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One vehicle transporting people and goods “rode over an improvised explosive device (IED) in the Barsalogho area” leaving at least 15 passengers dead, government spokesman Remis Fulgance Dandjinou said in a statement.
A security source said most were traders.
Meanwhile, around 50 kilometres (30 miles) away, 14 people were killed when food vans travelling in convoy were attacked, the spokesman added.
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“Military reinforcements have been deployed and a thorough search is under way,” Dandjinou said.
A former French colony that ranks among the world’s poorest countries, Burkina Faso has been struggling with an Islamist militant revolt since 2015.
The country’s army has been increasingly targeted by jihadists. Earlier this month, an attack on a military base in northern Burkina Faso killed 24 in an unprecedented blow to the army in its campaign against jihadists.
The insurgency, which came from neighbouring Mali, began in the north but has since spread to the east.
Since 2015, more than 500 people have died in attacks that have become increasingly violent especially in the north and the east, according to a toll compiled by AFP.
The capital Ouagadougou has been attacked three times, including a March 2018 jihadist assault on the military headquarters that left eight dead. A summit of regional heads of state is due to be held in Ouagadougou on Saturday to discuss the security situation.