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

Fehintola V Ajogbasile,Olugbenga A Mokuolu,Philomena Eromon ,Nma Jiya ,Onikepe A Folarin,Finimo Finimo,Uche Okafor ,Jessica N Uwanibe,Courage Philip,J P Ambe ,Stephen Oguche,Robinson D Wammanda,Go Emechebe ,Benjamin Adegboyega ,Nnenna Ogbulafor,Kazeem Akano ,Adeyemi T Kayode,Oluwagboadurami G John,Paul E Oluniyi,A Sowunmi ,Christian Happi

doi:10.1186/s12936-021-03734-x

Abstract

BackgroundMalaria 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.MethodsIn 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.ResultsEstimates 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).ConclusionThe 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.

Highlights

Malaria remains a public health burden especially in Nigeria
Parasite genetic diversity Of the 633 samples considered for analysis, microsatellite amplification was successful in 571 (90.2%)
This study represents the first use of 12 microsatellite loci to characterize parasite genetic diversity and structure in Nigeria across regions representing all the six geographical zones of the country

Summary

Introduction

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. The incidence of malaria infections and malariaassociated mortality has reduced in many African countries [1,2,3], transmission continues in endemic regions despite intensified efforts towards prevention, control and eradication [4, 5] This is due, in part, to the high genetic diversity of Plasmodium falciparum that contributes to increased transmission rate and spread of resistant parasites [6]. Molecular studies focused mostly on the use of polymorphic markers, such as merozoite surface protein 1 (msp-1), merozoite surface protein 2 (msp-2) and glutamate-rich protein (glurp) to characterize P. falciparum genetic diversity and structure in Nigeria [7,8,9]. The genotyping results provided by these markers can, potentially lead to a masked and distorted view of the population structure and transmission patterns which may account for observed variations across parasite populations circulating in a given environment [6]

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