Africa File

The Africa File is an analysis and assessment of the Salafi-jihadi movement in Africa and related security and political dynamics. 

March 16 BriefingCoronavirus Will Worsen Humanitarian Crises in African Conflict Zones

[Notice: The Critical Threats Project frequently cites sources from foreign domains. All such links are identified with an asterisk (*) for the reader's awareness.]

The global coronavirus (COVID-19) outbreak will worsen humanitarian crises caused by security and governance breakdowns in Africa. About half of the continent’s 54 countries have reported cases, and the number of cases is expected to grow. The pandemic may strain the continent’s fragile health care system. It is particularly dangerous to migrant, refugee, and internally displaced populations who suffer an acute lack of access to medical care, sanitation, and nutrition. The outbreak could also disrupt counterterrorism and peacekeeping missions if troop-contributing nations reprioritize their militaries to respond to the public health crisis.

In West Africa, a Salafi-jihadi insurgency is causing mass displacement that will compromise the pandemic response. Salafi-jihadi groups linked to al Qaeda and the Islamic State are waging a campaign to destroy and replace state and local governance across a large swath of Burkina Faso, Mali, and Niger. Salafi-jihadi violence has caused the world’s fastest growing displacement crisis in Burkina Faso, forcing hundreds of thousands of people to flee their homes.

Burkina Faso reported its first cases of coronavirus on March 9. The virus’ spread will likely compound the already severe crisis in Burkina Faso and further limit the state’s ability to respond to the Salafi-jihadi insurgency, which increasingly threatens neighboring countries.

In Libya, global and regional competition is fueling a conflict that is destroying the country’s institutions and harming vulnerable migrant populations in particular. Several foreign powers are perpetuating Libya’s civil war by providing arms, fighters, and funding. The conflict has severely degraded the Libyan health care system, and dozens of attacks have targeted health workers and facilities directly. An ongoing blockade of Libya’s oil resources is contributing to an economic crisis that also undermines the health sector.

The war and the pandemic are also dire threats to migrant populations trapped in Libya, where they lack access to basic services and have been the target of air strikes. The Libyan coast guard intercepted over 400 migrants and returned them to dangerous detention centers in Tripoli on March 15.

Also in this Africa File:

  • TUNISIA: Likely Islamic State militants conducted a suicide bombing at a checkpoint near the US embassy in Tunis. This attack may signal a trend of covert Islamic State operatives targeting US embassies across the Middle East and North Africa following a potentially related incident in Beirut, Lebanon.
  • LIBYA: Libyan warlord Khalifa Haftar met with European leaders but is unlikely to agree to a cease-fire while he retains significant foreign backing. Haftar, whose primary backers include the UAE, Egypt, Russia, and Saudi Arabia, has also begun to strengthen ties with Syrian President Bashar al Assad’s regime.
  • SAHEL: An al Qaeda–linked Salafi-jihadi group in the Sahel announced its willingness to negotiate with the Malian government if French and UN forces withdraw from the country.
  • LAKE CHAD: Members of the Islamic State’s West Africa Province reportedly mutinied over restrictions on the group’s rules of engagement. Leadership changes may make the group more lethal in the short term but could undermine its efforts to gain popular support.
  • SUDAN: The attempted assassination of Sudan’s prime minister indicates the country’s fragile new government may destabilize.
  • KENYA and SOMALIA: Al Shabaab will likely attempt to con duct a high-casualty attack in Nairobi, Kenya’s capital, in the coming months.

Read Further On:

North Africa

West Africa

East Africa


At a Glance: The Salafi-Jihadi Threat in Africa

Updated March 10, 2020

Global counterterrorism efforts are rapidly receding as the US shifts its strategic focus to competition with Iran, China, Russia, and North Korea. The US administration has begun to withdraw troops from Afghanistan after signing a peace deal with the Taliban on February 29. The future of Iraq, and US forces’ presence there, is uncertain. Indicators of the Islamic State’s return are apparent in both Iraq and Syria, however, as the group recovers from the death of its leader Abu Bakr al Baghdadi and other senior officials in late October 2019.

