What is the African BioGenome Project? A coordinated pan-African effort to build capacity (and infrastructure) to generate, analyze and deploy genomics data for the improvement and sustainable use of biodiversity and agriculture across Africa. We refer to this coordinated pan-African effort as the African BioGenome Project (AfricaBP), and the community of networks to deliver on this agenda as Digital Innovations in Africa for a Sustainable Agri-Environment and Conservation (DAISEA).

1. African BioGenome Project
(AfricaBP)
Genomics for the future of
biological diversity across
Africa
ThankGod Ebenezer, EMBL-EBI, United Kingdom
Anne Muigai, JKUAT, Kenya
Appolinaire Djikeng, CTLGH, United Kingdom
AfricaBP Master Slide 2021

2. Content
➢ Background
○ Goals and vision
○ Overarching aim and evolution of AfricaBP
○ About AfricaBP, DAISEA and Grand Challenges (GCs)
➢ Delivery pipeline
○ Timelines
➢ Value proposition
➢ Prospective partners and framework (AAS, AU-IBAR, EBP, VGP)
➢ Steering Committee
➢ Advisory Board
➢ What is next?

3. Coordinate
01
● all non-human genome sequencing
initiatives (existing and emerging) in
Africa.
● act as forum for the non-human space.
Deploy
03
● sequencing data to contribute to regional
biobanks, Africa CDC PGI, AU-IBAR, etc
● inform policy, and build capacity in Africa
Initiate, develop, &
support
02
● new non-human genome sequencing
efforts.
● sequence > 105,000 species in Africa.
Goals of the African BioGenome Project (AfricaBP)

4. The global biodiversity landscape is a shared heritage
Nearly all continent is endowed with a form of biodiversity
6th mass extinction event is upon us: but we can still turn the tide

5. Africa plays significant role in global biodiversity
Essential component of global biodiversity hotspots

6. Human activities poses significant threat to biodiversity
Source: https://earth.org/data_visualization/biodiversity-loss-in-numbers-the-2020-wwf-report/

7. Global biodiversity loss is happening at an unprecedented scale
We need unprecedented urgency to help reverse this trend
Africa must protect & ensure equitable use of BD across Africa

8. Two revolutionary global projects, one end goal...
20 years: Human genome revolutionised understanding of human health
20 years: BioGenomes will improve our understanding of the biosphere

9. Emergence and Evolution of AfricaBP
In the early days, DAISEA aims to build capacity in portable genome sequencing

10. Overarching aim
➢ AfricaBP is the umbrella project
○ DAISEA | EBP-Africa an exemplar initiative
○ Focus now is on DAISEA | EBP-Africa,
○ Evolution of AfricaBP
■ e.g. generate BioGenome data for African
Union, Africa CDC PGI, AU-IBAR
➢ Other sub-projects may spring up within AfricaBP
as Africa’s genomic community identifies the need.
Sequence the genomes of indigenous and
endemic biological species across Africa
DAISEA
AfricaBP:
Unified African
BioGenome

11. BioGenome for Food Systems and Conservation across Africa
An exemplar in AfricaBP

12. DAISEA for the AfricaBP: Background
➢ A flagship community network within AfricaBP to
support genome-guided sustainable agricultural
practises and conservation across Africa.
Overarching goal
➢ Sequence the genomes of endemic biological organisms
in the agri-environment and in the wild across Africa.
○ From sequence (diversity, variations) to applications (crop and
animal improvement).
○ Resilient food systems and well-being (human, animal, plants,
etc)

13. AfricaBP project activities will cover all eukaryotic lineages
Sources: https://forestrypedia.com https://www.vecteezy.com

14. What we envisage?
➢ Build and increase
collaborations and
capacities
➢ Contribute to genomic
resources in Africa
➢ Inform and drive policy,
socio-economics

15. What are the challenges?
How do we achieve the challenges of addressing the goals of the UN SDG02?

16. African scientists must contribute to global biogenome revolution
Biodiversity genomics in Africa must be driven by African scientists & agencies
Is it possible to sequence all eukaryotic organisms across Africa?

