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Nearly 3,600 people are without shelter after heavy rains in Bumba, 520 km northeast of Mbandaka, the main town in Congo's Equateur Province.
"Some of the victims have sought shelter with close relatives in surrounding villages, but most are still in Bumba and living in canoes," Charles Longoso, the provincial health inspector, said from the village of Iyonda, 15 km west of Mbandaka.
Several homes, most made of non-durable material, have been swept away or submerged in water. One child has died, he said.
Equateur Governor Yves Mobando Yogo said rice fields had been ruined, and an emergency committee had been set up to organise the relief effort.
The committee was comprised of the United Nations World Health Organization, the UN Children's Fund and the provincial medical office, he said, and was not expected to get help to the victims until Monday because of lack of transport.
Humanitarian agencies have already amassed 16 tonnes of food and six tonnes of non-food items and the UN Mission in the Democratic Republic of Congo will be asked to provide air transport.
Hundreds of people are also threatened in the towns of Lisala and Mankanza just west of Bumba, Longoso said.
The entire province has now been declared a disaster zone.
World Health Organization epidemiologist Jean-Robert Likofata said that while he awaited an evaluation of the epidemiological situation, "we expect there will be an increase in waterborne diseases and malaria".
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