Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing
- 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
- Silvia Portugal
- Awa B. Deme
- Issiaka Soulama
- Daouda Ndiaye
- Olusola Ojurongbe
- Simon Kariuki
- Ya Ping Shi
- Jonathan S. Schultz
- Moonga Hawela
- Daniel J. Bridges
- Jason A. Hendry
2026-05-11
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.