Weekly Health Update | Ebola Spreads, Cholera Surges and New Gains Against Malaria in Africa

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In this week's health update, the Bundibugyo Ebola outbreak affecting the Democratic Republic of Congo and Uganda remained the region's leading public health emergency, with 381 confirmed cases, placing it among the largest outbreaks on record. Progress was also reported in the fight against HIV and malaria, notably through the rollout of lenacapavir in South Africa and encouraging new data on the RTS,S/AS01 malaria vaccine. The week was marked by intensified efforts to develop vaccines against the Bundibugyo strain, controversies over biosafety practices and a proposed quarantine project in Kenya, as well as a resurgence of cholera across Southern Africa.

The Mosquirix vaccine (RTS,S/AS01) is effective against child mortality, according to a commentary published June 2 in The Lancet. The paper presents new data on the vaccine's impact in African rollout programs.

Results from African countries with moderate to high malaria transmission show a significant reduction in mortality among children under five, validating the protective efficacy of a vaccine that spent years as an experimental candidate. Ally Olotu of the Ifakara Health Institute in Tanzania and co-authors note that RTS,S/AS01 is the first vaccine effective against a human parasitic disease, and that it usefully complements insecticide-treated bed nets in prevention strategies.

If confirmed at scale, the data would strengthen the case for incorporating malaria vaccination into immunization schedules across high-endemic African countries, at a time when malaria kills more than 600,000 people annually, the vast majority of them African children.

Cholera: Angola and Mozambique drive resurgence in southern Africa

The cholera situation in sub-Saharan Africa remains a serious challenge. According to the ECDC's monthly report of June 1, 2026, more than 68,000 cases have been reported across the continent since the start of the year. Between late April and late May, Angola recorded 2,120 new cases, making it one of the hardest-hit countries.

Mozambique followed with 413 additional cases reported in late May. The country accounts for nearly 90% of southern Africa's cases and, at the World Health Assembly in May, unveiled a five-year, $500 million plan to eliminate the disease by 2030.

The Democratic Republic of Congo also recorded 115 recent cholera deaths, a sign that the preventable disease continues to kill on a large scale in areas where access to safe water and sanitation remains inadequate.

HIV: South Africa launches lenacapavir, but U.S. funding cuts threaten access

South Africa on June 5, 2026, officially launched lenacapavir (LEN) as a pre-exposure prophylaxis (PrEP) tool against HIV.

????? Today marks an important step forward in HIV prevention with the launch of lenacapavir in South Africa.

Developed by U.S. company Gilead Sciences, this groundbreaking twice-yearly HIV prevention medication has demonstrated 99.9% effectiveness in clinical trials. Through… pic.twitter.com/tQpiE2kaVs — U.S. Mission SA (@USEmbassySA) June 5, 2026

President Cyril Ramaphosa and Health Minister Aaron Motsoaledi presided over the ceremony at the Lilian Ngoyi Stadium in Secunda, Mpumalanga. Administered by injection twice a year, lenacapavir, an HIV-1 capsid inhibitor, provides six months of protection with each dose, reducing adherence challenges associated with daily oral PrEP.

South Africa becomes the ninth African country to adopt the treatment. An initial allocation of 37,920 doses has been made available across 360 public health facilities in high-prevalence areas.

U.S. aid cuts have nonetheless caused new PrEP initiations in Africa to fall by more than 40%, threatening the systems that are meant to support the large-scale rollout of lenacapavir.

Ebola epidemic in DRC and Uganda: toll and dynamics

The Bundibugyo strain Ebola outbreak continues to spread in the DRC and Uganda. As of June 4, the Congolese health ministry reported 381 confirmed cases, including 64 deaths, with 233 patients hospitalized in isolation.

Ituri remains the epicenter with 359 cases across 17 health zones; North Kivu accounts for 19 additional cases and South Kivu three. The epidemic now affects 24 health zones across three provinces. In Uganda, 19 confirmed cases and 2 deaths have been recorded, including several in Kampala and the neighboring district of Wakiso.

At a June 3 press briefing, WHO Director-General Tedros Adhanom Ghebreyesus said the number of suspected cases had been reduced from more than 1,000 to 116, following a systematic review and reclassification of pending samples. The clarification does not mean the outbreak is receding, but reflects improved diagnostic capacity. Contact tracing, however, remains insufficient, estimated at just 45%.

Already the third-largest Ebola outbreak in history

The outbreak is already ranked the third largest Ebola flare-up ever documented, behind the 2014-2016 West African epidemic and the 2018-2020 Congolese crisis, and is being worsened by several structural challenges. The Bundibugyo strain has no approved vaccine or treatment, unlike the Zaire strain, for which the Ervebo vaccine exists. Initial detection was also delayed by several weeks, after the first diagnostic kits, which targeted the Zaire strain, returned false negatives.

