More than 7,000 years ago, during the last Green Sahara period, when the vast north African desert was rain-fed and lush, a child was born with extraordinary powers – and the seed of a curse.

Locked inside the child was a genetic mutation that gave a heightened immunity to malaria. Over the following 259 generations, the disease would become the deadliest in human history. Indian scribes of the Vedic period called it “the king of diseases”. Malaria hastened Rome’s fall. It killed up to 300 million people in the 20th century alone – one in every 20 deaths.

The child survived because of a change in haemoglobin, the molecule in red blood cells that carries oxygen, which was then passed on to its descendants. The mutation persisted because it was a means of survival in malarial sub-Saharan Africa. But its potency held a dark secret.

Sometimes, when two of those descendants procreated, their children inherited two mutated genes, and their red blood cells collapsed into crescents, clogging their blood vessels. The result is what we now call sickle cell anaemia – a painful, sometimes deadly genetic disorder that afflicts 300,000 babies every year, mostly in Africa.

The link between sickle cell and malaria was established in the 1950s and had a profound impact on the field of human molecular genetics. But the existence of the child – which may be crucial in finding a cure – was not discovered until 2018, by Charles Rotimi and his colleague Daniel Shriner at the US National Institutes of Health.

Scientists in Africa are grappling with the complex ethical implications of practising an extractive science on a continent with a long history of exploitation from abroad © Diana Ejaita

The mapping of the entire human genome – a 13-year effort to list all of the roughly 3 billion “letters” that make up a person’s DNA – was completed in 2003. Since then, the reference genome that scientists use to conduct their research has steadily grown, adding different types of people to further our understanding of the fundamental building blocks of human life.

But it remains incomplete: nearly 20 years on, the vast majority of it is still European. Genetic material from people of African descent makes up just 2 per cent. It was this small portion that produced Rotimi’s groundbreaking research.

The lack of African genetic material constitutes a significant obstacle to understanding how our bodies and diseases function. African genomes are not only humanity’s oldest but our most diverse, and that diversity holds within it an almost unfathomable potential – from scientific breakthroughs to gene editing to the rewriting of our evolutionary history, the very story we tell ourselves about ourselves.

“The continent of Africa represents what I would like to call the root and trunk of human evolutionary history,” Rotimi tells me over the phone from Maryland, where he is the director of the Center for Research on Genomics and Global Health at NIH.

“We have lived the longest as humans on the African continent, and that has very, very important implications for understanding… how forces that existed on the continent helped shape present-day human genomes, either in terms of how to survive infectious diseases or survive the environment.”

Researchers, academics, drug companies and start-ups around the world have recently woken up to the potential that Africa offers. A consortium of roughly 500 African scientists is conducting groundbreaking research on the genetic causes of blindness, Alzheimer’s, cancer, kidney disease and other afflictions under the umbrella of the H3Africa programme – an initiative created by Rotimi, and funded by the NIH and the UK’s Wellcome Trust, in 2012.

‘There are things in the human genome that we cannot study anywhere else but on the African continent, because of the evolutionary history of humanity’ — Charles Rotimi of the US National Institutes of Health © Nate Palmer

Their work, Rotimi says, is just beginning to bear fruit. Meanwhile, pharmaceutical groups are on the hunt for genomic data from African populations – in some cases provided by new home-grown biotech start-ups – as they seek to develop the next generation of blockbuster gene-based therapies.

There is, however, concern about who will ultimately own Africa’s genomic data. A US official told the FT last month that the Trump administration wanted to block China’s plans to build an $80m headquarters for the Africa Centres for Disease Control and Prevention, in large part because of Africa’s “vast amounts of genomic data”. “The Chinese… want to eventually steal the data,” the official said (Beijing called the allegation “ridiculous”).

As the commercial possibilities become clear, and private companies from the US, Europe and China take an interest, scientists in Africa are grappling with the complex ethical implications of practising an extractive science on a continent with a long history of exploitation from abroad.

