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

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.

HairSplitter: haplotype assembly from long, noisy reads

“…Long reads with extremely low error rate, such as PacBio HiFi reads, have been used to distinguish finely strains with the help of specialized software such as hifiasm (Cheng et al, 2021) and stRainy (Kazantseva et al, 2023). However, this challenge has not been yet successfully tackled in the case of noisier reads such as “regular” PacBio data or Oxford Nanopore Technology (ONT) reads, the latter of which can be obtained very rapidly on cheap sequencers that are small enough to be carried into the field (Cesare et al, 2024; Runtuwene et al, 2019).…”