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

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.