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Background  Characterizing the genetic diversity of malaria parasite populations in different endemic settings (from low to high) could be helpful in determining the effectiveness of malaria interventions. This study compared  Plasmodium falciparum  parasite population diversity from two sites with low (pre-elimination) and high transmission in Senegal and Nigeria, respectively.    Methods  Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated  P. falciparum  malaria infected patients in Senegal (94) and Nigeria (93). Allelic polymorphism at  merozoite surface protein  1 ( msp1 ) and  merozoite surface protein - 2 ( msp2 ) genes were assessed by nested PCR.    Results  The most frequent  msp1  and  msp2  allelic families are the K1 and IC3D7 allelotypes in both Senegal and Nigeria. Multiplicity of infection (MOI) of greater that 1 and thus complex infections was common in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for  msp 1/2) than in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of  msp1  gene was higher in  P. falciparum  isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles was associated with heavy than with moderate parasite density. Meanwhile, equal proportions of K1 were observed in both heavy and moderate infection types in Nigeria. The IC3D7 subtype allele of the  msp2  family was the most frequent in heavily parasitaemic individuals from both countries than in the moderately infected participants.    Conclusion  The unexpectedly low genetic diversity of infections high endemic Nigerian setting compared to the low endemic settings in Senegal is suggestive of possible epidemic outbreak in Nigeria.

Allelic diversity of MSP1 and MSP2 repeat loci correlate with levels of malaria endemicity in Senegal and Nigerian populations