In addition to his wife, he is survived by a daughter, Yasmin; a son, Samy; and two sisters, Dorreya and Safa.
In 1978, he graduated second in his class of 800 from the Alexandria Medical School in Egypt. But he was less interested in practicing medicine than in unraveling mysteries, which had been an obsession of his ever since he was captivated by the novels of Enid Blyton as a child.
That obsession was at the heart of his work at the C.D.C. “We go into the basics of how a disease happens, the mechanism,” he said in an interview with Stat, a medical website, in 2016. “Putting pieces together. Solving puzzles.”
He earned a master’s in pathology from Alexandria University. But since autopsies were not permitted in Egypt for religious reasons, he did his residency in anatomic pathology at Emory University in Atlanta, where he also received a doctorate in experimental pathology.
He then went to work at the C.D.C. and became a naturalized American citizen.
Described by James LeDuc, a former colleague, as “kind of the secret weapon for a lot of what was done at C.D.C. on emerging diseases,” he was awarded the Department of Health and Human Services Secretary’s Award for Distinguished Service, the department’s highest honor, nine times.
“What distinguished him as a researcher was creativity, collaboration, solid scientific methodology and a broad knowledge base.,” Dr. Inger K. Damon of the C.D.C.’s National Center for Emerging and Zoonotic Infectious Diseases said in an email.
Dr. Zaki had no illusions that his work would ever be finished.
“We think we know everything,” he told The New York Times in 2007, “but we don’t know the tip of the iceberg.”
“There are so many viruses and bacteria we don’t know anything about, that we don’t have tests for,” he added. “A hundred years from now, people will not believe the number of pathogens we didn’t even know existed.”
