A nurse prepares a vaccine against Ebola in Goma, in the Democratic Republic of Congo on 7 August 2019.
The epidemic began in August 2018 in the province of North Kivu before spreading to neighbouring Ituri and South Kivu - a remote and largely lawless region bordering Uganda, Rwanda and Burundi. According to the World Health Organization, the virus kills between 25% and 90% of people who contract it.
MSF said in a statement on Tuesday that those receiving the first dose of the new vaccine would be asked to return to complete the process.
It will be available to adults and children over one, living in two areas of the DR Congo city of Goma, where there is no active transmission of the deadly disease.
The epidemic in Congo was declared in August 2018 and has so far killed almost 2,200 people, making it the second-worst outbreak of the virus on record behind the 2013-16 West African outbreak that killed more than 11,300.
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Four cases of the disease were recorded in Goma this year, but no new cases have been reported in the lakeside city since August. He now faces charges that he embezzled funds intended for the fight against Ebola.
Merck - which is known as MSD outside the United States and Canada - said: "Given the unique manufacturing requirements for ERVEBO, this approval allows MSD to initiate manufacturing of licensed doses in Germany, which are expected to start becoming available in the third quarter of 2020".
The new J&J vaccine had initially been rejected by DRC's former health minister Oly Ilunga, who cited the risks of introducing a new product in communities where mistrust of Ebola responders is already high. He is now under investigation for alleged embezzlement of Ebola funds. The WHO prequalified the vaccine just two days after the European Commission granted conditional marketing authorization for the vaccine. It is being marketed under the brand name of Ervebo.
This is often followed by vomiting and diarrhoea, skin eruptions, kidney and liver failure, and internal and external bleeding.
The virus's natural reservoir is suspected to be a tropical bat which does not itself fall ill but can pass on the microbe to humans who hunt it for food.