysts say they are not overly worried, noting the continued strong role of the Egyptian military and the fact that the United States gives Egypt more than $1.3 billion a year in military aid. Robert Grenier, the former head of the CIA’s counterterrorism center, said, “The Egyptians have as much interest in protecting themselves from violent extremism as everyone else.”

But with a new government, “the comfort level with the United States may not be so high. They will be more distrusting,” in part because of past U.S. efforts to prop up autocratic regimes, Grenier said.

Egypt’s intelligence cooperation is extensive. Its security services have numerous sources in places where the U.S. government does not, such as Gaza and Sudan, according to analysts.