Genomic-informed pathogen surveillance in Africa: opportunities and challenges

Abstract

The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics.

Figure 1

Next-generation sequencing capacity in Africa The circles show the number and distribution of NGS devices on the continent. Data was obtained primarily from manufacturers of the most used NGS equipment—ie, Illumina (Illumina, CA, USA), Oxford Nanopore (Oxford Nanopore Technologies, Oxford, UK), and Ion Torrent (Thermo Fisher Scientifics, MA, USA). However, these data might not be conclusive as they might not include equipment donated or bought outside Africa. Overall, we identified a total of 206 NGS devices in Africa, which includes South Africa (79), Kenya (28), Morocco (18), Nigeria (13), Egypt (10), Algeria (6), Ethiopia (5), Ghana (5), Uganda (5), Gabon (4), The Gambia (4), Senegal (4), Tanzania (4), Zambia (3), Botswana (2), Mali (2), the Democratic Republic of the Congo (2), Rwanda (2), and one each for Angola, Benin, Cameroon, Cote d'Ivoire, Guinea, Madagascar, Sierra Leone, Sudan, Tunisia, and Zimbabwe. NGS=next-generation sequencing.

Figure 2

Proposed pathogen genomics laboratory and bioinformatics network structure