Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing
Abstract
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.
Article Details
Authors (49)
Mulenga Mwenda
Karolina Mosler
Bernd Bohmeier
Miriam Chomba
Welmoed van Loon
Charité Center for Global Health, Institute of International Health, Charité–Universitätsmedizin Berlin
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
Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
Emma Schallenberg
Yuhana Sogoba
Christina Ntalla
Oumarou Ouedraogo
Kephas Otieno
Oluyinka Opaleye
Adekunle Olowe
Marley Gibbons
Chris Drakeley
Grit Schubert
Frank P. Mockenhaupt
Charité Center for Global Health, Institute of International Health, Charité–Universitätsmedizin Berlin
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