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Asymptomatic carriers of Plasmodium are considered a reservoir of the parasite in humans. Therefore, in order to be effective, new malaria elimination strategies must take these targets into account. The aim of this study was to analyse genetic diversity of Plasmodium falciparum among schoolchildren in three epidemiological areas in Côte d'Ivoire. This was a crosssectional study carried out from May 2015 to April 2016 in a primary school in rural and urban areas of San Pedro, Grand-Bassam and Abengourou, during the rainy season and the dry season. A total of 282 Plasmodium falciparum isolates were genotyped using Nested PCR of Pfmsp1 and Pfmsp2 genes. The overall frequency of K1, Mad20 and RO33 alleles was 81.6%, 53.4% and 57% for Pfmsp1 respectively. For Pfmsp2, this frequency was 84.3% and 72.2% for 3D7 and FC27. K1, Mad20 and FC27 Frequencies were significantly higher in Abengourou compared to other sites. Overall, the frequency of MIs was significantly higher in Abengourou for Pfmsp1 and Pfmsp2. However, Mad20 and RO33 alleles were significantly higher in the rainy season. No significant difference was observed between Pfmsp2 alleles in both seasons. Frequency of the 3D7 allele was significantly higher in symptomatic patients. MIs and COI increased with parasitemia for Pfmsp1and Pfmsp2. The data can be added to that available for monitoring and control of P. falciparum malaria. Further studies combining the entomological inoculation rate and the genetic diversity of P. falciparum will allow us to shed light on our understanding of the epidemiology of this parasite.

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