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The jihadist magazine made the announcement on Tuesday in an interview with Sheikh Abu Musab al-Barnawi, whom it referred to as the new “governor of West Africa”.
In the interview, Barnawi makes no clear reference to the Nigeria-based extremists’ previous leader, except for a mention of Shekau’s pledge of allegiance to the IS group last year.
Since the pledge, Barnawi has appeared in several videos distributed by Boko Haram, claiming responsibility for successive attacks, earning him the reputation of group spokesman, experts say.
Speculation over the fate – and alleged disappearance – of Shekau has been rife in recent months.
He last appeared in a video posted on YouTube in March, looking weak, and saying: “For me, the end has come.”
Sources close to Boko Haram say Shekau was injured in the abdomen.
With no proof of life since then, they say he has either been incapacitated and become unable to lead or he has died.
“If [Shekau] is still alive then ISIS chose to replace him,” Kyle Shideler of the Washington-based Center for Security Policy told AFP, using another acronym for the IS group.
“This (Barnawi) is their preferred choice,” Shideler added.
Boko Haram ‘lost its prestige’
Romain Caillet, a French expert on jihadist movements, agreed.
“There is no indication in the interview that Abubakar Shekau has been killed, which means he was likely sacked,” Caillet wrote on Twitter.
A Nigerian security analyst said he believed Shekau is alive, but that IS may be seeking to clean up Boko Haram’s reputation among jihadists, by getting rid of a leader seen as disorganised and unreliable.
Barnawi may have taken over from Shekau, said Yan St-Pierre, a specialist on jihadist groups who works for the Berlin-based Modern Security Consulting Group (Mosecon).
Under Shekau’s leadership, “Boko Haram has lost its prestige and become difficult to control. Today, Boko Haram is divided into several little groups.”
Shekau became Boko Haram leader after the Nigerian security forces killed the group’s founding chief Mohammed Yusuf in 2009, sparking an insurgency that has left 20,000 people dead and forced 2.6 million people to flee their homes.
In March 2015, Shekau declared that Boko Haram had become the Islamic State group’s West Africa Province. At the time, Boko Haram was the most powerful military force in northeast Nigeria, controlling a huge area and better equipped and motivated than Nigerian forces.
Since then the group has been pushed out of most of the territory it controlled, though it has continued to carry out suicide bombings in northeast Nigeria and neighbouring Cameroon, Niger and Chad, focusing on busy public areas such as markets and mosques.