Roughly 99 per cent of our evolutionary history occurred in Africa. Modern humans emerged there 200,000 years ago. About 100,000 years later, small groups of our collective ancestors began a procreational march around the world. They took with them just a fraction of our genetic diversity. Those in Africa held the vast majority, and as they intermarried and reproduced, that diversity remained, buffeted and transformed by environmental pressures including disease. Tapping into that diversity has implications for all of humanity.

Not long ago, a tailor came to my home in Lagos to take my measurements. I asked him if he could also make dresses for my daughters. He said he knew someone who could, his ex-business partner. Actually, he said, she was also his ex. Ah, I said, it’s always hard to mix business and love. No, no, it’s not that, he said. We’re both AS.

Inside each human cell is a nucleus with about 20,000 genes made up of strands of DNA that contain four chemicals called nucleotides, or bases. The entire human genome – which includes all of a person’s genes – contains 3.2 billion pairs of those bases – lettered A, C, T and G – which provide the blueprint for how our cells function.

Two copies of the haemoglobin gene sit in each of those cells. For some Africans, one of them is normal (A) and one of them is mutated (S). They carry the sickle cell trait but don’t suffer from the disease. Roughly a quarter of Nigerians are AS; the country accounts for half of the babies born with the disease each year.

When things between the tailor and his girlfriend got serious, they – like most young Nigerians – took a genetic test. He was unlucky, as many others across Africa and in the diaspora are, to have fallen in love with another descendant of the child born in the Green Sahara, hundreds of generations down the line.

Genomic research is the search for variation. Humans share roughly 99.9 per cent of their DNA but it is the difference in what remains that is important. These mutations are known as SNPs, or single-nucleotide polymorphisms – the equivalent of a single typo in all of the words in a thousand bibles. Most are benign, causing blue eyes or big ears or nothing at all. The ones scientists seek are more dangerous – causing cancer, Alzheimer’s, high cholesterol, Parkinson’s – and more heroic, protecting us from such afflictions.

Without including the genetic data of Africans, precision medicine, gene editing and other scientific advances risk becoming the province of the white and wealthy. Many genetic tests are already better at predicting breast cancer and type-1 diabetes in patients of European descent than clinical methods, because the tests are based on them. This bias is “the most critical limitation to genetics in precision medicine”, according to a 2019 paper in the journal Nature Genetics.

Broadening genetic research will benefit everyone. Years ago, Dr Olufunmilayo Olopade, one of America’s leading cancer researchers, began noticing higher rates of breast cancer, at earlier ages, in women in her native Nigeria. In 2018, she co-authored the first-ever study to use sophisticated genomics analysis of African women. The results could change the way we think about how breast cancer develops and how it should be screened for – regardless of where you come from.

‘We need to do more genetics research in Africa, because otherwise we will have the wrong policies, we will start in the wrong place’ — Dr Olufunmilayo Olopade, a leading cancer researcher at the University of Chicago © Jean Lachat/University of Chicago

“For a very long time, we have thought that cancer went through a systematic, slow growth, so you wait until 50 and you get your mammogram once every two years and you’re going to be OK,” says Olopade, a MacArthur genius grantee and director of the Center for Clinical Cancer Genetics and Global Health at the University of Chicago.

“I think this really has just turned that on its head, because you may need to start earlier…And it shows that we need to do more genetics research in Africa, because otherwise we will have the wrong policies, we will start in the wrong place, and that’s why we have not had the kind of progress we needed to have.”

Advances in sequencing mean finding mutations is increasingly easy. Determining which ones matter is far more difficult. Researchers have found that including even a few black people in studies can improve results. But most analysis is still done on European-ancestry populations, because they are the most common in scientific literature. Without robust data from African populations, scientists are missing out on the secrets of thousands of generations of human evolution.

