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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\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) in fifty-three\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      isolates from two epidemiologically different areas in the South and North of Senegal, was carried out.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A total of 76\n                      <jats:italic>Pfmsp1<\/jats:italic>\n                      and 116\n                      <jats:italic>Pfmsp2<\/jats:italic>\n                      clones were identified and 135 different alleles were found, 56 and 79 belonged to the\n                      <jats:italic>pfmsp1<\/jats:italic>\n                      and\n                      <jats:italic>pfmsp2<\/jats:italic>\n                      genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (\u03c0) were higher in the South than in the North for both genes. For\n                      <jats:italic>pfmsp1<\/jats:italic>\n                      , a high positive Tajima\u2019s D (TD) value was observed in the South (D\u2009=\u20092.0453) while negative TD value was recorded in the North (D\u2009=\u2009\u2212\u20091.46045) and F-Statistic (Fst) was 0.19505. For\n                      <jats:italic>pfmsp2<\/jats:italic>\n                      , 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 (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009\n                      <jats:italic>0.001<\/jats:italic>\n                      ).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      This study revealed a high genetic diversity of\n                      <jats:italic>pfmsp1<\/jats:italic>\n                      and\n                      <jats:italic>pfmsp2<\/jats:italic>\n                      genes and low genetic differentiation in\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      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\n                      <jats:italic>P. falciparum<\/jats:italic>\n                      infections.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12936-020-03471-7","type":"journal-article","created":{"date-parts":[[2020,11,10]],"date-time":"2020-11-10T07:25:09Z","timestamp":1604993109000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal"],"prefix":"10.1186","volume":"19","author":[{"given":"Tolla","family":"Ndiaye","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mouhamad","family":"Sy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy","family":"Gaye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katherine J.","family":"Siddle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel J.","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy K.","family":"Bei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Awa B.","family":"Deme","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aminata","family":"Mbaye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baba","family":"Dieye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaye Die","family":"Ndiaye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ibrahima Mbaye","family":"Ndiaye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mamadou Alpha","family":"Diallo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khadim","family":"Diongue","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah K.","family":"Volkman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aida Sadikh","family":"Badiane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daouda","family":"Ndiaye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,11,10]]},"reference":[{"key":"3471_CR1","unstructured":"WHO. 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