A second clinic serving patients affected by the escalating Ebola outbreak in the Democratic Republic of Congo has been set alight, as concerns mount over widespread distrust of health agencies.

Seven months since the start of the outbreak, which has claimed 548 lives, experts warned that the virus is still not under control and said suspicion of agencies is severely undermining Ebola services.

Médecins Sans Frontières, which runs treatment centres in Katwa and Butembo that were attacked, and is one of the agencies leading the wider Ebola response, said key partners needed to reconsider their approach.

“Within the response, and ourselves, MSF, we need to think what more we could have done, because right now it’s clear that we do not have enough trust within the community,” said Pierre Van Heddegem, project coordinator of the Ebola response in Katwa, adding that all agencies needed to engage in greater consultation with communities.

“In some neighbourhoods, you have to go back to square one, sit down, listen to people and not impose our views of how it [the response] should be organised,” said Van Heddegem.

An Ebola treatment centre in Butembo, North Kivu province, was torched on Wednesday, the second attack on a clinic in a week. MSF was earlier forced to close one of its treatment centres in Katwa, also in North Kivu province, after it was attacked on Sunday night. Assailants threw stones at the centre before setting parts of the structure on fire. The brother of a patient died while reportedly trying to escape the scene, MSF said, though the exact circumstances of his death remain unclear. Medical wards and equipment were destroyed.

On Tuesday, Tedros Adhanom Ghebreyesus, the World Health Organization’s director general, described the outbreak as unprecedented. “There has never been an Ebola outbreak in these conditions, with such a highly mobile population and with many gaps in the health system,” he said.

Efforts to contain the outbreak have also been hampered by conflict and political instability. Suspicion and rumours – including that Ebola is not real, or that it is being used for financial gain – are also rife.

Already health workers lack access to affected communities, and there are fears the outbreak could spread to more volatile areas. There are concerns that the use of police escorts in the Ebola response has worsened the situation for agencies who do not employ such protection, and added to fear among communities.

“How can you work without escorts in a place where other activities are held with escorts? Then you put yourself in an extremely difficult position, and that comes from this militarisation of the response,” said Heddegem.

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There have been 872 cases of Ebola since the start of the outbreak, according to the WHO. The source of transmission is unclear in one in five cases. Very few families are reporting signs of illness to the health workers’ surveillance system, designed to identify people with the virus at an early stage.

The WHO has warned that there is a very high risk of the outbreak spreading not only across DRC but to Uganda, Rwanda and South Sudan.

The agency is calling for $148m (£111m) for agencies to continue the response. So far, less than $10m has been pledged.