The health ministry said two new deaths have been tied to the cases, including one in a suburb of Mbandaka. There were no cases in the Congo during that outbreak.
"This is a major, major game-changer in the outbreak", Dr. Peter Salama, the World Health Organization's deputy director-general of emergency preparedness and response, warned Thursday.
"The arrival of Ebola in an urban area is very concerning and WHO and partners are working together to rapidly scale up the search for all contacts of the confirmed case in the Mbandaka area", WHO Regional Director for Africa, Matshidiso Moeti, said in a statement. It is paramount to trace the suspect case in order to have a clearer view on how it reached the city. It will be used to protect health workers and "rings" of contacts around each case.
If any of these elements fails, the vaccine's potential to protect 100 percent of those immunised will go unrealised.
Isolation zones have been set up in Mbandaka's main hospital, and in Bikoro, WHO said. "There's a lot of complex logistics and social science here". The disease killed over 11,000 people in West Africa between 2014 and 2015.
The outbreak, publicly declared on May 8, had previously been reported in a rural area of Equateur that lies roughly 150 kilometres (93 miles) from Mbandaka.
Of the 45 reported cases, 25 people have died but so far only one death has been linked to Ebola, it said.
REUTERS Kenny Katombe Congolese Health Ministry officials arrange the first batch of experimental Ebola vaccines in Kinshasa
The WHO said on Thursday it became more concerned when a case was confirmed in Mbandaka, a city of about a million people which is connected to Kinshasa by the Congo River.
"The EU is taking urgent action to help manage and contain the spread of this highly deadly disease".
Experts also caution that acting too hastily could jeopardise the potential success of a vaccine deployment.
In Mbandaka and Bikoro, 514 people who may have been in contact with infected people have been notified by national health authorities and are being monitored, according to Doctors Without Borders. They would be sending in experts to remote locations as well.
There is, however, a logistical challenge as the Canadian vaccine, which is called rVSV-ZEBOV, needs to be stored at minus 80 degrees Celsius and is only available in the capital, Health Minister Oly Ilunga told Reuters. "We are working closely with the Ministry of Health and the other organisations in the field to implement a coordinated, tailored and rapid response to stop the spread of Ebola".
The WHO said the risk of the disease spreading was "high" and announced it was preparing for the "worst case scenario".
"We want to make sure we are engaging whole communities so that the broader community understands what we are doing and why", said Salama.
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