Mulenga Mwenda, Karolina Mosler, Bernd Bohmeier, Miriam Chomba, Welmoed van Loon, Brenda Mambwe, Amy Gaye, Adedolapo Olorunfemi, Salma Suliman, Nassandba Julien Yanogo, Djiby Sow, Bassirou Ngom, Oumou Aïcha Zeïna Zoure, Yssimini Nadège Guillène Tibiri, Fiyinfoluwa Ojeniyi, Arsène Zongo, Etilé A. Anoh, Vincent Achi, Carol Chiyesu, Sheila Otieno, Bixa Ogola, Moussa Niangaly, Manuela Carrasquilla, Dagaga Kenea Goboto, Torsten Feldt, Tafese Beyene Tufa, Rafael Oliveira, Emma Schallenberg, Yuhana Sogoba, Christina Ntalla, Oumarou Ouedraogo, Kephas Otieno, Oluyinka Opaleye, Adekunle Olowe, Marley Gibbons, Chris Drakeley, Grit Schubert, Frank P. Mockenhaupt, Sílvia Portugal, Awa B. Dème, Issiaka Soulama, Daouda Ndiaye, Olusola Ojurongbe, Simon Kariuki, Ya Ping Shi, Jonathan Schultz, Moonga Hawela, Daniel J. Bridges, Jason A. Hendry
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. Here, we initiate a decentralised scale-up of P. falciparum genomic surveillance by locally sequencing and analysing 1065 samples across six African countries in one year. We achieve 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, hrp2/3 deletions, the vaccine target csp, and the polymorphic gene ama1. We couple this to a laptop-based bioinformatics dashboard that runs offline 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.