A large number of these insectivorous free-tailed bats - Mops condylurus in Latin - were collected by the villagers for food, but disposed of the next day after a government-led ban on bushmeat consumption was announced.
While bushmeat is thought to be a possible source of Ebola, the scientists believe it didn't trigger the outbreak.
Instead, it was Emile's exposure to the bats and their droppings as he played with his friends in the hollowed tree.
The scientists took and tested ash samples from the tree and found DNA traces that were a match for the animals.
While they were unable to test any of the bushmeat that the villagers had disposed of, they captured and tested any living bats they could find in and around Meliandou.
No Ebola could be detected in any of these hundred or so animals, however.
But previous tests show this species of bat can carry Ebola.
Dr Leendertz, from the Robert Koch Institute in Germany, and his colleagues say this must be a pretty rare occurrence though.
Meliandou is a small village of 31 houses.
It sits deep within the Guinean forest region, surrounded by towering reeds and oil palm cultivations - these are believed to have attracted the fruit bats carrying the virus passed on to Emile.
During their four-week field trip in April 2014, Dr Fabian Leendertz and colleagues found a large tree stump situated about 50m from Emile's home.
Villagers reported that children used to play frequently in the hollow tree.
Emile - who died of Ebola in December 2013 - used to play there, according to his friends.
The villagers said that the tree burned on March 24, 2014 and that once the tree caught fire, there issued a "rain of bats".
he Ebola victim who is believed to have triggered the current outbreak - a two-year-old boy called Emile Ouamouno from Guinea - may have been infected by playing in a hollow tree housing a colony of bats, say scientists.
They made the connection on an expedition to the boy's village, Meliandou.
They took samples and chatted to locals to find out more about Ebola's source.
The team's findings are published in EMBO Molecular Medicine.
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