Genetic Diversity of the Plasmodium falciparum Reticulocyte Binding protein Homologue-5 which is a potential Malaria Vaccine Candidate: Baseline data from areas of varying malaria endemicity in Mainland Tanzania
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Background
The limited efficacy of the two malaria vaccines, RTS,S/AS01 and R21/Matrix M, which were recently approved vaccines by the World Health Organization, highlights the need for alternative vaccine candidate genes beyond these pre-erythrocytic-based vaccines. Plasmodium falciparum Reticulocyte Binding Protein Homologue 5 ( Pfrh5) is a potential malaria vaccine candidate, given its limited polymorphism compared to other parasite’s blood stage antigens. This study evaluated the genetic diversity of the Pfrh5 gene among parasites from regions with varying malaria transmission intensities in Mainland Tanzania, to generate baseline data for this potential malaria vaccine candidate.
Methods
This study utilized secondary data of 697 whole-genome sequences from Mainland Tanzania, which were generated by the MalariaGEN Community Network. The samples which were sequenced to generate the data were collected between 2010 and 2015 from five districts within five regions of Mainland Tanzania, with varying endemicities (Morogoro urban district in Morogoro region, Muheza district in Tanga region, Kigoma-Ujiji district in Kigoma region, Muleba district in Kagera region, and Nachingwea district in Lindi region). The genetic diversity of the Pfrh5 gene was assessed using different genetic metrics, including Wright’s fixation index (F ST ), Wright’s inbreeding coefficient (Fws), Principal Component analysis (PCA), nucleotide diversity ( π ), haplotype network, haplotype diversity (Hd), Tajima’s D, and Linkage disequilibrium (LD).
Results
Of the sequences used in this study (n=697), 84.5% (n = 589/697) passed quality control and 313 (53.1%) were monoclonal, and these monoclonal sequences were used for haplotype diversity and haplotype network analysis. High within-host diversity (Fws <0.95) was reported in Kigoma-Ujiji (60.7%), Morogoro urban (53.1%), and Nachingwea (50.8%), while Muleba (53.9%) and Muheza (61.6%) had low within host diversity (Fws≥0.95). PCA did not show any population structure across the five districts and the mean F ST value among the study populations was 0.015. Low nucleotide diversity values were observed across the study sites with the mean nucleotide diversity of 0.00056. A total of 27 haplotypes were observed among the 313 monoclonal samples. The Pf 3D7 was detected as Hap_1, and it was detected in 16/313 (5.1%) sequences, and these sample sequences were from Muheza (62.5%, n=10/16), Kigoma-Ujiji (18.8%, n=3/16), and Muleba (18.8%, n=3/16). Negative Tajima’s D values were observed among the parasite populations in all the study sites.
Conclusion
In this study, we observed low levels of polymorphism in the pfrh5 gene, as it exhibited low nucleotide and haplotype diversity, a lack of population structure and negative Tajima’s D values as signatures of purifying selection. This study provides an essential framework of the diversity of the Pfrh5 gene to be considered in development of the next generation malaria vaccines. Robust and intensive studies of this and other candidate genes are required for characterization of the parasites from areas with varying endemicity, and are crucial to support the prioritization of the Pfrh5 gene for potential inclusion in a broadly cross-protective malaria vaccine.
