Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana

Abstract

Background Extensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The transmission intensity and rates of recombination within and between populations influence the extent of its 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. Methods Pfcsp sequences were retrieved from the Illumina-generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6–59 months presenting with clinical malaria at health facilities in Cape Coast (in 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 analysed for the allele frequency spectrum, genetic diversity both within the host and between 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. Results Pfcsp showed extensive diversity at the two sites, with the higher transmission site, Navrongo, exhibiting 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. Between 1 and 6 amino acid variations were observed in the TH2R and TH3R epitope regions of PfCSP. Tajima’s D was negatively skewed, especially for the population from Cape Coast, given the expected historical population expansion. In contrast, a 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. Conclusion The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines.

Genetic polymorphism and evidence of signatures of selection in thePlasmodium falciparumcircumsporozoite protein gene in Tanzanian regions with different malaria endemicity

“…The current RTS,S, recombinant vaccine was constructed with pfcsp of P. falciparum 3D7 strain, but in Tanzanian isolates, only 0.7% 3D7-matched Tanzanian pfcsp haplotypes. Low matching of the 3D7 to the natural Pfcsp has been reported in many other studies in Africa (8,38,64,68). This data is consistent with other studies conducted across Africa and worldwide, which demonstrate low 3D7 haplotypes and little population structure.…”

“…Similar findings were reported in Ghana where pfcsp sequences collected from two sites located over 784.4 km apart showed a largely homogeneous population with F ST below 0.05, and without any population structure as detected by PCA (62). This and other studies of the Pfcsp gene suggested a continued gene flow among parasites or human population mixing between the areas which might have contributed to the observed findings (62,64,65). High genetic diversity and a lack of population differentiation may have important implications related to the efficacy and emergence as well spread of vaccine-resistant parasites (66,67).…”

Genetic polymorphism of circumsporozoite protein of Plasmodium falciparum among Chinese migrant workers returning from Africa to Henan Province

“…For natural selection of the C-terminal region, both Tajima's D and Fu and Li's D and F values were positive, indicating that the region may be experiencing positive selection, but these observations might be somewhat different from the study of Huang et al [ 20 ]. Some previous studies revealed that the C-terminal region might be in a state of balanced selection to maintain or produce the genetic diversity of the global PfCSP population, and the value of Tajima's D in other regions were positive and highly polymorphic, which might be due to the balanced selection of this immunogenic epitope by host immune pressure [ 35 – 37 ]. The Rm value of imported PfCSP in Henan Province was close to that in Africa, possibly because these were people returning from Africa.…”

Population genomic evidence of adaptive response during the invasion history ofPlasmodium falciparumin the Americas

“…The variant filtration steps were performed using VCFtools v 0.1.16 (Danecek et al 2011) and BCFtools v1.10.2 (Li 2011; Danecek et al 2021). The within-host infection complexity was assessed by calculating the F WS values (Amegashie et al 2020) with vcfdo (github.com/IDEELResearch/vcfdo; last accessed July 2022). An F WS threshold of >0.95 was used as a proxy for monoclonal infection.…”