Identification and prevalence of single-nucleotide polymorphisms in the P. falciparum genes pfcoronin and pfubp1 associated with artemisinin resistance in Ghana and Benin

Abstract

Malaria remains a great public health concern, with an estimated 263 million cases and 597,000 estimated deaths in 2023. Artemisinin-based combination therapies (ACTs) are currently the first-line treatment for uncomplicated P. falciparum malaria in Sub-Saharan Africa (SSA), but the emergence of resistant parasites is threatening their efficacy. Single-nucleotide polymorphisms (SNPs) in the pfk13 gene are associated with artemisinin (ART) resistance. However, recent reports have shown that other genes, such as pfcoronin and pfubp1, may also confer a resistant phenotype.

This project aimed at screening 1100 P. falciparum-positive samples from Ghana and 226 samples from Benin for SNPs in the pfcoronin and pfubp1 genes. We created and optimized PCR protocols for the amplification of these genes and sequenced the samples using an Illumina MiSeq sequencing platform.

Results showed that the pfubp1 polymorphisms associated with ART resistance were detected at alarming prevalences, namely D1525E (12.8% in Ghana and 12.2% in Benin) and E1528D (18.5% in Ghana and 20.0% in Benin). E1531D and D1534E were also observed with very high prevalences in both countries (27.2% and 23.0% in Ghana and 22.2% and 13.9% in Benin, respectively), but their association with ART resistance remains to be explored. In pfcoronin, the P76S polymorphism was detected at a high prevalence (21% in Ghana and 29.1% in Benin). A prevalence map for P76S was also created, showing that this SNP is mostly present in West African countries.

Further studies are still necessary to validate the pfcoronin and pfubp1 genes as molecular markers for ACT resistance, as well as more information is needed on the relevance of the unknown mutations detected. Nevertheless, this project provides useful information regarding ART resistance in SSA and may encourage the incorporation of these genes in routine molecular monitoring in African countries.

Popular Abstract

Mapping malaria resistance genes in Ghana and Benin

Malaria is an infectious disease caused by Plasmodium parasites, with Plasmodium falciparum being the species causing the major burden in Africa. In 2023, there were an estimated 263 million malaria cases and 597,000 estimated deaths, mostly in Sub-Saharan Africa. Even though the global malaria case incidence and mortality have been greatly reduced since 2000, this progress is now being threatened by the emergence of drug-resistant parasites.

Currently, artemisinin-based combination therapies (ACTs) are the first-line care in treating uncomplicated P. falciparum malaria. Artemisinin (or a derivative) greatly reduces the number of P. falciparum parasites during the first hours of treatment, whilst a partner drug, with a longer half-life, eliminates the remaining parasites. In Ghana and Benin, artesunate-amodiaquine and artemether-lumefantrine are the first-line ACTs for treating uncomplicated P. falciparum malaria.

In 2007, the first reports of ACT-resistant P. falciparum parasites were recorded in Southeast Asia. These resistant parasites contained mutations (single-nucleotide polymorphisms, SNPs) in their Pfk13 gene, reducing the parasite’s uptake of hemoglobin, a crucial process to activate the ACT drugs. Resistant parasites have emerged in Sub-Saharan Africa, and new reports have shown that other genes, such as Pfcoronin and Pfubp1, may also confer resistance to ACTs.

This project aimed to identify SNPs in the P. falciparum genes Pfcoronin and Pfubp1, believed to be associated with ACT resistance, in 1326 P. falciparum–positive samples from Ghana and Benin. For this, we created and optimized amplification protocols for regions of interest within these genes, using polymerase-chain reaction (PCR) techniques. We then sequenced these fragments by an Illumina sequencing platform and compared the prevalence of mutations in both countries.

Results showed that SNPs associated with ACT resistance were detected at alarming prevalences, namely D1525E (12.8% in Ghana and 12.2% in Benin) and E1528D (18.5% in Ghana and 20.0% in Benin) in Pfubp1 (Fig. 1). The P76S polymorphism in Pfcoronin was also detected at high prevalences (21.0% in Ghana and 29.1% in Benin). P76S has been recently monitored in several African countries, so a prevalence map for this mutation was created. In the future, in vitro and in vivo studies are still necessary to validate the Pfcoronin and Pfubp1 genes as molecular markers for ACT resistance, as well as more information is needed on the relevance of the novel mutations in these two genes detected in this project. The goal of this project was to expand the focus from Pfk13 to other genes that may need to be monitored for antimalarial drug resistance in Africa.


Master’s Degree Project in Molecular Biology (MOBN03), 60 credits
Department of Biology, Lund University

Supervisors: Michael Alifrangis and Helle Hansson
Centre for Translational Medicine and Parasitology, University of Copenhagen

• author: Raposo, Madalena
• supervisor: Michael Alifrangis; Helle Hansson
• organization: Degree Projects in Molecular Biology
• course: MOBN03 20242
• year: 2025
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 9214779
• date added to LUP: 2025-11-03 12:10:56
• date last changed: 2025-11-03 12:10:56