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The Democratic Republic of Congo (DRC) declared a yellow fever epidemic in June after the haemorrhagic virus spread from Angola, where at least 360 people have died since last December in the worst outbreak in decades.
A wide effort to bring the outbreak under control by vaccinating more than 10 million people in DRC was due to start this week after delays due to shortages of vaccine and syringes.
"There is no known cure for yellow fever and it could go global," said Save the Children's country director for DRC, Heather Kerr, in a statement.
The yellow fever vaccine takes one year to manufacture. Save the Children said there are only 7 million emergency vaccines after stocks were depleted in a series of outbreaks earlier this year.
World Health Organisation (WHO) advisers have recommended using a fifth of the standard dose of vaccine in the event of a global shortage - enough to immunize temporarily but not to give lifelong immunity.
"We've got to urgently reach as many children and families as we can with the supplies that are left, and this is the only way we are able to do that right now," Kerr said.
The WHO aims to vaccinate 8.5 million people in Congo's capital Kinshasa and 3.4 million in DRC's border areas before the onset of the rainy season in October, to reduce the risk of mosquito-borne diseases spreading.
A total of 2,269 suspected cases and 16 deaths have been reported in DRC as of August 8, the WHO said.
Angola is starting a campaign this week to vaccinate 3 million people. The epidemic appears to be declining in the Southern African country with no confirmed cases reported in July or August, the WHO said.