Meanwhile, the Salafi-jihadi movement, including al Qaeda and Islamic State affiliates and allies, continues to make gains in Africa, including in areas where previous counterterrorism efforts had significantly reduced Salafi-jihadi groups’ capabilities. The movement is positioned to take advantage of the expected general reduction in counterterrorism pressure to establish new support zones, consolidate old ones, increase attack capabilities, and expand to new areas of operations. The Salafi-jihadi movement is on the offensive in Burkina Faso, on the counteroffensive in Libya, and stalemated in Mali, Somalia, and Nigeria. However, conditions in these last three countries favor the Salafi-jihadi movement rather than its opponents in the coming year.

Libya’s civil war, reignited on a large scale in April 2019, will continue to fuel the conditions of a Salafi-jihadi comeback, particularly as foreign actors prolong and heighten the conflict. Stalemates in Somalia and Mali rest on the continued efforts of international coalitions, support for which is eroding in both host and troop-contributing countries and on local partners that have demonstrated their inability to govern effectively or establish legitimacy in their people’s eyes.

Amid these conditions, US Africa Command (AFRICOM) is shifting its prioritization from the counterterrorism mission to great-power competition, a move also intended to reduce risk after a 2017 attack killed four servicemen in Niger. US and European powers aim to turn over counterterrorism responsibilities to regional forces of limited effectiveness—such as the G5 Sahel, which is plagued by funding issues, and the African Union Mission in Somalia, which is beginning a scheduled drawdown

The Salafi-jihadi movement currently has four main centers of activity in Africa: Libya, Mali and its environs, the Horn of Africa, and the Lake Chad Basin. These epicenters are networked, allowing recruits, funding, and expertise to flow among them. The rise of the Salafi-jihadi movement in these and any other place is tied to the circumstances of Sunni Muslim populations. The movement takes root when Salafi-jihadi groups can forge ties to vulnerable populations facing existential crises such as civil war, communal violence, or state neglect or abuse. Local crises are the incubators for the Salafi-jihadi movement and can become the bases for future attacks against the US and its allies.



North Africa


Likely Islamic State militants conducted the first suicide bombing in Tunis, Tunisia’s capital, in 2020. Two attackers detonated explosives attached to a motorbike at a security barrier near the US embassy in Tunis, killing one security officer and injuring several other officers and a passerby. The attackers were under a travel ban, and one had been imprisoned previously. Tunisian officials have arrested several suspects since the attack.

The attack continues a trend of suicide bombings against security positions and patrols in Tunis. Islamic State militants conducted a double suicide bombing targeting security personnel in June 2019. A female suicide bomber attacked police officers in an unclaimed attack in October 2018.

The latest bombing may be the work of a transnational Islamic State network targeting US embassies. This is a low-confidence assessment that requires further information to verify. In January 2020, Lebanese security forces arrested an Islamic State militant and Syrian national named Ibrahim al Salem for planning to attack the US embassy in Beirut, Lebanon, with a self-assembled, explosive-bearing drone. Salem confessed to online contact with a senior Islamic State militant based in Tunisia—Abdullah al Tunisi—who advised Salem to attack the US embassy.

Lebanese authorities reportedly warned Tunisian authorities that al Tunisi was *plotting to attack the US embassy in Tunis. Al Tunisi has not been linked to the March 6 attack in Tunis at the time of writing. His involvement would indicate the existence of an Islamic State network in at least two countries focused on attacking US diplomatic posts.