17. Genomics and Bioinformatics
Technologies for the
Agri-Environment
Technology Development,
Knowledge Exchange and
Industry
Crops and Livestock
Improvement and
Health
Socio-economics,
Ethics and Policy
Issues
Genomics for Conservation of
Endangered and Endemic Species
Value
Proposition
Capacity
Building
AfricaBP, DAISEA Grand Challenges (GCs)
Five GCs that will deliver value to the African people

18. 1
Sampling
Sign MoU with host communities & labs;
Nagoya Protocol; Build capacity in taxa
sampling & preparation techniques; work
with partners e.g. AWARD, CORAF.
3
Sequencing, assembly,
annotation
Build capacity in sequencing, assembly, &
annotation techniques across labs; use
existing labs in Africa; work with partners,
e.g. EBP, VGP, H3ABioNet, Sanger ToL
5
Value proposition and
empowerment
Bring different value players; Knowledge
exchange & breakthroughs; Build large
bioresources relevant to stakeholders &
partners; Increase genomics technology
expertise in non-human systems in Africa;
Provides data for zoonosis & anthroponosis;
Gender equality & sustainable
agri-environment; empowering women; work
with partners, e.g. AWARD, AU-IBAR, AAS
2
Sample preparation &
Nucleic acid extractions
Build capacity in molecular biology
techniques for respective taxa; use existing
labs in Africa; work with partners e.g. EBP,
VGP
4
Informatics, data
storage, databases, &
IT infrastructure
development
Build capacity in data storage
platforms; use existing DBs in
Africa; Build a critical mass of
genome and informatics
infrastructure; work with partners
e.g EBP, VGP, H3ABioNet, Sanger
ToL
AfricaBP will drive standards for BioGenomes in Africa

19. Sept. 2021
Inauguration
- Inaugural meeting
of AfricBP, DAISEA
- Launch at
Biodiversity
Genomics 2021
Oct. 2021 -
Mar. 2022
Consultations
- Genomics and
bioinformatics labs in
Africa; Sampling
communities.
- Policy makers; AAS,
AU, AU-IBAR, NEPAD
- Regional node
institutions; EBP
community e.g. VGP
- Funders Forum
Apr. 2022 -
Mar. 2024
Pilot: Trial
- Pilot project
- Sequence 2500
species endemic in
Africa.
- Distribute species
sequencing efforts
across regional
diversity and taxa
- Value proposition
Apr. 2024 -
Mar .2028
Phase I
- Large-scale: Phase I
- 45K plants & > 60K
animal species
- Invertebrates: 50K,
Fish: 3360,
Amphibians: 800,
Reptiles: 2026, Birds:
2341, Mammals:
1100
- Value proposition
Apr. 2028 -
Mar. 2032
Phase II
- Re-assess Phase I
& implement
recommendations.
- Sequence
additional taxa not
captured in Phase I
- Value proposition
- Looking ahead
Looking ahead: AfricaBP timeline will be a multi-step process

20. AfricaBP
,
DAISEA
EBP,
VGP,
WGCOP
African
genomics
labs,
PacBio,
Inqaba
Biotec
AWARD,
socio-ec
onomics
groups in
Africa
Regional
nodes
institutions,
H3ABioNet
AAS,
AU-IBAR,
Africa
CDC
AfricaBP will employ a Strategic Partnership Framework
Multi-national, multi-country Strategic Partnership Framework

21. AfricaBP Pilot Project

22. AfricaBP pilot studies will reveal strengths and weaknesses
2500 species across Africa in 3 years; we’re open to partnerships

23. AfricaBP pilot studies: challenges, more challenges & solutions
● 2500 native and
endemic species
(including endangered
species)
● Representatives of
animals, plants, fungi,
seaweeds, microalgae
and other unicellular
eukaryotes.
● Terrestrial, freshwater,
and coastal habitats

24. AfricaBP pilot studies will engage natural or approved custodians of samples
● Coordination: AfricaBP Pilot
Committee
● Fresh material collection in
collaboration with national and private
parks, nature conservation centres,
aquaria, and zoos
● Local taxonomists will be engaged
● Suitability of materials housed in the
local zoological collections and
herbaria will be explored

