A pan-African pathogen genomics data sharing platform to support disease outbreaks

Alan Christoffels^{1

2}, Gerald Mboowa³, Peter van Heusden⁴, Sello Makhubela⁵, George Githinji⁶, Sarah Mwangi³, Harris Onywera³, Ndodo Nnaemeka⁷, Daniel Gyamfi Amoako^{8

9}, Idowu Olawoye¹⁰, Amadou Diallo¹¹, Placide Mbala-Kingebeni¹², Samuel O Oyola¹³, Bright Adu¹⁴, Christopher Mvelase¹⁵, Pascale Ondoa¹⁶, Fred Athanasius Dratibi¹⁷, Abdourahmane Sow¹⁸, Nicksy Gumede¹⁵, Sofonias K Tessema¹⁹, Ahmed Ogwell Ouma³, Yenew Kebede Tebeje³

Affiliations

¹ Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia. alan@sanbi.ac.za.
² South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa. alan@sanbi.ac.za.
³ Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia.
⁴ South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa.
⁵ Nomazangwa Consulting, Haartbeesport, South Africa.
⁶ KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya.
⁷ Nigeria Centre for Disease Control, Abuja, Nigeria.
⁸ National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
⁹ College of Health Sciences, University of KwaZulu Natal, Durban, South Africa.
¹⁰ African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
¹¹ Institut Pasteur of Dakar, Dakar, Senegal.
¹² Institut National de Recherche Biomédicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
¹³ International Livestock Research Institute (ILRI), Nairobi, Kenya.
¹⁴ Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
¹⁵ WHO Regional Office for Africa, Brazzaville, Republic of Congo.
¹⁶ African Society for Laboratory Medicine (ASLM), Addis Ababa, Ethiopia.
¹⁷ Regional Emergency Hub, WHO Regional Office for Africa, Nairobi, Kenya.
¹⁸ West African Health Organization, Bobo-Dioulasso, Burkina Faso.
¹⁹ Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia. sofoniast@africa-union.org.

PMID: 37161068
PMCID: PMC12181013
DOI: 10.1038/s41591-023-02266-y

A pan-African pathogen genomics data sharing platform to support disease outbreaks

Alan Christoffels et al. Nat Med. 2023 May.

. 2023 May;29(5):1052-1055.

doi: 10.1038/s41591-023-02266-y.

Authors

Affiliations

¹ Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia. alan@sanbi.ac.za.
² South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa. alan@sanbi.ac.za.
³ Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia.
⁴ South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa.
⁵ Nomazangwa Consulting, Haartbeesport, South Africa.
⁶ KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya.
⁷ Nigeria Centre for Disease Control, Abuja, Nigeria.
⁸ National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
⁹ College of Health Sciences, University of KwaZulu Natal, Durban, South Africa.
¹⁰ African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
¹¹ Institut Pasteur of Dakar, Dakar, Senegal.
¹² Institut National de Recherche Biomédicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
¹³ International Livestock Research Institute (ILRI), Nairobi, Kenya.
¹⁴ Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
¹⁵ WHO Regional Office for Africa, Brazzaville, Republic of Congo.
¹⁶ African Society for Laboratory Medicine (ASLM), Addis Ababa, Ethiopia.
¹⁷ Regional Emergency Hub, WHO Regional Office for Africa, Nairobi, Kenya.
¹⁸ West African Health Organization, Bobo-Dioulasso, Burkina Faso.
¹⁹ Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia. sofoniast@africa-union.org.

PMID: 37161068
PMCID: PMC12181013
DOI: 10.1038/s41591-023-02266-y

Abstract

High-income countries have a wealth of genomics expertise that can be rapidly activated to deal with disease threats. African countries should invest in a federated data-management system for genomics epidemiology to deal with such threats better.

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Figures

**Fig. 1 ∣. A pathogen genomics ecosystem for Africa.**
The complexity of the genomics landscape in Africa to support disease surveillance requires integrated data streams among public health practitioners, scientists, technology providers, government and health workers. NPHIs, National Public Health Institutes.

See this image and copyright information in PMC

References

1. Mboussou F. et al. Epidemiol. Infect 147, e299 (2019). - PMC - PubMed
1. Tessema SK et al. Lancet Microbe 1, e227–e228 (2020). - PMC - PubMed
1. Inzaule SC, Tessema SK, Kebede Y, Ogwell Ouma AE & Nkengasong JN Lancet Infect. Dis 21, e281–e289 (2021). - PMC - PubMed
1. Tegally H. et al. Science 378, eabq5358 (2022).
1. Littler K. et al. Bull. World Health Organ 95, 243–243 (2017). - PMC - PubMed

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A pan-African pathogen genomics data sharing platform to support disease outbreaks

Affiliations

A pan-African pathogen genomics data sharing platform to support disease outbreaks

Authors

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources