More than 2,000 cases have been recorded in the DRC since the start of the outbreak in August, the country's 10th to date, and more than 1,400 people have died. He says 27 people who may have been exposed are being followed.
"EU humanitarian health experts in the Democratic Republic of Congo, in Uganda and in the region are coordinating and they are in daily contact with the health authorities in these countries, the World Health Organisation and operational partners", the statement added.
On Thursday, health workers in Congo's town of Beni began vaccinating pregnant women who have passed the first trimester and are considered contacts of an Ebola case.
A health ministry official told AFP on condition of anonymity that the two victims had "attended the burial of an Ebola patient in Congo, but returned to Uganda".
Congo's health ministry says all members of the Congolese-Ugandan family have agreed to be repatriated to Congo for experimental treatments as part of clinical trials.
Uganda's Health Minister Jane Ruth Aceng said challenges remained stopping people crossing at "unofficial entry points" between Congo and Uganda, which share a porous 875km (545 mile) border.
They and frontline health workers are due to be vaccinated Friday with a new drug created to protect them against the virus, the health ministry said.
South Sudan has also declared a state of alert and vaccinated health workers. Uganda, Rwanda and South Sudan have been preparing for possible cases.
WHO will hold an emergency meeting Friday to determine whether to declare the outbreak "a public health emergency of worldwide concern", a major shift in mobilisation against the disease. The decision in both instances was due to Ebola's containment within the DRC.
Meanwhile, new research from Cambridge University released on Thursday indicates that half of all Ebola outbreaks have gone undetected since the virus was discovered in 1976.
"The unfolding epidemic in the DRC demonstrates how hard it is to stop the disease once it has got out of control, even with global intervention", Emma Glennon from Cambridge's department of veterinary medicine said in a statement. There is no treatment as such for the virus which can spread quickly via close contact with bodily fluids of those infected and can be fatal in up to 90 per cent of cases.
It is the worst on record after an epidemic that struck Liberia, Guinea and Sierra Leone between 2014-2016, leaving more than 11 300 people dead.
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