25. AfricaBP Pilot Project Subcommittees
● Sample Collection and Processing Sub-committee
● Sequencing and Assembly Sub-committee
● Annotation Sub-committee
● Data Analysis Sub-committee
● IT & Informatics Sub-committee
● Ethics, Legal and Social Issues Sub-committee
● Communication and Public Affairs Sub-committee
● Partnership and Fundraising Sub-committee

26. Progress made so far within the AfricaBP (< 6 months)
● Defined goals, objectives, consultations and engagements
● Assembled members of various committees: e.g. pilot committee
● Developing of Terms of Reference by each subcommittee of PC
● Calls for sequencing of 2500 species endemic to Africa
● Surveys, permits, Nagoya Protocol, Access Benefit Sharing (ABS)
● Sample custodians for 18 vertebrate species; 1st genome to be sequenced
● AfricaBP policy document

27. Sample collection is the biggest bottleneck
Sample collection and processing SC will identify key elements

28. The foundation of genomics has been built across Africa
BioGenome capacity efforts are needed to sequence African species

29. 206 genomics capacities, 71 % concentrated in five countries.
70 % outside national public health institutes
Source: Inzaule, et al., 2021

30. Current gaps in Nagoya Protocol will need to be improved
Harmonizing policies and tracking ABS compliance will be effective
● No clear attribution of responsibility for the enforcement of ABS
● Ineffective mechanism for the participation of IPLC & aTK in ABS
● Unclear regulatory regime at national and regional levels
● Lack of shared guidelines for effective implementation of Nagoya

31. We’re conscious of the challenges AfricaBP faces
Hybrid of mobile & reference labs is of relevance in Africa
https://54gene.com/

32. Africa’s internet costs are the most expensive globally
Improved reliance of genomics data on internet is essential

33. Organogram for AfricaBP, DAISEA initiative
Steering Committee
(AfricaBP)
Science and Technology
Committee
Monitoring and Evaluation
Committee
Advisory Board
North Africa
Coordinator
Partners and
Collaborators
West Africa
Coordinator
Central Africa
Coordinator
Southern
Africa
Coordinator
East Africa
Coordinator
Nodes Nodes Nodes Nodes Nodes

34. Steering Committee of the AfricaBP

35. Steering Committee of the AfricaBP: Names
Anne Muigai - Chair | Jomo Kenyatta University of Agriculture and Technology, Kenya
Cathrine Ziyomo - co-Chair | Biosciences Eastern and Central Africa (BecA-ILRI), Kenya
Josiah Mutuku - co-Chair | Central and West African Virus and Epidemiology, Ivory Coast
Ntanga Mapholi - co-Chair | University of South Africa, South Africa
ThankGod Ebenezer - co-Chair (Diaspora) | European Bioinformatics Institute (EMBL-EBI), UK
Appolinaire Djikeng co-Chair (Diaspora) | Centre for Tropical Livestock Genetics and Health (CTLGH), UK
Roksana Majewska - Chair, Pilot Committee | North-West University, South Africa
Isidore Houaga - Secretary General | Centre for Tropical Livestock Genetics and Health (CTLGH), UK
Bouabid Badaoui - coordinator (North Africa) | Mohammed V University, Morocco
Chakirath Salifou - coordinator ( West Africa) | University of Abomey-Calavi, Benin Republic
Christian Tiambo - coordinator ( Central Africa) | Centre for Tropical Livestock Genetics and Health (CTLGH-ILRI), Kenya
Teklu Gerbaba & Josiah Kujah - coordinators (East Africa) | Addis Ababa University, Ethiopia; Jomo Kenyatta University, KY
Ntanga Mapholi & Cathrine Ziyomo- Coordinators (Southern Africa) | U of South Africa, SA; BecA-ILRI, Kenya,
Julian Osuji - Chair, Genomics for Conservation of Endangered Species | University of PortHarcourt, Nigeria
Santie De Villiers - Chair, Bioinformatics and Genomics Technologies | Pwani University, Kenya
Ntanga Mapholi - Chair, Crops and Livestock Improvement and Health | University of South Africa, South Africa
Aron Abera - Chair, Technology Development, Knowledge Exchange, Industry | Inqaba Biotec, South Africa
Michèle Mbo’o-Tchouawou - Chair, Socio-economics, Ethics and Policy Issues| AWARD, Kenya

