Continental-scale genomic surveillance of Plasmodium falciparum malaria | ESCMID Global 2026

Abstract: In sub-Saharan Africa, continental-scale genomic surveillance of Plasmodium falciparum malaria is needed to track the spread of drug and diagnostic resistance, as well as monitor parasite evolutionary responses to vaccine rollout. Yet continental-scale implementation is hindered by a lack of genomic approaches suitable for local laboratories, and the vastness of the continent.

In the last two years, we have initiated a decentralised scale-up of P. falciparum genomic surveillance across multiple African countries, sequencing and analysing thousands of samples locally. We achieved this with a novel nanopore sequencing protocol that is rapid (∼5 hr) and cost-effective (<$25 USD/sample), providing surveillance of antimalarial drug resistance genes, the diagnostic test antigens hrp2/3, the vaccine target csp, and the polymorphic gene ama1. We coupled this to a laptop-based bioinformatics dashboard, called Nomadic, that runs offline and displays mapping and variant calling results in real-time. In this talk, I discuss how we developed, validated, and deployed our nanopore-based approach across sub-Saharan Africa, and highlight major opportunities and challenges to future growth.