Genetic diversity and natural selection of Plasmodium falciparum Pf41 vaccine candidate in clinical isolates from Senegal.

The merozoite surface antigen Pf41 was previously identified among the top 10 of new malaria vaccine candidates. Pf41 possesses red blood cell binding regions and conserved domains. We used population genetics approaches to determine the genetic diversity and to identify regions under balancing selection for the potential inclusion of Pf41 as candidate in a multicomponent vaccine. We screened 116 clinical isolates collected from different administrative regions in Senegal for P. falciparum positivity, Pf41 amplification and sequencing. We analyzed Pf41 sequences for polymorphism, natural selection, haplotype prevalence and linkage disequilibrium. Neutrality tests (Tajima's D, FLD, FLF and MEME) were computed using DnaSP v6. and Datamonkey Hyphy. Population Analysis with Reticulate Trees (Popart) version 1.7 software was used to construct haplotypes network showing the distribution of haplotypes per study site. P. falciparum positivity from the 116 successfully tested samples was 93.1% of which 73 were successfully sequenced for Pf41. We found a low genetic diversity (π = 0.00144 ± 0.00022) and high haplotype diversity (Hd = 0.765 ± 0.037) of Pf41 sequences that can be attributed to linkage disequilibrium. We identified several substitutions under positive selection and negatively selected codons at inter-species level in the central and 6-Cys domains of Pf41, respectively. The predominant SNP S232R was found fixed by positive selection in Senegalese isolates. The genetic diversity of Pf41 antigen is low in clinical isolates from Senegal. With a central domain under balancing selection and two highly conserved 6-Cys domains under negative selection due to functional constraints, the Pf41 antigen appears as a good vaccine candidate. Further monitoring of allelic variants on larger and diverse sets of samples would justify the rational for functional assays and Pf41 integration in a multicomponent vaccine.