36. Advisory team of the AfricaBP
Nicola Mulder
PI, H3ABioNet,
South Africa
Simplice Nouala
Head of Agriculture and Food
Security (African Union),
Ethiopia
Rob Davey
Head, e-Infrastructure,
Earlham Institute, United
Kingdom

37. Three funding mechanisms likely possible for AfricaBP
105K species, ~ $1bn USD sequencing & computing costs in 10 years
Core funding
Supplementary funding 1:
Leverage on global communities
Supplementary funding 2:
Leverage on existing projects
across Africa

38. Should Africa commit $1bn USD to BD genomics in face of poverty?
Africa can directly feed population; but this is a short-term solution
Build capacity to produce food of the future; is a long-term solution
Source: https://blog.wallstreetsurvivor.com

39. HGP costed $3.3 bn USD; revenue > $108 bn USD in 2019 alone
The impact of EBP will be far-reaching in our biosphere by 2038

40. Why must Africa act now? Why must Africa invest?
As the EBP gains momentum, Africa must avoid the mistakes of the HGP.
Africa must invest now to derive long-term benefits and breakthroughs

41. Project-based capacity building is at the heart of AfricaBP
African scientists can solve food insecurity problems where capacity exists
Empowering indigineous communities helps maximise long-term gains

42. What is the charge to African scientists in the era of biogenomics?
We should look back at this era with hope & confidence; but we must act.
African scientists must lead the way in sequencing African biogenomes
A Call to Action
For AfricaBP to be
successful, African
scientists must galvanise
efforts at the national levels

43. A Call to Action for African Scientists

44. Taking off and moving on…….What is next?
● Publish AfricaBP position paper
● Finalise AfricaBP white paper
● Commence pilot studies in collaboration with the VGP (18 + 482 species)
● Populate list of 2000 eukaryotic species for sequencing across Africa
● Anchor AfricaBP onto the African Academy of Sciences (AAS) programmes

45. AfricaBP website: https://africanbiogenome.org/

46. Social media, email address, mailing list, & website….
Check AfricaBP website or Social Media to know more
africabp-chairs@googlegroups.com
africabp-all@googlegroups.com
Over to 450 email
subscribers

47. Acknowledgements…...1/2
All members of the AfricaBP committees….A village
● Anne Muigai, Cathrine Ziyomo
● Julian Osuji
● Ntanganedzeni Mapholi
● ThankGod Ebenezer
● Appolinaire Djikeng
● Isidore Houaga
● Roksana Majewska
● Bouabid Badaoui
● Michèle Mbo’o-Tchouawou
● Josiah Kuja
● Teklu Gerbaba
● Aron Abera
● Michèle Mbo’o-Tchouawou
● Verena Ras
● Katali K. Benda
● Joseph Kirangwa
● Alan Buddie, Dr.
● Abdoallah Sharaf
● Yves Hermandez Tchiechoua
● Slimane Khayi
● Simon Morgan
● Rose A. Marks
● Mark Blaxter
● Taiwo Crossby Omotoriogun
● Yedomon Ange Bovys Zoclanclounon
● Yasmina Jaufeerally Fakim
● Girish Beedessee
● Anisah Ghoorah
● Anmol Kiran
● Fatma Guerfali
● Suresh Maslamoney
● Julien Alban Nguinkal
● Nidhal Ghanmi
● Sally Mueni Katee
● Justin Ideozu
● Varsha Nagaraj Shetty
● Paballo Chauke
● Fatu Badiane Markey
● Samuel Eziuzor
● Anneke Lincoln Schoeman
● Charlotte Ndiribe
● Harry Akligoh
● Cyprien Ndikuryayo

48. Acknowledgements…..2/2
These institutions, companies, and projects have signed AfricaBP’s MoU

49. Thank you for listening