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Background   Plasmodium falciparum  malaria remains a major health challenge in Nigeria despite the global decline of its incidence and mortality rates. Although significant progress has been made in preventing the transmission of  P. falciparum  and controlling the spread of the infection, there is much to be done in the area of proper monitoring, surveillance of the parasite, investigating the population dynamics and drug resistance profiling of the parasite as these are important to its eventual eradication. Polymorphic loci of  msp1 ,  msp2  and/or  glurp  genes or microsatellites have been traditionally used to characterize  P. falciparum  population structure in various parts of Nigeria. The lack of standardization in the interpretation of results, as well as the inability of these methods to distinguish closely related parasites, remains a limitation of these techniques. Conversely, the recently developed 24 single nucleotide polymorphism (SNP)-based molecular barcode assay has the possibility of differentiating between closely related parasites and offer additional information in determining the population diversity of  P. falciparum  within and between parasite populations. This study is therefore aimed at defining the population diversity of  P. falciparum  in and between two localities in Nigeria using the SNPs barcode technique.    Methods  The 24-SNP high-resolution melt (HRM) barcode assay and  msp2  genotyping was used to investigate both intra and inter population diversity of the parasite population in two urban cities of Nigeria.    Results  Based on SNP barcode analysis, polygenomic malaria infections were observed in 17.9% and 13.5% of population from Enugu and Ibadan, respectively, while  msp2  analyses showed 21% and 19.4% polygenomic infections in Enugu and Ibadan, respectively. Low levels of genetic diversity (π) of 0.328 and 0.318 were observed in Enugu and Ibadan parasite populations, respectively, while the F ST  value of 0.02 (p = 0.055) was obtained when the genetic divergence of both populations was considered.    Conclusions  The 24-SNP barcode assay was effective in analysing  P. falciparum  population diversity. This study also showed that  P. falciparum  populations in Enugu and Ibadan had a degree of intra-population diversity, but very low divergence between the population. A low degree of polygenomic infections were also observed in the two parasite populations unlike previous years. This maybe as a result of the effect of artemisinin-based combination therapy (ACT), long-lasting insecticide-treated nets (LLITNs) and intermittent preventive treatments in the study populations.

Characterization of Plasmodium falciparum structure in Nigeria with malaria SNPs barcode