A Regional Approach to Malaria Molecular Surveillance in Southern Africa: Lessons from the GenE8 Initiative

The growing threat of artemisinin partial resistance prompted the WHO to recommend routine monitoring of drug efficacy and resistance. Advances in sequencing technologies and expanded laboratory capacity across Africa have made malaria molecular surveillance (MMS) a viable option for many countries. Despite improved access to next-generation sequencing platforms, the uptake of MMS for programmatic decision-making and the availability of antimalarial resistance marker data in southern Africa have lagged behind those in other regions. The Genomics of Malaria in the Elimination Eight (GenE8) initiative implemented a regional MMS model comprising 1) regional consensus-building and governance, 2) capacity strengthening, and 3) evidence generation. Through this initiative, standardized parasite genomic data across five southern African countries (Angola, Eswatini, Namibia, South Africa, and Zambia) were generated using a targeted amplicon deep-sequencing workflow. Regional laboratory and analytical skills were strengthened, and national malaria programs (NMPs) were capacitated to use genomic data for decision-making through a regional MMS fellowship and training workshops. Although the initiative achieved important successes, persistent challenges limited its overall impact despite the implementation of integrated mitigation strategies. Challenges included constraints in regional bioinformatics capacity, delays in sample shipment and cross-border data sharing, and a lack of sustained funding. In the present case study, the GenE8 model, operational experiences, and cross-cutting lessons learned are described. The GenE8 experience reveals that regional MMS is feasible in southern Africa and that near-real-time resistance data can inform policy and intervention decisions, but that it requires sustained investment in governance mechanisms, bioinformatics expertise, and institutionalized NMP capacity to be sustainable.