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

Abstract

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.

Evidence of a Recent Bottleneck in Plasmodium falciparum Populations on the Honduran–Nicaraguan Border

“…In this study, the allele frequencies of the pfmsp-1 and pfmsp-2 genes were assessed. Both genes encode antigens with highly polymorphic regions that have been used extensively to study the epidemiology of malaria [27,28,36]. The most frequent allelic subfamily of pfmsp-1 was K1 (84.4%) followed by RO33 (61.2%) and MAD20 (23.8%).…”

The diversity of Plasmodium falciparum isolates from asymptomatic and symptomatic school-age children in Kinshasa Province, Democratic Republic of Congo

“…[ 65 ] showed that the MOI was significantly higher in a rural area than in an urban setting. To date, the majority of studies have established: i) a correlation between the genetic diversity of P. falciparum populations and the intensity of transmission in malaria-endemic areas, ii) that P. falciparum genetic diversity is higher in hyperendemic areas than in low-endemic settings [ 41 , 65 – 67 ], and iii) that polyclonal infection prevalence decreases with a reduction in malaria transmission [ 67 – 72 ]. These findings suggest that pfmsp1 and pfmsp2 allelic diversities are not influenced by the level of transmission between the two zones.…”

Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention

“…In this study, evidence of a single, admixing parasite population included 1) the fact that Pikine and Thiès are geographically proximal (~30 miles), 2) the post-2014 mutation frequencies in Thiès and Kedougou follow similar trajectories, and 3) the mutation frequencies observed in sites not included in the model (Kolda, and Kaolack) tended to be consistent with the model predictions. Previous parasite population genetic analyses in Senegal based on the time-serial allele frequency data of neutral sites and Fst from msp-typing have consistently suggested a well-mixed parasite population 43,44 . While we cannot exclude the possibility of site-specific differences in mutation frequency, there is little evidence that the parasite population genetic structure in Senegal is as fragmented as those seen in the Greater Mekong region of Southeast Asia 45 .…”