A recent study of just 910 people of African descent revealed that 300 million base pairs – out of more than 3 billion – are not found in the reference genome. “That’s massive. That means that potentially you have 10 per cent of the area that you just don’t know… and that completely harms our capacity as scientists to do good science,” says Dr Ambroise Wonkam, associate professor in the division of human genetics at the University of Cape Town, who is studying the longevity of sickle cell patients.

“So when we say equity in science now is important, specifically with the African population, it’s not about charity… It’s something that is absolutely necessary for us to do the science the way it should be done. Otherwise, we all lose.”

Point G Hospital is a dusty complex of low-slung buildings on a sandstone bluff above Bamako. Down below, the Niger river winds through Mali’s sleepy, sandblasted capital. I meet Dr Guida Landouré, an H3Africa-funded researcher, in the faded baby-blue neurology building where his office is lit by fluorescent bulbs and the midday Sahelian sun.

His white coat hangs from the curtain rod. Stacks of bursting Manila folders are piled half-a-metre high around his small laptop. He grins wanly as he unfolds his gangly frame to greet me, moving a hand towel in a bashful effort at cleaning up.

‘My goal is not to go somewhere... where I can get better paid. My goal is to get knowledge that I can transmit to other people back in my country’ — Dr Guida Landouré, an H3Africa-funded researcher in Bamako, Mali © Oman Seth Ahouansou

Landouré was born in central Mali, the last of 28 children to a Koranic schoolteacher and his three wives. His family tended cattle. After he completed his PhD at University College London, Landouré returned for two weeks to the US, where he’d previously worked at the NIH. “People were saying, ‘Why don’t you stay?’ I said, ‘No, I came to the country to look for something I could not get at home’,” he says.

“PhDs are thousands in the US, thousands in the UK, but a PhD in neurology or neurogenetics in Mali? There are none. My goal is not to go somewhere where it is easy for me to work, or where I can get better paid. No. My goal is to come here to get knowledge that I can also transmit to other people back in my country, those who did not get the opportunity to come here, to train them.”

In 2013, Landouré received his H3Africa grant to study the genetic roots of hereditary neurological disorders such as muscular dystrophy or Huntington’s disease. Many such disorders are being studied elsewhere. Some even have a cure. “But we have not even done the survey of these diseases in Africa,” he says.

I think it’s more acceptable to the African population if they see their African peers doing the research, rather than people from outside. That can remind people of the old days

Five months ago, Landouré’s lab discovered a form of progressive myoclonic epilepsy caused by a genetic mutation that had previously only been documented in two other patients, a German and an Italian. The disorder can be treated with an inexpensive compound called folinic acid.

“The patient could not even hold their head up, and was completely absent. But when we saw him later, he was playing!” he says. “So you can see how genetics can change that child’s life. This is what makes us think that we should continue.”

Walking through the lab, it is impossible not to recognise the extreme limitations most African scientists must work under. “It’s completely different,” Landouré says. An NIH lab in the US comes fully kitted-out, with expert colleagues to bounce ideas off. “But here, when I came, they give you an empty space. You bring everything.”

The lab has a number of state-of-the-art instruments, kept under floral plastic sheeting. Shipping costs and diesel for the generator eat up a lot of the budget. Landouré’s H3Africa funding is being used for the entire neurology department. It funds bursaries for students, the clinic downstairs and training for students and faculty alike – important capacity building, though it takes away from the research.

But he hopes it will sustain medical research in Mali for years to come, instilling trust in people who might otherwise be wary. “I think it’s more acceptable to the African population if they see their African peers doing the research, rather than seeing people from outside,” he says. “That can remind people of the old days, of people coming in and taking the resources and going out.”

In 1996, the Nigerian city of Kano was hit by the worst meningitis outbreak in Africa’s history, infecting 120,000 people. Médecins Sans Frontières and other non-governmental organisations convened at the infectious disease hospital. Another team arrived from Pfizer, the global pharmaceuticals company, which was in the late stages of testing a meningitis drug.

