Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing

Mariateresa Cesare, Mulenga Mwenda, Anna E. Jeffreys, Jacob Chirwa, Chris Drakeley, Kammerle Schneider, Brenda Mambwe, Karolina Glanz, Christina Ntalla, Manuela Carrasquilla, Silvia Portugal, Robert J. Verity, Jeffrey A. Bailey, Isaac Ghinai, George B. Busby, Busiku Hamainza, Moonga Hawela, Daniel J. Bridges and Jason A. Hendry ()
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Mariateresa Cesare: University of Oxford, Wellcome Centre for Human Genetics
Mulenga Mwenda: PATH
Anna E. Jeffreys: University of Oxford, Wellcome Centre for Human Genetics
Jacob Chirwa: National Malaria Elimination Centre, Chainama
Chris Drakeley: PATH
Kammerle Schneider: PATH
Brenda Mambwe: PATH
Karolina Glanz: Max Planck Institute for Infection Biology
Christina Ntalla: Max Planck Institute for Infection Biology
Manuela Carrasquilla: Max Planck Institute for Infection Biology
Silvia Portugal: Max Planck Institute for Infection Biology
Robert J. Verity: Imperial College London
Jeffrey A. Bailey: Brown University
Isaac Ghinai: University of Oxford, Wellcome Centre for Human Genetics
George B. Busby: University of Oxford, Wellcome Centre for Human Genetics
Busiku Hamainza: National Malaria Elimination Centre, Chainama
Moonga Hawela: National Malaria Elimination Centre, Chainama
Daniel J. Bridges: PATH
Jason A. Hendry: University of Oxford, Wellcome Centre for Human Genetics

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3–4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.

Date: 2024
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DOI: 10.1038/s41467-024-45688-z

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