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Background  Molecular epidemiology can provide important information regarding the genetic diversity and transmission of  Plasmodium falciparum , which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure of  P. falciparum  and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform.    Methods  Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) in fifty-three  P. falciparum  isolates from two epidemiologically different areas in the South and North of Senegal, was carried out.    Results  A total of 76  Pfmsp1  and 116  Pfmsp2  clones were identified and 135 different alleles were found, 56 and 79 belonged to the  pfmsp1  and  pfmsp2  genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. For  pfmsp1 , a high positive Tajima’s D (TD) value was observed in the South (D = 2.0453) while negative TD value was recorded in the North (D = − 1.46045) and F-Statistic (Fst) was 0.19505. For  pfmsp2 , non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas ( p  =  0.001 ).    Conclusion  This study revealed a high genetic diversity of  pfmsp1  and  pfmsp2  genes and low genetic differentiation in  P. falciparum  population in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology of  P. falciparum  infections.

Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal