According to the agency, attacks by armed opposition groups in Beni "have occurred with alarming frequency." The most recent attack on September 22 left 21 people killed.
"As a result, WHO and its UN partners were asked to halt operations in Beni, while the city mourns its dead. As of today, some operations have begun to resume, but even a gap of two days has resulted in health workers not being able to reach contacts of Ebola patients to monitor their health; or investigate alerts of potential cases," the statement read.
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WHO said it was worried that some people sick with Ebola traveled to look for alternative care, bringing infections to new locations.
As of September 25, the Ebola disease had affected 151 individuals, and killed 101 in North Kivu and Ituri provinces, according to WHO.