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Genomic surveillance using Nanopore sequencing

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  • Genomic surveillance using Nanopore sequencing

    Researchers from the United Kingdom and Ghana have teamed up to improve the genomic surveillance of Plasmodium falciparum, the deadliest species responsible for malaria.

    Malaria continues to be one of the major causes of death worldwide, with a more significant impact across African countries (World Health Organization). Efforts are in place to distribute vaccines against P. falciparum that target its circumsporozoite protein (csp). However, there aren’t proper surveillance measures in place to accurately monitor mutations in csp, and thereby potential resistance of P. falciparum to the current vaccines.

    Genomic surveillance is typically prohibitive in the countries that require it the most due to the high costs and infrastructure needed, which lead to the current study's design. The research team wanted to test the feasibility of surveillance in these regions using devices from Oxford Nanopore Technologies (ONT) that are affordable, portable, and can provide real-time genomic analysis.

    Testing began by isolating DNA from clinical samples and applying it to a multiplexed PCR assay that targeted several drug resistant marker genes. The resulting amplicons were used to build sequencing libraries and were then sequenced in a series of runs on the MinION mk1b device. A custom informatics pipeline in Nextflow called nano-rave, was built to provide real-time analysis and variant calling. All work was conducted at two field sites in Ghana to ensure its applicability in rural settings.

    The results showed mutations in key resistance genes (dhfr and dhps) that likely corresponded with the changes in antimalarial treatment available in the area. Several high-frequency SNPs were also detected in the C-Terminal Region (CTR) of csp; the same region that is incorporated in the current vaccines. These mutations were not confirmed to disrupt the efficacy of the vaccines, but provide evidence of a successful multiplex surveillance panel that can be performed in the regions most impacted by malaria.

    This study provides the framework for monitoring malaria resistance in key communities. Read the current preprint of this work here.

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