As the World Health Organization announces the next step in its distribution of the world’s first authorised malaria vaccine in three African countries, concerns about its value have come from an unlikely source: the Bill and Melinda Gates Foundation, arguably the vaccine’s biggest backer.

WHO endorsed the vaccine last fall as a “historic” breakthrough in the fight against malaria but the Gates Foundation told The Associated Press (AP) news agency this week it will no longer financially support the shot.

Some scientists say they are mystified by that decision, warning it could leave millions of African children at risk of dying from malaria as well as undermine future efforts to solve intractable problems in public health.

The vaccine, sold by GlaxoSmithKline (GSK) as Mosquirix, is about 30-percent effective and requires four doses.

The malaria vaccine has “a much lower efficacy than we would like,” Philip Welkhoff, the Gates Foundation’s director of malaria programmes, told the AP.

Explaining its decision to end support after spending more than $200m and several decades getting the vaccine to market, he said the shot is relatively expensive and logistically challenging to deliver.

“If we’re trying to save as many lives with our existing funding, that cost-effectiveness matters,” he said.

The Gates Foundation’s decision to pivot away from supporting the rollout of the vaccine in Africa was made years ago after detailed deliberations, including whether the foundation’s money would be better spent on other malaria vaccines, treatments or production capacity, Welkhoff said.

Some of the resources that might have gone into getting the vaccine to countries have been redirected to buy new insecticidal nets, for example.

“It’s not the greatest vaccine in the world, but there are ways of using it that could have a big impact,” said Alister Craig, the dean of biological sciences at Liverpool School of Tropical Medicine.

The world is struggling to contain the spike in malaria seen since the coronavirus pandemic disrupted efforts to stop the parasitic disease, which killed more than 620,000 people in 2020 and caused 241 million cases, mainly in children under five in Africa, Craig said.

“It’s not like we have a lot of other alternatives,” Craig said. “There could be another vaccine approved in about five years, but that’s a lot of lives lost if we wait until then,” he said, referring to a shot being developed by Oxford University.

BioNTech, creator of the Pfizer COVID-19 vaccine, plans to apply the messenger RNA technology it used for the coronavirus to malaria, but that project is in its infancy.

Another big obstacle is availability; GSK says it can only produce about 15 million doses per year until 2028. WHO estimates that to protect the 25 million children born in Africa every year, at least 100 million doses every year might be needed.

Although there are plans to transfer the technology to an Indian drugmaker, it will be years before any doses are produced.

“All the money in the world” would not alleviate the vaccine’s short-term supply constraints, said Welkhoff, of the Gates Foundation.

He noted that the Gates Foundation continues to support the vaccines alliance Gavi, which is investing nearly $156m into making the shot initially available in three African countries: Ghana, Kenya and Malawi.

“We’re supporting the roll-out via the Gavi funding, but we decided we would not dedicate additional direct funding to extend the supply of the vaccine,” Welkhoff said.

On Thursday, WHO and Gavi invited developing countries to apply for funding to pay for the malaria vaccine in their countries.

“If delivered to scale, the vaccine will help to prevent millions of cases of malaria, save tens of thousands of lives and ensure a brighter future for the continent,” said Dr Matshidiso Moeti, WHO’s Africa director.

The Gates Foundation’s withdrawal of financial support for the malaria vaccine might unnerve others, Dr David Schellenberg of the London School of Hygiene and Tropical Medicine, said.

“There is a risk that this could discourage others who are considering financing the malaria vaccine or even be a disincentive for people working on other vaccines,” he said. He said that combining the vaccine’s use with other measures, like distributing drugs during malaria’s peak season could dramatically reduce cases and deaths.

“We still see people coming in with four or five episodes of malaria a year,” he said. “We don’t have a magic bullet, but we could make better use of the tools we do have.”

An imperfect distribution of the vaccine would still save lives, Dr Dyann Wirth, an infectious diseases expert at Harvard University, said.

“We would love to have 100 million doses, but that kind of money doesn’t exist for malaria,” she said. “The 15 million doses we have is still 15 million opportunities to protect children that we didn’t previously have.”

The Gates Foundation had done its part in bringing the vaccine to market and it is now up to countries, donors and other health organisations to ensure it is used, she said.

The vaccine, even with its imperfections, is eagerly awaited in Malawi.

Nolia Zidana, 32, said she is keen to get her two young sons immunised after seeing malaria sicken them numerous times – and surviving it herself.

“Growing up with my parents and siblings, we have been sick from malaria all the time,” said Zidana, who lives in Malawi’s central Ntcheu district. “My elder son has had malaria countless times within the four years that he has been around. While just at seven months old, twice my younger son has already been down with malaria,” she said.

She said although they sleep under mosquito nets, sometimes they get bitten before going to bed as they are preparing meals for supper in the dark of the evening.

“We hear other people use mosquito repellents or burn anti-mosquito incense coils, which we cannot afford as we are just peasant farmers that live from hand to mouth,” she said.

Dr Michael Kayange of Malawi’s health ministry urged everyone in the country to take whatever measures they can to curb malaria. Immunisation itself is insufficient to stop the disease and people should adopt multiple strategies, he said.

“Even just by sleeping under a mosquito net, you have played your role in reducing the malaria burden in the country,” he said.