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Such assessments are currently scarce in Madagascar. The study presented here aimed to bridge this gap by investigating the genetic diversity of <jats:italic>P. falciparum<\/jats:italic> populations in three epidemiological strata (Equatorial, Tropical and Fringes) in Madagascar.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Two-hundred and sixty-six <jats:italic>P. falciparum<\/jats:italic> isolates were obtained from patients with uncomplicated malaria enrolled in clinical drug efficacy studies conducted at health centres in Tsaratanana (Equatorial stratum), Antanimbary (Tropical stratum) and Anjoma Ramartina (Fringes) in 2013 and 2016. Parasite DNA was extracted from blood samples collected before anti-malarial treatment. <jats:italic>Plasmodium<\/jats:italic> species were identified by nested PCR targeting the <jats:italic>18\u00a0S rRNA<\/jats:italic> gene. The genetic profiles of <jats:italic>P. falciparum<\/jats:italic> parasites were defined by allele-specific nested PCR on the polymorphic regions of the <jats:italic>msp<\/jats:italic>-<jats:italic>1<\/jats:italic> and <jats:italic>msp<\/jats:italic>-<jats:italic>2<\/jats:italic> genes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Fifty-eight alleles were detected in the <jats:italic>P. falciparum<\/jats:italic> samples tested: 18 alleles for <jats:italic>msp-1<\/jats:italic> and 40 for <jats:italic>msp-2<\/jats:italic>. K1 (62.9%, 139\/221) and FC27 (69.5%, 114\/164) were the principal <jats:italic>msp-1<\/jats:italic> and <jats:italic>msp-2<\/jats:italic> allele families detected, although the proportions of the <jats:italic>msp-1<\/jats:italic> and <jats:italic>msp-2<\/jats:italic> alleles varied significantly between sites. Polyclonal infections were more frequent at sites in the Equatorial stratum (69.8%) than at sites in the Tropical stratum (60.5%) or Fringes (58.1%). Population genetics analyses showed that genetic diversity was similar between sites and that parasite flow within sites was limited.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study provides recent information about the genetic diversity of <jats:italic>P. falciparum<\/jats:italic> populations in three transmission strata in Madagascar, and valuable baseline data for further evaluation of the impact of the control measures implemented in Madagascar.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12936-021-03776-1","type":"journal-article","created":{"date-parts":[[2021,5,27]],"date-time":"2021-05-27T20:11:25Z","timestamp":1622146285000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Genetic diversity of Plasmodium falciparum populations in three malaria transmission settings in Madagascar"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4755-4241","authenticated-orcid":false,"given":"Fanomezantsoa","family":"Ralinoro","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tovonahary Angelo","family":"Rakotomanga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rianasoambolanoro","family":"Rakotosaona","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danielle A.","family":"Doll Rakoto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Didier","family":"Menard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor","family":"Jeannoda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arsene","family":"Ratsimbasoa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,5,27]]},"reference":[{"key":"3776_CR1","volume-title":"World Malaria Report 2020","author":"WHO","year":"2020","unstructured":"WHO. 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