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Ndiaye T, Sy M, Gaye A, Siddle KJ, Park DJ, Bei AK, Deme AB, Mbaye A, Dieye B, Ndiaye YD, Ndiaye IM, Diallo MA, Diongue K, Volkman SK, Badiane AS, Ndiaye D. Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal. Malar J 2020; 19:403. [PMID: 33172455 PMCID: PMC7654156 DOI: 10.1186/s12936-020-03471-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/30/2020] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Tolla Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal.
| | - Mouhamad Sy
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Amy Gaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | | | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy K Bei
- Yale School of Public Health, 60 College Street, New Haven, CT, 06510, USA
| | - Awa B Deme
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Aminata Mbaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Baba Dieye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Yaye Die Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mamadou Alpha Diallo
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Khadim Diongue
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard University, Cambridge, MA, USA
| | - Aida Sadikh Badiane
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Daouda Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard University, Cambridge, MA, USA
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