Genetic Diversity of the Malaria Vaccine Candidate PfRIPR in a High Transmission Region of Senegal

Summary RH5-Interacting Protein (RIPR) is essential for the invasion of Plasmodium into host red blood cells and is currently being studied as a novel malaria vaccine candidate in Phase 1a clinical trials. To study the genetic diversity of RIPR, deep amplicon sequencing was used to identify RIPR mutations in Plasmodium falciparum clinical isolates (n=89) collected in Kédougou, a high malaria transmission region of Senegal. We identified nonsynonymous single nucleotide polymorphisms (SNPs) in 64/89 (71.9%) of the samples. In total, 26 non-synonymous SNPs were identified, of which 15 were novel. 16/26 SNPs were able to be threaded onto existing RIPR crystal structures to predict the effects of SNPs on RIPR stability. 7/16 mutations were predicted to destabilize RIPR while 2/16 increased the stability of RIPR. Additionally, we identified 3 SNPs (Q737K, T738K, V840L) in the EGF5-8 domains of RIPR where neutralizing antibodies are known to bind. Competing Interest Statement The authors declare no competing interests. Funding Statement This work was supported 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 A.K.B. This work was also supported by National Institute of Allergy and Infectious Diseases of the NIH (R61 AI176583) to Z.S. 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. Additional funding for student exchange and research was provided by the Yale School of Public Health Wilbur Downs Fellowship (M.N., K.A.H., Y.T.), the Yale Collaborative Action Project Fellowship (K.A.H., Y.T., N.G., M.N., G.G.), the Yale Lindsay Fellowship for Research in Africa (K.A.H, Y.T.), the Ambrose Monell PhD Research Fellowship (K.A.H.), the Yale Tetelman Fellowship (A.C., R.L., N.G.), the Yale Richter Summer Fellowship (A.C., N.G.), the Yale Global Health Awards for Research (N.G.), and the Yale College Dean Office Perspectives on Biological Research Fellowship (to G.G.). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study protocol was approved by National Ethics Committee of Senegal (CNERS) (SEN19/36 and SEN23/09), the regulatory board of the Senegalese Ministry of Health and the Institutional Review Board of the Yale School of Public Health (2000025417). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability The sequencing data generated by this study have been deposited in the NCBI SRA under the following BioProject accession number: PRJNA1204383