Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing

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.

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Journal
Nature Communications
Published
2026-05-11
DOI
https://doi.org/10.1038/s41467-026-72358-z
Primary Topic
Malaria Research and Control
Type
article
Field-Weighted Citation Impact
0.00

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article

Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing

Frank P. Mockenhaupt, Jonathan Schultz, Yuhana Sogoba, Sílvia Portugal et al.
Nature Communications
Malaria Research and Control
article

Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing

Frank P. Mockenhaupt, Jonathan Schultz, Yuhana Sogoba, Sílvia Portugal, Bixa Ogola, Grit Schubert, Brenda Mambwe, Welmoed van Loon, Manuela Carrasquilla, Tafese Beyene Tufa, Arsène Zongo, Miriam Chomba, Adekunle Olowe, Moussa Niangaly, Sheila Otieno, Vincent Achi, Amy Gaye, Torsten Feldt, Yssimini Nadège Guillène Tibiri, Nassandba Julien Yanogo, Emma Schallenberg, Christina Ntalla, Carol Chiyesu, Olusola Ojurongbe, Karolina Mosler, Dagaga Kenea Goboto, Bernd Bohmeier, Fiyinfoluwa Ojeniyi, Awa B. Dème, Mulenga Mwenda, Moonga Hawela, Issiaka Soulama, Daouda Ndiaye, Daniel J. Bridges, Adedolapo Olorunfemi, Chris Drakeley, Jason A. Hendry, Salma Suliman, Marley Gibbons, Oumou Aïcha Zeïna Zoure, Bassirou Ngom, Rafael Oliveira, Etilé A. Anoh, Kephas Otieno, Ya Ping Shi, Oumarou Ouedraogo, Simon Kariuki, Oluyinka Opaleye, Djiby Sow
article en

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. 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.

Nature CommunicationsVol. 17(1)
Robert Koch Institute (DE), Université Alassane Ouattara (CI), Kenya Medical Research Institute (KE), Max Planck Institute for Infection Biology (DE), Düsseldorf University Hospital (DE), Université des Sciences, des Techniques et des Technologies de Bamako (ML), Centre National de la Recherche Scientifique et Technologique (BF), Institute of Health Research, Epidemiological Surveillance and Training (SN), National Center for Emerging and Zoonotic Infectious Diseases (US), Asossa University (ET), Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE), Max Planck Institute for the History of Science (DE), National HIV/AIDS/STI/TB Council (ZM), Arsi University, Heinrich Heine University Düsseldorf (DE), Ladoke Akintola University of Technology (NG), Charité - Universitätsmedizin Berlin (DE)
Bill and Melinda Gates Foundation
Good health and well-being
Openalex Percentile: Top 6%
Malaria Research and Control
DOIOpen Access PDFOpenAlex
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