Malaria remains a major global health concern, with 249 million cases and 608,000 deaths reported in 2022. Artemisinin-based combination therapies (ACTs) are currently one of the main strategies in the fight against this parasitic disease. However, the emergence of partial artemisinin resistance in Africa is threatening the significant progress made in malaria control over the last twenty years. To ensure the continued effectiveness of antimalarial drugs, it is important to determine whether the malaria parasites in a patient’s blood after malaria treatment are the same or different from those before treatment.
Distinguishing between recrudescence and new infections
This distinction between recrudescence (i.e. recurrence of an infection and therefore treatment failure) and new infections is known as PCR correction. It relies heavily on genotyping, the analysis of the DNA and its composition. However, the use of different molecular techniques and genetic markers in PCR correction makes it difficult to properly compare the results and confirm the emergence of resistance.For the first time, scientists from Swiss TPH systematically assessed the most commonly used techniques and markers for PCR correction against the malaria parasite Plasmodium falciparum. The study, published yesterday in the peer-reviewed journal The Lancet Microbe, identified one of the five techniques evaluated as particularly promising for assessing the efficacy of antimalarial drugs.
A promising genotyping technique
The authors assessed the efficacy of five genotyping methods currently in use in terms of how well each method could detect small numbers of parasites (sensitivity), how reliable the results were (reproducibility), and how many different types of malaria it could identify (genetic diversity of markers). They used both P. falciparum laboratory strains and patient samples collected from a clinical trial assessing the efficacy of a new antimalarial drug.The data show that targeted amplicon deep sequencing (TADS) is the most sensitive and accurate technique for distinguishing between recrudescence and newly infected malaria, outperforming the currently recommended method. TADS is based on new generation sequencing techniques, and each marker is sequenced at least ten thousand times. Each marker is sequenced at least tens of thousands of times, allowing parasites to be detected at very low densities and providing consistent results between markers. The high sensitivity of the technique and the consistency between the markers used are the main advantages of this technique.
"Recently, the World Health Organization (WHO) updated its guidelines to distinguish recrudescence from new infection, recommending to replace the marker glurp with microsatellites for PCR correction," said Annina Schnoz, PhD candidate and first author of the new study. "Our study indicates that TADS outperforms both glurp and microsatellites."
Christian Nsanzabana, leader of the Genotyping Group at Swiss TPH and last author, is convinced that TADS has all the required characteristics to become the gold standard for genotyping to distinguish recrudescence from new infections. "This will pave the way for better surveillance and response strategies in the fight against malaria and could potentially shape future WHO guidelines."
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