Two people have fallen ill with Ebola in Guinea, the World Health Organisation has said, dashing hopes of an imminent end to the worst recorded outbreak of the disease after a two-week spell without any new cases across west Africa.

Guinea was weeks away from joining Liberia in being declared free of the virus that has killed more than 11,000 people in a near two-year rampage. Neighbouring Sierra Leone is also halfway through the 42-day countdown to being Ebola-free.

Authorities in Guinea said on Friday one of the cases in Forécariah, western Guinea, appeared to be linked to a previously known chain of infection, while the other in the capital, Conakry, seemed to be new.

“On the bumpy road we keep talking about – the high risk of recurrence – once again we are navigating a few bumps,” Margaret Harris, a WHO spokeswoman, told a briefing in Geneva. “Of course we didn’t want it, but we did expect it. Guinea hadn’t got to the stage where we were looking at 42 days.”

Ebola transmission is considered to be over once a locality has gone 42 days without a new case.

A spokesman for Guinea’s anti-Ebola taskforce said the patient in Forécariah was discharged on Friday after being cured, leaving a 21-year-old man admitted to the Nongo treatment centre in Conakry, who was not on the contact list of any previous registered victims.

“We suspect that he contracted the disease by another means, perhaps sexual, but we cannot be sure for the time being,” said Fodé Tass Sylla.

A study this month showed the semen of male survivors can harbour the virus for nine months and the virus can also live on in other parts of the body.

A British nurse fell critically ill this week, 10 months after recovering from Ebola, underlining the lingering risks from the virus.

Liberia was declared transmission free on 3 September and Sierra Leone is counting down another 22 days until it is clear.

The medical toolkit for tackling Ebola has been transformed in the past few months by the success of a trial vaccine that is now used to treat each new case and their contacts who may be at risk from the highly contagious virus.

But Harris said that the trial comes to an end in mid-November, potentially putting a question mark over the use of the vaccine beyond that date.