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

Abstract

BackgroundIn 2021 and 2023, the World Health Organization approved RTS,S/AS01 and R21/Matrix M malaria vaccines, respectively, for routine immunization of children in African countries with moderate to high transmission. These vaccines are made ofPlasmodium falciparumcircumsporozoite protein (Pfcsp)but polymorphisms in this gene raises concerns regarding strain-specific responses and the long-term efficacy of these vaccines. This study assessed thePfcspgenetic diversity, population structure and signatures of selection among parasites from areas of different malaria transmission in mainland Tanzania, to generate baseline data before the introduction of the malaria vaccines in the country.MethodsThe analysis involved 589 whole genome sequences generated by and as part of the MalariaGEN Community Project. The samples were collected between 2013 and January 2015 from five regions of mainland Tanzania: Morogoro and Tanga (Muheza) (moderate transmission areas), and Kagera (Muleba), Lindi (Nachingwea), and Kigoma (Ujiji) (high transmission areas). Wright’s inbreeding coefficient (Fws), Wright’s fixation index (FST), principal component analysis, nucleotide diversity, and Tajima’s D were used to assess within-host parasite diversity, population structure and natural selection.ResultsBased on Fws(< 0.95), there was high polyclonality (ranged from 69.23% in Nachingwea to 56.9% in Muheza). No population structure was detected in thePfcspgene in the five regions (mean FST= 0.0068). The average nucleotide diversity (π), nucleotide differentiation (K) and haplotype diversity (Hd) in the five regions were 4.19, 0.973 and 0.0035, respectively. The C-terminal region ofPfcspshowed high nucleotide diversity at Th2R and Th3R regions. Positive values for the Tajima’s D were observed in the Th2R and Th3R regions consistent with balancing selection. ThePfcspC-terminal sequences had 50 different haplotypes (H_1 to H_50) and only 2% of sequences matched the 3D7 strain haplotype (H_50).ConclusionsThe findings demonstrate high diversity of thePfcspgene with limited population differentiation. ThePfcspgene showed positive Tajima’s D values for parasite populations, consistent with balancing selection for variants within Th2R and Th3R regions. This data is consistent with other studies conducted across Africa and worldwide, which demonstrate low 3D7 haplotypes and little population structure. Therefore, additional research is warranted, incorporating other regions and more recent data to comprehensively assess trends in genetic diversity within this important gene. Such insights will inform the choice of alleles to be included in the future vaccines