“[Pfizer] saw an opportunity for a phase 3 clinical trial,” says Babatunde Irukera, the lawyer who represented Nigeria in the lawsuit that followed. “They scrambled together a team and… started conducting their clinical trial.” Pfizer staff wore no badges differentiating themselves from the humanitarian workers, he says. “People were sending their children to them thinking they were going to treat them,” adds Irukera, now head of Nigeria’s Federal Competition and Consumer Protection Commission.

In 2009, Pfizer paid $75m to settle the resulting lawsuit. “It was an indication of the kinds of things that had been going on in this country for years: pharma companies conducting tests without proper controls,” says Irukera. “Pfizer claims it conducted informed consent, but we have no evidence of that. These are people who don’t speak English.”

In a 2009 statement announcing the settlement, in which Pfizer denied any wrongdoing or liability, the group said that “the 1996 study was conducted with the approval of the Nigerian government and the consent of the participants’ parents or guardians, and was consistent with Nigerian laws”.

Commercialisation has long been a fraught subject in scientific research, especially when it comes to informed consent and compensation. Questions over whether the subject should be paid have been debated for years. Perhaps the most famous example is Henrietta Lacks, the African-American woman whose unique “immortal” cells were harvested by researchers without her knowledge before she died. Their indefinite ability to grow means they have been used in nearly every major medical advance in the past half century, but her descendants have never received compensation.

‘When we say equity in science now is important, specifically with the African population, it’s not about charity... It’s something that is absolutely necessary’ — Dr Ambroise Wonkam of the University of Cape Town © Lee-Ann Olwage

The Lacks case is a relic of a time before informed consent. But researchers in Africa today must figure out how to obtain it from everyone, including those who may not yet have words like “DNA” or “gene” in their native tongue.

The UK’s Wellcome Sanger Institute was recently embroiled in a controversy over whistleblower complaints that it planned to misuse samples obtained in Uganda and elsewhere in Africa. These include accusations that it was attempting to commercialise the products of the research without proper consent.

Sanger, one of the world’s leading genomics institutions, has denied the allegations, citing two independent investigations it commissioned that found no wrongdoing. In a statement, it said: “The cause of concern was a potential commercialisation proposal from an individual working at the Institute at the time. The Institute did not pursue this proposal.”

Separately, during the 2014 Ebola epidemic, doctors and researchers from around the world took more than 269,000 blood samples from patients in Guinea, Sierra Leone and Liberia. None gave consent for them to be used for research. But thousands of samples were sent to foreign labs including Public Health England, according to reporting by the journalist Emmanuel Freudenthal. Beyond the lack of patient consent, this left researchers in those countries without access to the samples that in many cases they themselves collected.

Christian Happi, one of Africa’s leading scientists, was part of the team that sequenced Ebola during the outbreak. The Cameroonian, now based in Nigeria, tells me over the phone that the team made the data public immediately so that it could be used to find treatment. “We were not really interested in terms of storing the samples or keeping the samples or making the fancy Nature or Science paper,” he says. “And that’s what’s different between us that are on the ground and care about our people, and those that are called ‘parachute scientists’”.

Happi grows animated as he describes how Africa has the skills, facilities and knowledge to hold on to its genetic endowment. “We have many, many centres of excellence, we have plenty of people who trained in the best schools in the world that are back on the continent. There shouldn’t be any room for samples to keep going out of Africa any more,” he says. “There’s no point saying that you maintain and keep all this in Europe, and anytime there’s [a crisis] you parachute in with all the skills and all the tools and eventually go back. That is no longer acceptable.

What if a company came and requested data and 10 years down the line were able to make a [blockbuster] drug? How do the people who contributed that data benefit?

“We should be collaborating but… you can’t go to America and then take DNA samples out just anyhow. You can’t go to Europe and take DNA samples or virus samples out anyhow. Why should that be different here?”

