Characterization of Plasmodium falciparum structure in Nigeria with malaria SNPs barcode

Abstract

BackgroundPlasmodium 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.MethodsThe 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.ResultsBased 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 FST value of 0.02 (p = 0.055) was obtained when the genetic divergence of both populations was considered.ConclusionsThe 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.

Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

“…DNA was extracted from DBS for parasite genetic diversity and population structure studies as previously described [ 26 ]. DNeasy Blood and Tissue extraction kit (Qiagen, Germany) was used to extract parasite DNA from DBS following the manufacturer's protocol.…”

Bias-corrected maximum-likelihood estimation of multiplicity of infection and lineage frequencies

“…Some authors calculate MOI for each sample in a dataset as the maximum number of alleles observed across several marker loci (typically STR markers, e.g., [ 18 , 25 ]), or the mean number of alleles across all loci [ 26 ]. For SNP data, in [ 27 ] counts of the number of heterozygous SNPs are used in each sample to define multiclonal infections relating to MOI. Because haplotypes super- or co-infecting a host can carry the same allele at one or many loci, these approaches might substantially underestimate MOI.…”

Genetic Diversity and Population Structure of Plasmodium Falciparum in Nigeria: Insights From Microsatellites Loci Analysis

“…This may largely be attributed to the adoption and deployment of ACTs in Nigeria. In addition, other concurrent interventions such as broader distribution of long-lasting insecticide treated net (LLIN), may be a contributing factor [26]. Another measure of parasite diversity is the number of effective alleles (Ne) detected per microsatellite locus.…”