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Microsatellite markers and DNA sequencing were used to determine diversity and molecular characterization of <jats:italic>P. falciparum<\/jats:italic> parasite populations in Uganda.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A total of 147 <jats:italic>P. falciparum<\/jats:italic> genomic DNA samples collected from cross-sectional surveys in symptomatic individuals of 2\u201310 years were characterized by genotyping of seven highly polymorphic neutral microsatellite markers (n\u2009=\u200985) and genetic sequencing of the Histidine Rich Protein 2 (<jats:italic>pfhrp2<\/jats:italic>) gene (n\u2009=\u200962). ArcGIS was used to map the geographical distribution of isolates while statistical testing was done using Student's t-test or Wilcoxon's rank-sum test and Fisher\u2019s exact test as appropriate at P\u2009\u2264\u20090.05.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Overall, 75.5% (95% CI 61.1\u201385.8) and 24.5% (95% CI14.2\u201338.9) of parasites examined were of multiclonal (mixed genotype) and single clone infections, respectively. Multiclonal infections occurred more frequently in the Eastern region 73.7% (95% CI 48.8\u201389.1), P\u2009&lt;\u20090.05. Overall, multiplicity of infection (MOI) was 1.9 (95% CI 1.7\u20132.1), P\u2009=\u20090.01 that was similar between age groups (1.8 vs 1.9), P\u2009=\u20090.60 and regions (1.9 vs 1.8), P\u2009=\u20090.43 for the\u2009&lt;\u20095 and\u2009\u2265\u20095 years and Eastern and Western regions, respectively. Genomic sequencing of the <jats:italic>pfhrp2<\/jats:italic> exon2 revealed a high level of genetic diversity reflected in 96.8% (60\/62) unique sequence types. Repeat type AHHAAAHHATD and HRP2 sequence Type C were more frequent in RDT\u2212\/PCR\u2009+\u2009samples (1.9% vs 1.5%) and (13% vs 8%), P\u2009&lt;\u20090.05 respectively. Genetic relatedness analysis revealed small clusters of gene deleted parasites in Uganda, but no clustering with Eritrean parasites.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>High level of genetic diversity of <jats:italic>P. falciparum<\/jats:italic> parasites reflected in the frequency of multiclonal infections, multiplicity of infection and variability of the <jats:italic>pfhrp2<\/jats:italic> gene observed in this study is consistent with the high malaria transmission intensity in these settings. Parasite genetic analysis suggested spontaneous emergence and clonal expansion of <jats:italic>pfhrp2<\/jats:italic> deleted parasites that require close monitoring to inform national malaria diagnosis and case management policies.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12936-021-03763-6","type":"journal-article","created":{"date-parts":[[2021,5,31]],"date-time":"2021-05-31T08:04:21Z","timestamp":1622448261000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Genetic diversity and genetic relatedness in Plasmodium falciparum parasite population in individuals with uncomplicated malaria based on microsatellite typing in Eastern and Western regions of Uganda, 2019\u20132020"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4601-5171","authenticated-orcid":false,"given":"Bosco B.","family":"Agaba","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Anderson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karryn","family":"Gresty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christiane","family":"Prosser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joaniter I.","family":"Nankabirwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Nsobya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adoke","family":"Yeka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rhoda","family":"Namubiru","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Arinaitwe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Mbaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Kissa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chae Seung","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Karamagi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joan K.","family":"Nakayaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moses R.","family":"Kamya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,31]]},"reference":[{"key":"3763_CR1","unstructured":"WHO. 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Agaba has been corrected: previously, the name had been miswritten as Agaba B. Bosco.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Ethical approval for the primary study was obtained from the Makerere University School of Medicine Research and Ethics Committee, the Uganda National Council of Science and Technology, the London School of Hygiene & Tropical Medicine Ethics Committee, and the University of California, San Francisco Committee on Human Research. Ethical approval to access and use participants\u2019 samples from the primary study was obtained from the school of Medicine Research and Ethics Committee (SOMREC), the Uganda National Council of Science and Technology (UNCST) and the Australian Department of Defence and Veterans\u2019 Affairs Human Research Ethics Committee (DDVA HREC 096\u201318).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All authors read and approved the manuscript for publication.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"All authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"242"}}