PfCSP in Senegal. Plasmodium falciparum circumsporozoite protein study in Senegal

In addition to effective malaria control measures in the past decades such as effective case management and prevention measures, vaccine has been seen as promising tools to expect to interrupt the transmission and eliminate malaria. Important progress has been made, with the RTS,S/AS01 vaccine currently in the pilot study pipeline; however, this vaccine confers a moderate protection against malaria. The extensive genome plasticity and rapid adaptation of Plasmodium parasites could explain the difficulty of developing an effective vaccine. With regard to malaria epidemiological patterns in Senegal, we surveyed the dynamics of the target antigens of the RTS,S/AS01 malaria vaccine among Plasmodium falciparum isolates over the last decades in Senegal. Samples in this study were obtained from a WHO therapeutic efficacy study (TES) for monitoring antimalarial drug efficacy which was conducted in 2018 the health posts of Tomboronkoto (Kedougou region, high transmission) and Keur Serigne Mbaye Sarr (Diourbel region, moderate transmission). Dried blood spots were collected for PCR amplification of a 1020 fragment encompassing both the central repeat region and the C-terminal region of P. falciparum circumsporozoite protein (PfCSP). Amplicon products were sequenced using Sanger method. PfCSP sequences were compared to those retrieved from the Pf3k genome database (samples collected from 2001 to 2011) in order to determine the temporal dynamics of the variability in the RTS,S/AS01 vaccine target antigens. Among the 86 samples sequenced samples in the central repeat region of PfCSP, 38 unique haplotypes were identified at amino acid level. The number of repeat motifs of tetrapeptides asparagine–alanine–asparagine–proline (NANP) and asparagine–valine–aspartic acid–proline (NVDP) resulted in size polymorphism. The six haplotypes shared between Kedougou and Diourbel predominated in both regions. The distribution of unique haplotypes differed significantly between the two study sites with frequencies of 64.7% in Diourbel vs 42.3% in Kedougou (p = 0.042). No 3D7 vaccine strain haplotype was observed at this locus. In the C-terminal region, 33 distinct haplotypes were identified among the 88 successfully sequenced samples. The seven haplotypes were homogeneously shared between the two localities, whereas there were significantly more unique haplotypes in Kedougou than in Diourbel (p = 0.0081). A 21 single nucleotide polymorphisms (SNPs) barcode across the C-terminal region showed new amino acids in 2018 samples which were not found in the Pf3k samples. Only three of the clustering barcodes in the 2018 samples matched previously observed haplotypes in the Pf3k database. Among those, the 3D7 haplotype frequency was 6.3% in 2007. It expanded to 18.2% in 2008; but then contracted in the subsequent years. The proportion of unique haplotypes significantly decreased between 2007 and 2018 (p = 0.033) while increasing identical alleles were observed. Overall, extensive PfCSP variations were observed between 2011 and 2018 in Senegal. The extensive plasticity of the genes coding the RTS,S/AS01 vaccine target antigens may influence the immune responses to circulating alleles. Monitoring the genetic diversity baseline and its dynamics over time and space would be instrumental in rationally improving the malaria RTS,S/AS01 vaccine and/or its implementation schedule.