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. 2025 Aug 26:29:100611.
doi: 10.1016/j.ijpddr.2025.100611. Online ahead of print.

A novel intron variant is associated with emerging pfdhps mutant haplotypes in West and Central African Plasmodium falciparum

Emma Filtenborg Hocke  1 , Helle Hansson  2 , Ana Chopo-Pizarro  3 , Adebanjo Jonathan Adegbola  4 , Oluseye Bolaji  4 , Peter Thelma Ngwa Niba  5 , Innocent Mbulli Ali  6 , Akindeh Nji  7 , Wilfred Mbacham  7 , Vito Baraka  8 , Neema B Kulaya  9 , Gauthier Mesia Kahunu  10 , Hypolite Muhindo Mavoko  11 , Papy Mandoko Nkoli  12 , Eric Mukomena Sompwe  13 , Destin Mbongi  14 , Patrick Mitashi  11 , Valérie A Bédia  15 , Paterne A Gnagne  16 , Abibatou Konaté  16 , William Yavo  15 , Hervé Menan  17 , Khalid Beshir  3 , Andria Mousa  18 , Colin J Sutherland  3 , Michael Alifrangis  2 , Cally Roper  3
Affiliations

A novel intron variant is associated with emerging pfdhps mutant haplotypes in West and Central African Plasmodium falciparum

Emma Filtenborg Hocke et al. Int J Parasitol Drugs Drug Resist. .

Abstract

Sulfadoxine-pyrimethamine plays a key role in Plasmodium falciparum chemoprevention across Africa, yet the protective efficacy of SP is undermined by mutations conferring resistance in the genes encoding dihydrofolate reductase (pfdhfr) and dihydropteroate synthase (pfdhps). The emergence and spread of the pfdhps 431V mutation suggests that this may confer resistance and be selected by drug use. Here, we report a non-coding mutation a548383t, which expands a di-nucleotide repeat in the first intron of pfpppk-dhps. The first intron and second exon of the pfdhps gene were analysed by target amplicon sequencing of 929 P. falciparum-positive blood samples from Nigeria, Cameroon, Tanzania, The Democratic Republic of Congo, and Côte d'Ivoire. The intron mutation was found in Nigeria, Côte d'Ivoire, and Cameroon in association with the 431V mutation. In particular, the intron mutation was most highly associated with the VAGKGS haplotype (OR = 211.7, P < 0.001), followed by the VAGKAS (OR = 39.2, P < 0.001), and VAGKAA (OR = 33.6, P < 0.001) haplotypes. Additionally, a reduced di-nucleotide repeat diversity was observed in 431V-positive variants. The intron variant is significantly associated with the 431V mutation which is consistent with previous reports of selective sweeps around VAGKGS. The association of the 548383t mutation with both VAGKGS, VAGKAS and VAGKAA might indicate these lineages either have a common ancestor or that the intron variant 548383t has a functional association with 431V. More research is needed to determine if the association is simply genetic hitchhiking, or if the intron variant confers a phenotypic advantage.

Keywords: Drug resistance; Evolution; Pfdhps; Plasmodium falciparum; Sulfadoxine-pyrimethamine.

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Conflict of interest statement

Conflict of interest The authors declare no conflict of interest.

Figures

Image 1
Graphical abstract
Fig. 1
Fig. 1
Illustrated representation of the intron variant at position 548383 in the first intron of the pppk-dhps gene expanding a microsatellite. The red letter T indicates the 548383t mutation. The alignment demonstrates the observed variation in the microsatellite, with the microsatellite region highlighted in light blue and light red color. Arrows denote the positions of resistance mutations 431V, 436A, 437G, 540E, 581G, and 613S located in exon 2. Created with BioRender.com.
Fig. 2
Fig. 2
Distribution of the a548383t intron variant in I431V containing -genotypes and 431V-containing haplotypes in samples from Nigeria and Cameroon. A) Frequency of the pfdhps a548383t intron variant in I431V-containing genotypes. B) Frequency of the intron variant observed in 431V-containing haplotypes (codons 431-436-437-540-581-613). The samples included in this study were selected based on a combination of previously identified 431V haplotypes as reported from previous published studies, and novel population samples. Consequently, the plots should not be interpreted as representative of geographical prevalence of the 431V variant.
Fig. 3
Fig. 3
Weighted scatterplot of microsatellite length in pfdhps showing counts of I431 wildtypes and 431V mutants and the intron mutant 548383t (ATA) or Wildtype (AAA) across Five African countries. A&B) the I431V variants in Cameroon, C&D) the I431V variants in Nigeria, E&F) the I431V variants in Cõte d’Ivoire, G) the I431 wildtype in DRC. H) the I431 wildtype in Tanzania. The samples included in this study were selected based on a combination of previously identified 431V haplotypes as reported from previous published studies, and novel population samples. Consequently, the plots should not be interpreted as representative of geographical prevalence of the 431V variant.
Fig. 4
Fig. 4
Barplots showing frequencies in number of microsatellite repeats and whether the intron mutation is present (ATA) or the intron wildtype (AAA) for each pfdhps haplotype group. Haplotypes containing an ‘x’ indicates that both the mutant and Wildtype at the codon position was grouped together for analysis. The samples included in this study were selected based on a combination of previously identified 431V haplotypes as reported from previous published studies, and novel population samples. Consequently, the plots should not be interpreted as representative of geographical prevalence of the 431V variant.
See this image and copyright information in PMC

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