Such questions have been pondered inside H3Africa for years, says Jenniffer Mabuka, head of the programme at the African Academy of Sciences. “What if a commercial company, for example, came here and requested data and 10, 15 years down the line were able to make a [blockbuster] drug out of it?” she says. “How do the people who contributed that data benefit?”

Options for compensation could include free access to diagnostic services, discounted access to the drugs developed from their genetic material, donations to local clinics – or, most simply and far more controversially, cash.

Many researchers contend that subjects shouldn’t be compensated as it could compromise the science. It also takes years of analysis before anyone can tell whether a mutation means anything. “The idea that I would learn something from your genome and then exploit [it] is actually pretty rare,” says Lawrence Brody, director of the division of genomics and society at the National Human Genome Research Institute at NIH.

But the issue is complicated by the west’s history of plunder in Africa. From diamonds to gold, oil, bauxite, rare earths and, of course, people – the continent is rich in resources but has seen almost no benefit from its bounty. Big Pharma’s record is no better than Big Oil’s. What is to keep Africa’s great genetic diversity from becoming yet another resource that is extracted and refined into multibillion-dollar drugs abroad?

Funding for H3Africa will dry up in two years. There is no sign of any government or institution ready to step in, even as its research is only beginning to reveal the promise the continent holds. Its leaders believe the investments they’ve made will allow African scientists to better compete for funding with their global peers. But those researchers will also have to get creative about how to fund their work.

Since the Human Genome Project there has been a dramatic reduction in the cost of sequencing – from $500m-$1bn in the early 2000s, to under $1,000 per genome today. That has made Africa a more attractive destination for research dollars, despite being higher risk and logistically complex. But the allure of African genomics, both commercially and scientifically, has elevated a familiar debate that is particularly acute in a continent with a history of exploitation: profit versus purpose.

‘The [sheer] number of companies that have reached out — there is a real interest in studying diseases in this population’ — Abasi Ene-Obong, chief executive of 54gene © Kemka Ajoku

This became apparent in my discussions with Happi and, separately, Abasi Ene-Obong. His company, 54gene, raised $4.5m in venture funding last year to create Africa’s first private biobank and has just launched a programme to sequence the DNA of 100,000 Nigerians.

Both geneticists trained at world-class institutions (Happi at Harvard and Ene-Obong at the University of London), and both speak about broadly similar goals: to advance science by tapping into Africa’s potential, to give back to the continent and bring Africans into the genomics revolution. But Happi’s approach suggests a choice must be made between profit and purpose; Ene-Obong believes you can have it all.

This summer, Happi will open a $4m genomics centre on the campus of Redeemer’s University in Nigeria, funded mainly by the World Bank. The centre will primarily be a research institution, but it will also offer consulting, sequencing and training courses for academics and public health officials. “Our goal is to see how we can use genomic information to actually address problems in Africa… saving lives, making impact, without thinking about enriching ourselves first,” he says. “It’s about making it sustainable.”

Ene-Obong’s office in Lagos still bears the popping primary colours of 54gene’s early history as an African version of Ancestry.com or 23andMe, the US consumer genetics unicorn. He is a big guy with a gentle disposition who smiles easily. His mission for 54gene has some crucial differences to Happi’s.

“The question is, are we just building a research tool or is it a business?” he says. “It’s a business. But we want to build a better reference set… because the current leading reference set that is used in the world doesn’t even contain my tribe.”

Older academics see us moving fast, being successful and they are threatened because, you know, suddenly the light is leaving them and coming towards us

He is referring to the 1,000 Genomes Project, which followed the Human Genome Project and was meant to address the dearth of non-European populations. In fact, it includes neither his father’s Efik tribe nor his mother’s Igbo, of whom there are more than 30 million in Nigeria.

The company’s planned 100,000-Nigerian database – which it is sourcing from hospitals and academic institutions – is something that pharmaceutical companies would likely pay hefty fees to access.