The Africa CDC, the African Union's health agency, has designated 10 neighboring countries as being at high risk of importing cases. Community mistrust of healthcare workers, rooted in previous crises, is also directly complicating contact tracing operations.

Funding increases but remains insufficient

The international community stepped up its funding pledges in response to the epidemic between May 29 and June 5.

The U.S. State Department announced $112 million in bilateral aid earmarked for personal protective equipment procurement, border surveillance, contact tracing and diagnostic supplies.

The United Kingdom committed 20 million pounds for affected communities, while the European Union allocated 15 million euros, including 5 million euros paid directly to the WHO for field operations. Taken together, these formal pledges total the equivalent of nearly $175 million.

That funding falls short of the $319 million Africa CDC has deemed necessary for its six-month continental plan. Director-General Jean Kaseya had warned that pledged funding had already dropped from $500 million to around $290 million within a matter of days in late May, and said he would publicly identify countries that failed to deliver promised funding.

Race for a Bundibugyo vaccine accelerates

On the vaccine front, the Coalition for Epidemic Preparedness Innovations announced on June 4 its financial support for three Bundibugyo virus vaccine candidates, according to French vaccine information website Mes Vaccins.

U.S. company Moderna receives $50 million to develop an mRNA candidate for preclinical and Phase 1 trials. The University of Oxford receives $8.6 million to prepare clinical trials for a vaccine based on the ChAdOx1 platform, the same platform behind the Oxford/AstraZeneca COVID-19 vaccine. IAVI, the International AIDS Vaccine Initiative, a non-profit global biomedical research organization, receives $3.2 million to produce a reference strain via the rVSV platform.

On that last point, the WHO stated in its May 28 technical report that the rVSV-ZEBOV vaccine, licensed against the Zaire strain, should not be used in this outbreak due to a lack of evidence of cross-protection.

The experimental treatments MBP134, Maftivimab, and remdesivir, an antiviral used against SARS-CoV-2 during the COVID-19 pandemic, remain the only options currently under clinical evaluation for treatment and post-exposure prophylaxis.

Epidemic worsens food insecurity

Ituri, the outbreak's epicenter, is one of the DRC's most severely food-insecure areas in 2026. Some 1.7 million people, more than a third of the province's population, are in crisis-level food insecurity or worse, including 500,000 in emergency conditions. Nationally, 26.5 million Congolese are living in acute food insecurity.

The World Food Programme is deploying a multi-pillar response including meals for hospitalized patients, their caregivers and affected households, aimed at reducing uncontrolled departures from isolation centers. "The window to contain this epidemic is narrow," WFP DRC Country Director David Stevenson said. MSF is meanwhile building a 65-bed treatment center in Ituri and supporting several health facilities in Bunia. Both organizations are calling for urgent additional funding.

Kenya: court blocks U.S. quarantine center project at Laikipia

A U.S. plan announced in late May for a 50-bed quarantine center for American citizens exposed to Ebola at Kenya's Laikipia Air Base triggered a triple reaction: judicial, popular and diplomatic. Nairobi's High Court, seized by the Katiba Institute and the Law Society of Kenya, suspended the project on May 30, citing public health risks and a lack of contractual transparency. Separately, hundreds of protesters blocked roads leading to Nanyuki base on June 1.

President William Ruto sought to defuse the crisis by stating the facility would not be reserved exclusively for Americans. Washington announced $13.5 million in funding to strengthen Kenya's health preparedness. American public health experts described the project as problematic on clinical, ethical, operational and legal grounds.

Ghana and Nigeria: proactive preparedness with no confirmed cases

Further from the Great Lakes region, other countries are maintaining vigilance. On June 3, the WHO delivered a batch of essential medical equipment and supplies to Ghana in response to a request from the government.

Health Minister Kwabena Mintah Akandoh conducted an assessment tour of Accra's airport, the Noguchi Memorial Institute for Medical Research and the Ga East Municipal Hospital to assess weaknesses in surveillance and diagnostic systems.

Ghana has recorded no Ebola cases. In a similar vein, Oyo State in Nigeria activated its emergency operations centers and reinforced epidemiological surveillance in health facilities and at points of entry, mobilizing community health workers. These initiatives reflect a pattern of proactive preparedness that contrasts with the early detection failures observed in Ituri in April. Nigeria, the continent's most populous country, had notably succeeded in containing the 2014 Ebola outbreak rapidly.

Ayi Renaud Dossavi