When Abdoulaye Djimdé returned to his home city of Bamako, Mali, after receiving a grant to set up his first lab, he naturally went to see the university’s finance office.

The conversation was not what he expected. Frustratingly, the grant, which had been transferred to the University’s bank account, had been mixed up with funds from various other sources. Eventually, after a small percentage had been deducted to cover the institution’s running costs, Djimdé was handed the remaining amount – some $20,000 (£13,000) – in cash.

That was 2001. Djimdé had returned to Mali after completing a PhD in malaria genetics at the University of Maryland. During his time in the United States he had authored ground-breaking research identifying the first genetic markers for chloroquine-resistant malaria, and a method for tracking drug-resistant malaria parasites in the field. He was a world-class scientist, but obtaining access to his research funds had been an uphill battle and, with no systems for research procurement or accounting in place at the University of Bamako, Djimdé was tasked with setting up an internationally recognised genetics lab virtually unaided.

Nevertheless, Djimdé and many other leading researchers are convinced that the best place to do malaria research is in sub-Saharan Africa, where the disease is a massive health burden and there is a pressing need for better methods of prevention and new treatments. A key partnership for the lab was with the Wellcome Trust Sanger Institute in Cambridge, which meant that although the resources locally were scarce, he was able to sequence malaria parasite DNA by sending back samples to the UK.

Following the same logic, we should be doing Ebola research in Sierra Leone, basic science on HIV in South Africa, and malaria genetics in Mali. Why then are we more used to seeing the latest developments in these areas being pioneered in the universities of California, Oxford or Zurich, rather than KwaZulu-Natal, Accra, or Harare? Inevitably, it is down to lack of investment, by both governments and the international community, in research infrastructure, training and programmes. Djimdé is one of many African scientists who have gone to study at a non-African university, and – crucially – he’s one of the very few to have come back. It is common for a scientist to move around the world to do research, but not to move to Africa to set up a research base.

The figures are stark, and the task of developing African science and its future scientists is daunting. Government money is spent on development and security, not research and innovation. According to the World Economic Forum, Africa produces only 1.1% of global scientific knowledge. The continent has just 79 scientists per million of inhabitants compared to countries like Brazil and United States where the ratio stands at 656 and 4,500, respectively. Worst of all, of those scientists and engineers who are trained in Africa, most work elsewhere due to the lack of infrastructure and resources.

Under-investment has knock-on effects, both on the stability of the healthcare systems, as we saw in West Africa during the Ebola epidemic, but also on the economy. There are clear links between investment in basic science and innovation in the form of spin-outs and large-scale commercial research and development. Similar arguments are made all over the world, but so far in Africa they are not being won.

But one new organisation hopes to turn this story around. AESA (the Alliance for Accelerating Excellence in Science in Africa), of which I am the director, has been founded by the African Academy of Sciences and the African Union’s New Partnership for African Development as a body that will award research grants to African universities, advise them on financial best practice and develop a science strategy for Africa. Our vision is to make research an attractive, recognised career option in Africa, creating scientists who stay in the continent and can win their own grants to address local problems.

Initially we have been working in partnership with the Wellcome Trust, the Bill and Melinda Gates Foundation and the UK Department for International Development to develop our resources and capacity. The Wellcome Trust and BMGF are working towards handing over control of their African research funding programmes to AESA. The active grants in these portfolios total more than $70m (£45m). But the real story is the step-change in governance. AESA will be directing the strategy for future funding, convening decision-making committees of international experts, and providing advice on finance and grant management – all of which is desperately needed if money is going to be reliably spent on research.

Abdoulaye Djimdé is one of the first awardees. The University of Bamako has made great strides in the past 15 years, and Djimdé will be using a $7m award to bring sequencing capacity to Mali and regionally, creating the first permanent genomics hub in sub-Saharan Africa, and training the next generation of biomedical scientists across nine African countries.

Tom Kariuki, an immunologist and biomedical scientist, is the director of the African Academy of Sciences’ Alliance for Accelerating Excellence in Science in Africa based in Nairobi, Kenya.