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“The U.S. will have to nurture relations with various political actors and negotiate its interests,” he said. “The relationship might become a little more complex, but it can become a much healthier one.”

Foreign policy vs. economic policy

The Morsi administration’s commitment to the 1979 Egyptian-Israeli peace treaty is the biggest unknown in the new relationship.

Mubarak received $1.3 billion in U.S. aid annually for keeping the peace with Israel. Brotherhood leaders have said they want to amend the treaty.

Morsi will be looking for a more robust economic relationship, and perhaps a relationship that contains more strategic dialogue on economic as well as political issues, and less a relationship that is simply delivery of a lot of military aid in exchange for a certain set of military and security cooperation,” Ms. Dunne said.

Mr. Morsi, in his first televised speech as president-elect, sought to allay concerns in the U.S. and Israel by declaring his intention to preserve all of Egypt’s international accords.

Secretary of State Hillary Rodham Clinton this week described such statements as positive, but added, “We’ll have to wait and judge by what is actually done.”

Some analysts view the president-elect’s comments with skepticism.

“The U.S. is not as certain as it was in the case of Mubarak that the Muslim Brotherhood will respect the peace treaty,” Ms. Ottaway said.

Mr. Trager said: “Morsi has said that he will abide by all agreements, but has frequently carved out exceptions for popular will and strategic priorities, and the consensus in Egypt is that peace with Israel is not a strategic priority.”

Peace with Israel hinges on stability in the Sinai Peninsula, where a flare-up could set the region ablaze.

The Brotherhood’s support for closer ties with Iran also has set off alarm bells in Washington.

Mr. Morsi, however, is unlikely to come to office with a big foreign policy agenda, largely out of necessity, analysts say.

One of his biggest challenges will be to put the country’s economy back on track.

Egypt’s tourism industry, its main source of income, has been ravaged since the start of the anti-Mubarak uprising in January 2011.

Story Continues →