African effort to sequence continent’s biodiversity seeks $1 billion over 10 years | Science

When ThankGod Echezona Ebenezer left southeast Nigeria to start a biochemistry Ph.D. at the University of Cambridge in 2013, he soon realized little information on the genomes of plants and animals from Africa were in existing global sequencing databases. To help protect the continent’s biodiversity and aid its agriculture, he and colleagues founded the African BioGenome Project (AfricaBP) to sequence every plant, animal, and other eukaryotes native to the continent, estimated at more than 100,000 species.

Coordinated from Jomo Kenyatta University of Agriculture and Technology in Nairobi, Kenya, AfricaBP officially launched in June 2021 and now includes 109 African scientists and 22 African organizations, representing researchers and organizations from all five regions in the African Union. The plan is to develop a knowledge hub that helps build scientific capacity and equitably shares the benefits realized from this genome sequencing effort. AfricaBP is already trying to sequence more than 2000 species and is partnering with three global genomic efforts: the 10,000 Plants Genomes Project (10KP), the Vertebrate Genomes Project (VGP), and the Earth BioGenome Project (EBP).

But the project needs funding to move beyond its pilot efforts. Ebenezer, in a commentary in Nature today, calls on governments, in Africa and beyond; international partners; and donors to commit $1 billion over the next decade. Science spoke to the scientist about why the work is needed and the future of biogenomics in Africa.

This interview has been edited for brevity and clarity.

Q: Tell us about the Africa Biogenome Project?

A: When I started my Ph.D. I searched sequence databases for genomes of plants and animals in Africa—not much was there. About 12 years ago I was interested in how fishes adapt to environmental conditions through the help of parasites. I came across Bostrychus africanus, which is mainly found around the Gulf of Guinea and communities across West Africa. This fish is host to the nematode parasite, Raphidascaroides africanus. Since encountering this fish I would check sequence databases every now and then for its genome, but this was missing. I would also check the genomes of other African species and limited information existed. It became apparent to me that African species are neglected by the global genomic community. This is mainly because such genome sequencing and bioinformatics capacities are limited across Africa.

Q: What has been done in Africa so far?

A: AfricaBP became an affiliated project of the EBP in 2020. With the VGP partnership, we have been working to sequence about 10 vertebrate species. With the 10KP we have assembled 100 plant species to sequence. We are now in discussions with scientists in South Africa to get a top five sequenced there.

Echezona Ebenezer
ThankGod Echezona Ebenezer Jeff Dowling/EMBL-EBI/UK

Q: Has the pandemic been a major hurdle?

A: It is, actually. In Africa generally, scientists prefer face-to-face conversations as this works best for most people due to limited internet access and electricity. So far we have been working remotely. In future we would want to meet physically in Africa.

Q: What sort of knowledge hub do you intend to develop?

A: We aim to ensure that at least 80% or more of the sequencing happens on the continent by African scientists through our programme, the AfricaBP Open Institute for Genomics and Bioinformatics. We want African scientists to collect samples and analyze them. Even if they are going to be supported by scientists from the global north they should play a leading role in the process because it is only by doing so they will be able to do it on their own in the future. Another reason: it is good to sequence on the continent since it is not easy to transport a sample from Nigeria to Zimbabwe, for example—there are so many regulatory and legal issues. But if I could do it in Nigeria, it eliminates all those issues. And of course, Nigerians will be able to have more confidence in the system and even bring more samples for sequencing.

Q: What about building sustained investment in the early career pipeline for African scientists?

A: There has to be core funding for a sustainable AfricaBP. Scientists in Africa need funds in order to be able to run the project. We estimate that it will cost about $1 billion over 10 years, $100 million per year for sequencing, storing information, workshops, and funding early career researchers. We believe that knowledge exchange is key in a project like this. We aim to transfer knowledge from countries that have more genomics and bioinformatics capacity to those with less in Africa. Scientists in Burundi, could for example have a fellowship at the University of Cape Town in South Africa. After 3 years they will have the capacity they need to go back to their communities and contribute on genomics.

Q: And where do you intend to get the funds?

A: We aim to obtain funds from international partners, African science agencies, and the African Union. Several other continental partners will be happy to connect with this because we believe this project is something that we need to do for Agenda 2063, Africa’s blueprint for development, which has three goals that are related to biological resources. In 2022, we should start to understand the genetics of these biological resources.

Q: What is the importance of doing this in Africa and by Africans?

A: Africa is not yet where it needs to be when it comes to a capacity for genomics and bioinformatics. Although several groups across Africa have been involved in genomics and bioinformatics, especially within the human space, more still needs to be done on nonhumans. By doing this in Africa it helps build the capacity that we need. It provides the fundamental knowledge that Africa needs in order to solve her food and security problems, and conservation issues, such as how many elephants are there in Africa now compared to 10 to 15 years ago and how can we use genetic or genomic information to actually improve this. People in Africa are closer to this biodiversity than someone outside Africa, so they will be able to mix cultural and traditional knowledge into genomic practices.

Q: How do you feel about the future of bio-genomics in Africa?

A: I see the future as bright. I have had so much interest from students from the continent. There is a huge buy-in from early career scientists to established scientists and governments officials. The next step for us is being able to secure a multiyear core funding that would help to establish the project itself across the continent. There are several biobanks across Africa—this project should be able to feed into those biobanks.