European leaders are attempting to convince Libyan National Army (LNA) commander Khalifa Haftar to accept a cease-fire but are unlikely to succeed while Haftar retains other external backing. Haftar met with French President Emmanuel Macron in Paris on March 9 and German Chancellor Angela Merkel in Berlin on March 10. In Paris, Haftar signaled openness to a cease-fire only if the militias aligned with the UN-backed Government of National Accord (GNA) accept it. This statement is likely cover for Haftar’s intent to continue pursuing a military solution.

Haftar’s forces initiated the battle for Tripoli in April 2019. GNA Prime Minister Fayez al Serraj agreed to a cease-fire in Moscow in January, but Haftar walked out without signing the deal. Merkel urged Serraj to commit to a cease-fire during a phone call on March 12.

The French and German outreach is an attempt to preserve momentum from the late January Berlin conference on Libya, which sought to address the issue of foreign involvement. The conference led to a series of talks in Geneva, which have stalled. The UN Special Envoy for Libya Ghassan Salame resigned on March 2, citing the effects of stress on his health.

Choosing Salame’s successor will likely be another source of deadlock. Salame’s deputy, American diplomat Stephanie Williams, is currently acting envoy. The UN secretary general is reportedly considering former Algerian Foreign Minister Ramtane Lamamra as Salame’s successor.

Foreign involvement is a key driver of Libya’s war, which has become increasingly international since Haftar’s forces launched the assault on Tripoli in April. The offensive has stalled despite extensive military support from the UAE, Egypt, Russia, and Saudi Arabia, including the deployment of hundreds of Russian Wagner Group mercenaries and thousands of UAE-financed Sudanese fighters. Turkey intervened on the GNA’s side in late 2019 to stop the LNA’s advance. Turkey now provides military advisers and Syrian mercenaries to support the GNA.

The frontlines have largely stalled since Turkey increased its support for the GNA and associated forces in late 2019. Ankara has sustained its Libya footprint even while responding to a Syrian regime offensive in northwestern Syria’s Idlib province. Turkey and Russia, which backs Assad, struck a cease-fire deal on Idlib in early March. The LNA renewed an offensive push from the south at the end of February.

The LNA is strengthening ties with Syrian President Bashar al Assad’s regime. LNA-aligned officials reopened the Libyan embassy in Damascus on March 2. Libyan and Syrian officials announced their unified fight against Turkish-backed armed groups. Syrian sources have *reported that pro-Assad and pro-Russian groups are *recruiting Syrian fighters to support the LNA and Russia’s Wagner Group in Libya.

The GNA’s Ministry of Interior is attempting to leverage its improved position to wrest power from militia cartels that control Tripoli. Turkish backing has bolstered the GNA, which has held power in Tripoli through an uneasy deal with militias that have controlled parts of the capital for years. GNA Interior Minister Fathi Bashagha is attempting to bring policing and security operations under his authority. He *denounced the Nawasi Brigade militia for making arrests on February 23.

Nawasi and other militias *blocked Bashagha from the Ain Zara neighborhood on February 25 in response, which the GNA countered by establishing a new checkpoint and patrol on March 12. A GNA-aligned militia also accused Nawasi of assassinating one of its commanders on March 9.

Forecast: Foreign support for Libyan factions will continue, and the UN-brokered peace process will not yield a sustainable cease-fire. The most likely case is a grinding stalemate in a configuration similar to the current front lines. It is possible but less likely that the LNA will claim an initial victory by luring Misratan forces away from Tripoli and securing defections among Tripoli-based militias, particularly if arms embargo enforcement disproportionally affects Turkey.


This outcome would set conditions for insurgency, likely quickly. Either branch—the stalemate or the LNA advance—preserves and worsens the conditions that will allow Salafi-jihadi groups to strengthen. Alternately, diplomatic efforts paired with Haftar’s backers’ growing frustration could constrain the LNA and possibly marginalize Haftar over time. This could create space for others in the LNA camp to pursue a cease-fire, though it also increases the risk of the LNA coalition’s fragmenting. (Updated February 25, 2020)



West Africa

The Western Sahel (Burkina Faso, Mali, and Niger)

The Salafi-jihadi movement is ascendant in the western Sahel region. Militants aligned with both al Qaeda in the Islamic Maghreb (AQIM) and the Islamic State are growing more lethal and may soon establish de facto control over a large swath of the region. Militant attacks in this region have increased fivefold since 2016 and are concentrated in central Mali, northern Burkina Faso, and western Niger. The tactics that these groups use to overrun military bases could someday  enable attacks in Western capitals.

