Population Genetic Analysis of Plasmodium falciparum Circumsporozoite Protein (CSP) in Two Distinct Ecological Regions in Ghana

Abstract

Malaria caused by Plasmodium falciparum parasite continues to be of major public health concern in Ghana. RTS,S/AS01 is the most advanced malaria vaccine candidate designed based on the 3D7 laboratory Plasmodium falciparum Circumsporozoite protein (PfCSP). Extensive diversity of the gene encoding the PfCSP (Pfcsp) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The intensity of malaria transmission influences the extent of genetic variation within and between malaria parasite populations. However, the extent and dynamics of genetic diversity of Pfcsp in Ghana is poorly understood. Therefore, this study sought to investigate the extent of genetic diversity of Pfcsp parasite populations within and between two eco-epidemiologically distinct regions in Ghana and ascertain how forces of evolution such as selection shapes this diversity. Illumina generated paired-end short-read DNA sequences of P. falciparum parasites were retrieved from 101 and 131 blood samples taken from children between the age range of 6-59 months presenting with Clinical malaria at Cape Coast (located on the coastal belt) and Navrongo (in the Northern savannah region) respectively. The sequences were mapped to the genome of the 3D7 reference strain yielding high-quality genome-wide coding sequence data. After which data filtering and quality checks were done to remove missing data. There remained a total of 220 isolates which were analysed for allele frequency spectrum, genetic diversity both within host and between the populations and signatures of selection. Pfcsp was extensively diverse at the two sites with the higher transmission site, Navrongo, recording both higher within host and population level diversity as seen in higher malaria transmission regions. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences respectively indicating that the RTS,S vaccine might be more efficacious in Cape Coast than Navrongo. Amino acid variations ranging between 1 and 6 were observed specifically in the TH2R (CD4+) and TH3R (CD8+) immunodominant epitope regions of the PfCSP which could potentially reduce vaccine efficacy. Tajima’s D was negatively skewed mainly Cape Coast isolates as expected from historical population expansion. On the contrary, positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immunodominant TH2R and TH3R vaccine epitopes. These results have implications on the efficacy of the vaccine in Ghana and will inform the choice of alleles to include in future multivalent or chimeric vaccines.