Abstract
The Plasmodium falciparum cysteine-rich protective antigen (PfCyRPA) is a promising target as a next-generation blood-stage malaria vaccine and together with PCRCR complex members, the reticulocyte binding-like homologous protein 5 (PfRh5) and the Rh5-interacting protein (PfRipr), are currently being evaluated in clinical trials. PfCyRPA is essential for merozoite invasion and appears to be highly conserved within the P. falciparum parasite populations. Here, we used a targeted deep amplicon next-generation sequencing approach to assess the breadth of PfCyRPA genetic diversity in 93 P. falciparum clinical isolates from Kédougou, an area with a high seasonal malaria transmission in Senegal. Our data show the dominant prevalence of PfCyRPA wild type reference allele, while we also identify a total of 15 single nucleotide polymorphisms (SNPs). Of these, only five have previously been reported, while the majority of the SNPs were present as singletons within our sampled population. The population prevalence of these SNPs ranges from 1.1% (singletons) to the most prevalent SNP V292F at 9.7% population prevalence. The reference 3D7 allele was predominant in the population. We also applied a structure-based modelling approach to thread these SNPs onto PfCyRPA crystal structures and showed that these polymorphisms have different predicted functional impacts on the interactions with binding partner PfRH5 or neutralizing antibodies. Our prediction revealed that the majority of these SNPs have minor effects on PfCyRPA antibodies, while others alter its structure, stability, or interaction with PfRH5. Altogether, our present findings reveal conserved PfCyRPA epitopes which will inform downstream investigations on next-generation structure-guided malaria vaccine design.
Data availability
Sequencing Reads associated with this study have been deposited in the NCBI SRA with the BioProject Accession: PRJNA1109877.
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Acknowledgements
We would like to thank Souleymane Ngom from Dalaba, Lt. Dr Charles Latyr Diagne and Lamine Kane from Camp Militaire, Moctar Mansaly and Gerald Keita from Bandafassi, Safietou Sane and Astou Ndiaye from Mako, Adama Gueye from Bantaco, Der Ciss from Tomboronkoto and all the healthcare workers at these sites for their partnership with Institut Pasteur Dakar. We would also like to thank the people of Kédougou for their invaluable contributions to this work. We would like to thank the Yale Center for Genome Analysis (YCGA).
Funding
This work was supported by the by the Fogarty International Center of the NIH (K01 TW010496), National Institute of Allergy and Infectious Diseases of the NIH (R01 AI168238), and G4 group funding (G45267, Malaria Experimental Genetic Approaches & Vaccines) from the Institut Pasteur de Paris and Agence Universitaire de la Francophonie (AUF) to AKB. This work has been produced with the financial assistance of the European Union (Grant no. DCI-PANAF/2020/420 − 028), through the African Research Initiative for Scientific Excellence (ARISE), pilot program. ARISE is implemented by the African Academy of Sciences with support from the European Commission and the African Union Commission. The contents of this document are the sole responsibility of the authors and can under no circumstances be regarded as reflecting the position of the European Union, the African Academy of Sciences, and the African Union Commission. AB and LGT are partially supported by an ARISE grant from the African Academy of Sciences (ARISE-PP-FA-056).
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A.K.B. conceived the experiments. A.K.B., L.S., and Z.S. supervised the research. A.B., L.G.T., M.N.P., S.D.S., F.D., R.L., A.C., N.G., K.M., A.J.M, A.T., B.D.S., and A.M. collected the samples. A.K.B and A.B. assisted with geolocation. A.B., L.G.T., M.N.P. S.D.S., and F.D. conducted the experiments. Y.G., Z.S., S.D.P. performed structure modelling. A.B., L.G.T., S.L. N.G., and A.K.B. analysed the results. A.B., L.G.T., A.K.B. wrote the manuscript. A.B., L.G.T., A.K.B. J.L.A.N., I.V.W., Z.S., S.D.P. and L.S. reviewed and edit the manuscript. All authors reviewed and approved the final manuscript.
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Ba, A., Thiam, L.G., Pouye, M.N. et al. Genetic diversity in the Plasmodium falciparum next-generation blood stage vaccine candidate antigen PfCyRPA in Senegal. Sci Rep (2026). https://doi.org/10.1038/s41598-026-36257-z
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DOI: https://doi.org/10.1038/s41598-026-36257-z