The rapid deterioration of security in West Africa is happening as the US Department of Defense considers withdrawing most, if not all, US troops from the region. This reduction could include ceasing intelligence and logistics support for the French counterterrorism mission in the Sahel. The US Department of State created a new special envoy position for the Sahel in early March in recognition of the regional crisis. The African Union has also announced its intent to send a 3,000-man temporary force to the Sahel.

AQIM’s affiliate in the Sahel expressed willingness to negotiate with the Malian government if French and UN forces withdraw from the country. Jama’at Nusrat al Islam wa al Muslimeen (JNIM) framed its willingness to engage in talks as heeding the Malian people’s will. The group’s statement claimed Malians have held “massive marches” against the French presence, an overstatement meant to capitalize on a more modest uptick in anti-French political rhetoric and protest this year.[1] Malian President Ibrahim Boubacar Keita acknowledged on February 10 that his government had contacted senior JNIM leaders to pursue talks, citing peace talks with the Afghan Taliban as a model.

Likely JNIM militants intensified attacks near Kidal in Gao region as the Malian government seeks to project authority there. Malian Army troops deployed to Kidal as part of the implementation of the 2015 peace agreement on February 10. Mali’s Prime Minister visited the northern town on March 4. Militants ambushed Irish peacekeepers on the Gao-Kidal road on February 25, injuring three soldiers. JNIM claimed an attack on the French Army in Kidal on March 9.[2]

JNIM is capitalizing on violence against civilians to gain popular support. JNIM claimed an attack on a Malian Army post in Mondoro in central Mali’s Mopti region as retaliation for a reported massacre of Fulani civilians in early March.[3] JNIM had previously denied an attack on a market in Mopti region and condemned attacks on churches on February 26.[4]

Salafi-jihadi groups in the Sahel  gain popular support by presenting themselves as the defenders of vulnerable populations while stoking retaliatory violence. This cycle is escalating in northern Burkina Faso, where gunmen massacred dozens of civilians in villages where Salafi-jihadi militants reportedly sought shelter on March 9.

JNIM’s disavowal of attacks on Christian worship sites reflects al Qaeda senior leadership guidance and may be another indicator of strategic divergence with the Islamic State in the Greater Sahara.

Two hostages escaped in northern Mali. Canadian Edith Blais and Italian Luca Tacchetto escaped their captors near Kidal in northern Mali. They arrived in the capital Bamako on March 14. Blais and Tacchetto were kidnapped while traveling to Bobo-Dioulasso in southwestern Burkina Faso in late 2018. The Macina Liberation Front, a component of JNIM, operates in this region of Burkina Faso and may have been responsible for the kidnapping. JNIM also operates in Kidal.

Sweden will contribute a rapid reaction force to the French-led international counterterrorism mission in Mali. The force will include 150 troops and helicopters.

Forecast: Salafi-jihadi groups will begin to establish governing institutions—such as courts—in the Burkinabe-Malian-Nigerien tri-border area in the next six months, though it may mask these efforts to facilitate a deal with the Malian government. Salafi-jihadi groups may also work through local governance structures to present themselves as legitimate interlocutors and avoid scrutiny. Attacks on Fulani civilians will drive greater popular support to JNIM, which will present itself as a more moderate alternative. (Updated February 25, 2020)



The Lake Chad Basin

Infighting may weaken both the Islamic State’s West Africa Province (ISWA) and Boko Haram in the near term but could lead to the groups’ merger. ISWA and Boko Haram split in 2016. ISWA has previously gained popular support by demonstrating more restraint than Boko Haram does and eschewing certain attacks. A change in strategy could make ISWA more lethal in the short term but may undermine the group’s effort to establish governance.

