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High-throughput Plasmodium falciparum hrp2 and hrp3 gene deletion typing by digital PCR to monitor malaria rapid diagnostic test efficacy

Vera-Arias, C. A. and Holzschuh, A. and Oduma, C. O. and Badu, K. and Abdul-Hakim, M. and Yukich, J. and Hetzel, M. W. and Fakih, B. S. and Ali, A. and Ferreira, M. U. and Ladeia-Andrade, S. and Sáenz, F. E. and Afrane, Y. and Zemene, E. and Yewhalaw, D. and Kazura, J. W. and Yan, G. and Koepfli, C.. (2022) High-throughput Plasmodium falciparum hrp2 and hrp3 gene deletion typing by digital PCR to monitor malaria rapid diagnostic test efficacy. eLife, 11. e72083.

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Abstract

Most rapid diagnostic tests for Plasmodium falciparum malaria target the Histidine-Rich Proteins 2 and 3 (HRP2, HRP3). Deletions of the hrp2 and hrp3 genes result in false negative tests and are a threat for malaria control. A novel assay for molecular surveillance of hrp2/hrp3 deletions was developed based on droplet digital PCR (ddPCR). The assay quantifies hrp2, hrp3, and a control gene with very high accuracy. The theoretical limit of detection was 0.33 parasites/microL. The deletion was reliably detected in mixed infections with wild-type and hrp2-deleted parasites at a density of >100 parasites/reaction. For a side-by-side comparison with the conventional nested PCR (nPCR) assay, 248 samples were screened in triplicate by ddPCR and nPCR. No deletions were observed by ddPCR, while by nPCR hrp2 deletion was observed in 8% of samples. The ddPCR assay was applied to screen 830 samples from Kenya, Zanzibar/Tanzania, Ghana, Ethiopia, Brazil, and Ecuador. Pronounced differences in the prevalence of deletions were observed among sites, with more hrp3 than hrp2 deletions. In conclusion, the novel ddPCR assay minimizes the risk of false-negative results (i.e. hrp2 deletion observed when the sample is wild type), increases sensitivity, and greatly reduces the number of reactions that need to be run.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Epidemiology and Public Health (EPH) > Health Interventions > Intervention Effectiveness and Impact (Hetzel)
UniBasel Contributors:Holzschuh, Aurel
Item Type:Article, refereed
Article Subtype:Research Article
ISSN:1534-4983
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:28 Dec 2022 08:49
Deposited On:28 Dec 2022 08:49

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