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

Abstract

BackgroundExtensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. Transmission intensity and the rates of recombination within and between populations influence the extent of genetic diversity. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria endemic areas such as Ghana. MethodsPfcsp sequences were retrieved from Illumina generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6-59 months with clinical malaria presenting at health facilities in Cape Coast (on the coastal belt) and Navrongo (Guinea savannah region) respectively in Ghana. The sequences were mapped onto the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analyzed for allele frequency spectrum, genetic diversity both within host and between the populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. ResultsPfcsp was extensively diverse at the two sites with the higher transmission site, Navrongo, recording both higher within host and population level diversity. 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. Amino acid variations ranging between 1 and 6 were observed in the TH2R and TH3R epitope regions of the PfCSP. Tajima’s D was negatively skewed especially for the population from Cape Coast given expected 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 immuno-dominant TH2R and TH3R vaccine epitopes. ConclusionThe low frequencies of Pfcsp vaccine haplotype in the populations analyzed calls for additional molecular and immuno-epidemiological studies with temporal and wider geographic sampling in endemic populations targeted for RTS,S application. 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.