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Ebola prevention activities have been suspended in the city of Beni, Democratic Republic of Congo, after a deadly attack by the rebels.
The treatment centers will remain open but vaccinations and searches for people who have been in contact with patients suspected of Ebola have stopped for the time being.
About 100 people have died in the current epidemic in the east of the country, according to the Ministry of Health.
It started in July and is the tenth to hit the country since 1976.
The rebel attack in Beni began on Saturday afternoon and lasted several hours. Eighteen people have died, including 14 civilians, the army said.
According to local sources, the Allied Democratic Forces, a Ugandan Islamist militant group active in the region since the 1990s, were behind the attack, but this has not been confirmed.
Louise Dewast of the BBC in the capital Kinshasa reports that representatives of aid agencies working on the Ebola response are meeting to assess the increase in security measures in Beni.
Some Beni residents took to the streets to protest security issues.
The World Health Organization (WHO) had warned in August that insecurity in the region could affect the response to Ebola.
At the time, Peter Salama, of the WHO, described it as a "dreaded" scenario.
This is the second Ebola outbreak in the country this year. The previous outbreak in the west of the country killed 33 people, according to the government.
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