As Matthew Nelson, head of genetics at GlaxoSmithKline, tells me: “If I was able to access a full medical history of 500,000 people across five countries in Africa, and analyse genetic data from that, that would be a far better investment in understanding genes and disease than another 500,000-person study in Europe.”

But Ene-Obong also wants 54gene to work along the drug discovery chain, from contract research for pharma companies to clinical trials to potentially doing drug discovery themselves. He wants the company to be a “precision-medicine powerhouse” so that it can create targeted treatments for Africans.

“But that’s a side effect of the work,” he tells me. “We want to be able to build value, and that value could be drugs that treat people across the world but with a preference also for drugs from diseases that affect Africans disproportionately.”

The plan is to partner with pharma companies, research institutions, governments and biotech. “The [sheer] number of companies that have reached out – there is a real interest in studying diseases in this population, and we just want to make sure that it’s all done sustainably and done well,” he told me, a month after the company publicly launched last July. Ene-Obong insists the company can contribute to science, give back to Africa and make a profit.

Happi is not convinced. “What are we doing to ensure that there is equity, that there is fairness, that you have properly compensated for the gift – I mean it is a gift – that they have donated to mankind?” Happi says he effectively asked Ene-Obong in a recent H3Africa teleconference. He says he’s fine with the private sector engaging transparently, but wasn’t satisfied with what he says were Ene-Obong’s vague answers.

54gene’s ethics chief, Aminu Yakubu, served as chair of H3Africa’s ethics committee before joining the company last year in September. He tells me 54gene’s ethical framework aligns broadly with H3Africa’s, though it is evolving. Roughly 5 to 20 per cent of the profits from its research contracts with companies will go to a foundation in each country it operates in. Committees of eminent scientists and societal leaders will decide where the money goes.

For the first time in human history, we now have the necessary tools…and the scientific understanding of how to interrogate human genomes

Yakubu notes that the ethics of compensation are complicated. Would mentioning the prospect of compensation from a hypothetical billion-dollar drug in a consent form improperly induce someone living on $2 a day into participating? Should any benefits go only to those who participated in the study or their entire community? Their ethnic group? Their country? Still, if a single person’s genes are used to create a drug sometime down the line, Yakubu says the company would want that person to get a portion of the profits.

Ene-Obong tells me he’d noticed something among “old academics, researchers” doing genetics in Africa. “They see us moving fast and they see us being successful and they are threatened because, you know, suddenly the light is leaving them and coming towards us.”

Still, he says that he wants to work with academia. He already has collaborations with researchers and institutions in Nigeria, including some affiliated with H3Africa. This is essential to 54gene’s work and he wants to do more.

“The people who will suffer if [such] tensions continue are African, because the two sides will be focused on each other and people won’t be getting the benefits of either,” he says. “In other countries, you have a situation where private [companies] and academics come together to partner… [but] I can understand why there is contention in Africa – we are the first private entity doing this.”

With H3Africa’s funding running out, such collaboration will become increasingly important. Whatever happens, genomic research in Africa must continue, says Rotimi. “For the first time in human history, we now have the necessary tools in terms of biotechnology, computational infrastructure and the scientific understanding of how to interrogate human genomes… and we know that Africa is the home of humanity,” he says.

Rotimi is the godfather of African genomics research, widely credited with pushing the notion that we should study the continent’s populations. Bringing in more African scientists and studying African genomes is, he says, both a scientific imperative and a matter of social justice.

“The scientific imperative is that there are things in the human genome that we cannot study anywhere else but on the African continent, because of the evolutionary history of humanity,” he says. “The social justice issue is that if we don’t engage this part of the world, then whatever gains we’re going to get from using genomics to improve health or agriculture or even the economy, that part of the world is going to be left behind, just like a lot of other revolutions passed over Africa.”

Neil Munshi is the FT’s West Africa correspondent

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