Haplotype diversity of Plasmodium falciparum circumsporozoite protein prior to malaria vaccine implementation in Kaelé Health District, Cameroon, 2022–2023

Malaria remains a major public health concern in Cameroon, with Plasmodium falciparum responsible for most morbidity and mortality, particularly among children under five. In response to rising cases, Cameroon began implementing the RTS,S/AS01 malaria vaccine in early 2024. Given the vaccine’s strain-specific efficacy, understanding haplotypic diversity is critical for evaluating long-term impact. We analyzed 100 P. falciparum -positive dried blood spots collected in Mapoussere, Kaele Health District (2022–2023). Using the 4CAST amplicon sequencing assay, we targeted four genes: csp (circumsporozoite protein), ama1 (apical membrane antigen 1), sera2 (serine repeat antigen 2), and trap (thrombospondin-related anonymous protein). Haplotypes were identified using SeekDeep, and diversity metrics including heterozygosity (He), nucleotide diversity (π), and selection statistics (Tajima’s D , Fu and Li’s D* , F* ) were computed. We successfully genotyped csp in 35% of samples, identifying 22 haplotypes (He = 0.908; π = 0.021). The vaccine-matched haplotype was present in 20% of genotyped infections. The T cell TH2 and TH3 epitopes of csp showed signs consistent with balancing selection. Both ama1 and sera2 exhibited higher genotyping success and diversity, with ama showing significant Tajima’s D values. Within-participant haplotype counts were highest for ama1 (mean = 2.8), followed by sera2 (2.1), csp (1.3), and trap (1.2). This study provides a baseline of P. falciparum haplotype diversity in a vaccine-targeted region. The presence of vaccine-matched strains and high diversity in TH2/TH3 epitopes in csp may influence vaccine efficacy. Continued molecular surveillance is essential to monitor antigenic shifts and guide future strategies.