The cases were announced just hours after Sierra Leone officially heralded the end of its recent Ebola flare-up, again dashing hopes that the deadly disease was gone from West Africa.
The new cases occurred in a remote region of southeast Guinea, 10 00km from the capital.
In a statement Friday, WHO said Guinea officials reported three unexplained deaths in Koropara on Wednesday.
It said a mother and her 5-year-old son then tested positive for the disease and were taken to a treatment facility.
The deadliest Ebola outbreak in history has killed more than 11 300 people, mostly in Sierra Leone, Liberia and Guinea.
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