ISWA members reportedly mutinied over a disagreement over the group’s rules of engagement. They allegedly killed ISWA leader Abu Abdullah ibn Umar al Barnawi and militants Abu Maryam and Abu Zainab for "going soft" after they introduced a new regulation in February. The new regulation required fighters to stop pursuing soldiers fleeing during attacks and to cease killing captured soldiers. ISWA named Amir Abba Gana as al Barnawi's successor, according to local sources that shared this news with the Nigerian military on February 24. ISWA militants also murdered four members of ISWA’s shura council in early March. These ousters are likely not sanctioned by Islamic State leadership. The Islamic State has not commented on the removal of Islamic State–sanctioned ISWA emir Abu Musab al Barnawi in early 2019.

Boko Haram is also experiencing infighting over strategy. Militants are allegedly planning to assassinate the group’s leader Abubakar Shekau because of his unpredictability and nonadherence to Islamic tenets or Boko Haram’s original doctrine and ideology, particularly his use of women and children in attacks. Boko Haram tends to target Muslim civilians and is frequently condemned for its treatment of women and children. Shekau’s extreme tactics prompted Boko Haram ISWA to split into separate groups in 2016.

ISWA promoted its control of a local economic hub in northeastern Nigeria. An ISWA official, interviewed in the Islamic State’s al Naba bulletin, emphasized the economic and military value of Baga, a fishing town in Borno State located on a highway to the regional capital Maiduguri.[5] ISWA seized Baga in December 2018.



East Africa


The attempted assassination of Sudan’s prime minister indicates the country’s fragile new government may destabilize. Sudanese Prime Minister Abdalla Hamdok survived an assassination attempt targeting his convoy in Khartoum on March 9. He was unharmed. Witnesses reported an explosion caused by either a projectile or a car bomb. Sudan's Sovereign Council appointed Hamdok to become prime minister in August 2019 after the ousting of longtime leader Omar al Bashir in April. Hamdok is attempting to reform the country toward civilian rule by 2022 but has faced resistance from the military. Security forces linked to al Bashir instigated a gunfight in Khartoum over severance reforms in mid-January.

For more on the implications of instability in Sudan, see Emily Estelle’s “Chaos in Sudan and the rest of North Africa threatens all of us,” originally published in the Los Angeles Times in May 2019.

Kenya and Somalia

The al Shabaab insurgency in Somalia is largely stalemated, but conditions—including political instability and the planned withdrawal of African Union peacekeeping forces—are evolving in al Shabaab’s favor. Al Shabaab has recently intensified its efforts targeting American interests and Kenya, including a January 5 raid on a US-Kenyan military position that killed three Americans.

Al Shabaab may be planning a high-casualty attack in Nairobi, Kenya’s capital. The US embassy in Nairobi warned in late February that the group is planning an attack on a popular tourist hotel in Nairobi.

Al Shabaab has escalated its campaign in Kenyan counties bordering Somalia. Al Shabaab is targeting *military posts, police, police reservists, and telecommunications infrastructure in eastern Kenya, a longtime area of recruitment for the group.[6] Al Shabaab has also sustained attacks on police targets and telecommunications infrastructure. Kenyan President Uhuru Kenyatta gave a group of eastern Kenyan politicians and administrators 14 days to come up with a solution to the deteriorating security situation on February 26.

Al Shabaab’s spokesman attempted to persuade ethnic Somalis in eastern Kenya to support al Shabaab in a February 16 recording.[7] He argued that non-Muslim Kenyans treat ethnic Somalis in its eastern provinces like second-class citizens and appealed to economic anxieties driven by unemployment.

