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

Abstract

Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

Plasmodium malariae structure and genetic diversity in sub-Saharan Africa determined from microsatellite variants and linked SNPs in orthologues of antimalarial resistance genes

“…The low genetic distance observed in this study require further validation since there are no studies on P. malariae for direct comparison. However, the results obtained are consistent with a recent P. falciparum study in Nigeria 21 howbeit in sharp contrast with an older study in Senegal 22 , suggesting relatively high levels of panmixia in the current sampled populations despite the varying transmission patterns. Indeed, multi-locus genotypes were rare across all populations, an indication of recombination and absence of the clonal expansion observed in some P. falciparum populations with low or seasonal malaria transmission 23 .…”

Evidence of a Recent Bottleneck in Plasmodium falciparum Populations on the Honduran–Nicaraguan Border

“…Most studies have analyzed polymorphic coding genes (P. falciparum glutamate rich protein pfglurp, merozoite surface proteins pfmsp-1 and pfmsp-2, P. vivax apical membrane antigen pvama-1, merozoite surface proteins pvmsp-1, pvmsp-142, circumsporozoite protein pvcsp, and the surface protein pvs48 / 45) to assess the diversity of P. falciparum and / or P. vivax in some countries of the isthmus [14][15][16][17][18][19], whereas other studies have used microsatellite markers [20,21] or next generation sequencing using a selectively amplified whole genome approach (sWGA) [22]. Despite differences in the methods, most of these studies conclude that the parasite populations in Central America present a low diversity in relation to parasites of Sub-Saharan Africa [23]. This is much less clear in the Americas, where some of the regions with high incidence of malaria are still within the low to medium transmission levels and accordingly show low diversity of the parasite populations [24].…”

Evolutionary analysis of Babesia vulpes and Babesia microti-like parasites

“…Our examination of haplotypes in this study revealed that six and five of the 43 detected haplotypes were common in populations from different geographical regions and different hosts, respectively, thereby signifying that most of the identified haplotypes (> 86.0%) are unique to specific regions or hosts. Correspondingly, our AMOVA analyses revealed considerably greater genetic variation among populations than within populations (in terms of both geographical origins and hosts), thereby indicating that once having established infestation within a given area or host, B. microti-like parasites tend to evolve within the respective areas or hosts [31]. Furthermore, we detected a higher percentage of variation within populations of different geographical origin than in different hosts (Table 1).…”