Continental-scale genomic surveillance of Plasmodium falciparum malaria with rapid nanopore sequencing

In sub-Saharan Africa, continental-scale genomic surveillance of Plasmodium falciparum malaria is needed to track the spread of antimalarial drug resistance and diagnostic test evasion, as well as to monitor parasite evolutionary responses to vaccine rollout. Yet implementation of malaria genomic surveillance at a continental-scale is hindered by resource constraints, the vastness of the continent, and the lack of sequencing protocols suitable for most local laboratories. To address this, we developed an approach to enable a decentralized scale-up of P. falciparum genomic surveillance and established it in six African countries in one year, locally sequencing 1,065 samples. The approach includes a rapid ([~] 5 hours) and cost-efficient (<$25 USD/sample) nanopore sequencing protocol that provides surveillance of drug resistance-associated genes, hrp2/3 deletions, the vaccine target csp, and the polymorphic gene ama1. We coupled this to a bioinformatics dashboard that runs offline on a laptop and displays mapping and variant calling results in real-time. We demonstrate robust sequencing coverage across parasitemia levels and laboratories, accurate identification of antimalarial resistance markers and hrp2/3 deletions; and, with a novel variant caller, sensitive detection of mutations carried by minor clones. Our approach will accelerate genomic surveillance of P. falciparum malaria across sub-Saharan Africa at a time of urgent need.