London Calling 2023: Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum

Malaria is a global public health priority causing over 600,000 deaths annually, mostly in young children living in sub-Saharan Africa. Molecular surveillance can provide key information for malaria control, such as the prevalence and distribution of antimalarial drug resistance. However, genome sequencing capacity in endemic countries can be limited. We implemented an end-to-end workflow for Plasmodium falciparum genomic surveillance in Ghana using Oxford Nanopore sequencing targeting antimalarial resistance markers and the leading vaccine antigen circumsporozoite protein (CSP). The workflow was rapid, robust, accurate, affordable, and straightforward to implement. We found that P. falciparum parasites in Ghana had become largely susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine resistance and no evidence of artemisinin resistance. Multiple single-nucleotide polymorphism differences from the vaccine CSP sequence were identified, although their significance is unclear. This study demonstrates the potential utility and feasibility of malaria genomic surveillance in endemic settings using nanopore sequencing.