In the early 1990s, Zaki contributed to the discovery that hantaviruses were causing a previously unexplained series of deaths among members of the Navajo Nation. He participated in the processing and identification of the anthrax strain used during the 2001 anthrax attacks. He contributed to research into the use of the experimental antiviral drug remdesivir against the Nipah virus, finding a protective effect in animal trials. During the COVID-19 pandemic, Zaki studied the causes of fatality related to SARS-CoV-2 and the virus' impact on pregnancy.