Genetic Variations and Performance of Malaria Rapid Diagnostic Tests

Malaria rapid diagnostic tests (RDTs) are indispensable tools for the timely detection of Plasmodium falciparum infections in resource-limited settings. Most RDTs rely on the detection of parasite histidine-rich proteins 2 and 3 (PfHRP2 and PfHRP3), yet genetic variations such as gene deletions, polymorphic repeat structures and chromosomal rearrangements can undermine test sensitivity and lead to false-negative results. Emerging genomic analyses reveal that deletions of pfhrp2 and pfhrp3 often arise through chromosomal breakage followed by telomere healing or segmental duplications, generating distinct deletion patterns across geographic regions. Concurrently, antigenic diversity in remaining HRP epitopes and co-occurring mutations associated with drug resistance (for example in kelch13) present a compound threat to both diagnosis and case management. Ongoing surveillance using advanced molecular methods, coupled with strategic selection of alternative antigen targets, is critical to preserving diagnostic accuracy and to informing global malaria elimination strategies.

Research from Nature Portfolio

In a nationwide survey encompassing symptomatic patients at 100 health facilities in Tanzania, gene-targeted genotyping revealed that dual deletions of pfhrp2 and pfhrp3 were exceedingly rare, accounting for fewer than 0.3% of rapid test false negatives. Most parasites retained both genes, supporting continued reliance on HRP2-based RDTs in this setting while underscoring the value of periodic deletion monitoring to detect emerging risks.

Earlier foundational work in two endemic regions of Kenya established the presence of pfhrp2-deleted parasites in asymptomatic and clinical cases. Although HRP2-based tests remained largely effective at moderate to high parasite densities—possibly due to cross-reactivity with intact pfhrp3—the study highlighted the need for systematic surveillance of hrp gene deletions across East Africa and the potential benefits of integrating non-HRP2 antigen targets into diagnostic algorithms.

Genetic Variations and Performance of Malaria Rapid Diagnostic Tests publication trend

The graph below shows the total number of articles in genetic variations and performance of malaria rapid diagnostic tests across all publications each year (not limited to Nature Index journals).

Technical terms

PfHRP2 and PfHRP3: Histidine-rich proteins expressed by P. falciparum and targeted by most HRP-based RDTs; deletions reduce test sensitivity.

Rapid diagnostic test (RDT): A lateral-flow immunoassay designed to detect specific parasite antigens in a small volume of blood within 15–20 minutes.

Gene deletion: The loss of a DNA segment encoding an antigen or functional protein, often leading to absence of the corresponding antigen in the parasite.

Droplet digital PCR (ddPCR): A highly sensitive quantitative method that partitions a PCR reaction into thousands of droplets for precise measurement of target DNA copy numbers.

Kelch13 mutation: Single-nucleotide changes in the kelch13 gene associated with reduced artemisinin susceptibility and partial treatment failure.

Telomere healing: The process by which broken chromosome ends acquire new telomeric repeats, stabilising chromosomal fragments after breakage and enabling gene deletions.

References

1. Interchromosomal segmental duplication drives translocation and loss of P. falciparum histidine-rich protein 3. eLife (2024).
2. A Countrywide Survey of hrp2/3 Deletions and kelch13 Mutations Co-occurrence in Ethiopia. The Journal of Infectious Diseases (2024).
3. Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients enrolled at 100 health facilities throughout Tanzania: February to July 2021. Scientific Reports (2024).
4. Assessment of the Performance of Lactate Dehydrogenase-Based Rapid Diagnostic Test for Malaria in Djibouti in 2022–2023. Diagnostics (2024).
5. Plasmodium falciparum parasites with histidine-rich protein 2 (pfhrp2) and pfhrp3 gene deletions in two endemic regions of Kenya. Scientific Reports (2017).