Kenyan involvement in a Somali political crisis is causing backlash in Kenya. Kenyan Defense Forces (KDF) support regional security forces in southern Somalia’s Jubbaland State. Parliamentarians from Kenya’s Mandera County criticized the Kenyan government for the *skirmishes between the Somali National Army (SNA) and Jubbaland State security forces in early March in southwestern Somalia’s Gedo region. Some Kenyan Muslims have called for the KDF to pull out of Somalia completely. Kenyan officials announced in early March that they would begin scheduled negotiations to withdraw the KDF from Somalia by 2021.

Somali political crises are drawing resources away from the fight against al Shabaab. Federal SNA forces *clashed with Jubbaland State security forces on March 2.  The skirmishes follow a month of increasing tensions after the SNA took over the Gedo region from Jubbaland State security forces in early February.

The Jubbaland crisis has spiked tensions between the Kenyan government and the Somali Federal Government, but the debacle may be resolving. The Kenyan government accused the SNA of violating its territory during clashes with Jubbaland State security forces on March 4. Somali President Mohamed Farmajo *accepted an invitation from Kenyan President Uhuru Kenyatta to resolve the Jubbaland conflict at an upcoming meeting in Nairobi.

SNA forces have also clashed with a regional militia in Galmudug state in central Somalia. The leader of the Ahlu Sunna wa al Jama’a militia surrendered to the SNA on February 29.

The death of the al Shabaab commander responsible for the Manda Bay attack in Kenya in early January may help the leader of al Shabaab, Ahmad Umar, solidify his control over the group. US Africa Command confirmed that an air strike in late February killed Bashir Mohamed Mahamoud (Bashir Qoorgaab), a senior al Shabaab commander who planned the attack that killed three Americans. Umar had dismissed Qoorgaab from al Shabaab's executive council for disagreeing with Umar over targeting civilians in attacks in the Somali capital, Mogadishu.

Al Shabaab members also arrested and *executed Muse Moalim, the former chief coordinator of the group’s intelligence brigade, on March 9. Moalim had *resigned in mid-February amid escalating tensions between Ahmad Umar and several top commanders.

Forecast: Al Shabaab will attempt a spectacular attack in Kenya in the first half of 2020. The group will also sustain a campaign of bombings in Mogadishu and elsewhere as part of a broader campaign to disrupt the planned 2020 elections. (Unchanged since January 9, 2020)



Russian mercenaries are conducting counterinsurgency operations in Mozambique that risk worsening popular grievances and inflaming the Salafi-jihadi insurgency they are meant to counter. A second contingent of Russian Wagner Group mercenaries arrived in Mozambique. For more on the objectives of Russian counterterrorism missions in Africa, see the October 16 Africa File.


[1] “Echoing Taliban, JNIM expresses openness to negotiations with Malian government if France, UN withdraws,” SITE Intelligence Group, March 9, 2020, available by subscription at

[2] “JNIM claims bombing French and MINUSMA military vehicles in Mali, armored vehicle in Burkina Faso,” SITE Intelligence Group, March 9, 2020, available by subscription at

[3] “JNIM claims attack on Malian Army post as vengeance for massacre of civilians,” SITE Intelligence Group, March 5, 2020, available by subscription at

[4] “JNIM denies attack on Dogo market, disavows strikes on churches,” SITE Intelligence Group, February 26, 2020, available by subscription at

[5] “ISWAP military official speaks to IS’ Naba newspaper on enemy offensives in Baga,” SITE Intelligence Group, March 13, 2020, available by subscription at

[6] “Shabaab claims attacks in Kenya’s Garissa and Mandera counties, firing 30 mortars at Ugandan bases in Lower Shabelle,” SITE Intelligence Group, February 26, 2020, available by subscription at

[7] “Shabaab spokesman threatens non-Muslims in northeastern Kenya, cautions Muslims from supporting government,” SITE Intelligence Group, February 26, 2020, available by subscription at

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