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Genetic diversity of surface exposed and stage specific Plasmodium falciparum immunogenic proteins pose a major roadblock to developing an effective malaria vaccine with broad and long-lasting immunity. We conducted a prospective genetic analysis of candidate antigens (msp1, ama1, rh5, eba175, glurp, celtos, csp, lsa3, Pfsea, trap, conserved chrom3, hyp9, hyp10, phistb, surfin8.2, and surfin14.1) for malaria vaccine development on 2375 P. falciparum sequences from 16 African countries. We described signatures of balancing selection inferred from positive values of Tajima’s D for all antigens across all populations except for glurp. This could be as a result of immune selection on these antigens as positive Tajima’s D values mapped to regions with putative immune epitopes. A less diverse phistb antigen was characterised with a transmembrane domain, glycophosphatidyl anchors between the N and C- terminals, and surface epitopes that could be targets of immune recognition. This study demonstrates the value of population genetic and immunoinformatic analysis for identifying and characterising new putative vaccine candidates towards improving strain transcending immunity, and vaccine efficacy across all endemic populations.

Background Vaccines are the most reliable alternative to elicit sterile immunity against malaria but their development has been hindered by polymorphisms and strain-specificity in previously studied antigens. New vaccine candidates are therefore urgently needed. Highly conserved Plasmodium falciparum reticulocyte-binding protein homologue-5 (PfRH5) has been identified as a potential candidate for anti-disease vaccine development. PfRH5 is essential for erythrocyte invasion by merozoites and crucial for parasite survival. However, there is paucity of data on the extent of genetic variations on PfRH5 in field isolates of Plasmodium falciparum. This study described genetic polymorphisms at the high affinity binding polypeptides (HABPs) 36718, 36727, 36728 of PfRH5 in Nigerian isolates of P. falciparum. This study tested the hypothesis that only specific conserved B and T cell epitopes on PfRH5 HABPs are crucial for vaccine development. Methods One hundred and ninety-five microscopically confirmed P. falciparum samples collected in a prospective cross-sectional study of three different populations in Lagos, Nigeria. Genetic diversity and haplotype construct of Pfrh5 gene were determined using bi-directional sequencing approach. Tajima’s D and the ratio of nonsynonymous vs synonymous mutations were utilized to estimate the extent of balancing and directional selection in the pfrh5 gene. Results Sequence analysis revealed three haplotypes of PfRH5 with negative Tajima’s D and dN/dS value of − 1.717 and 0.011 ± 0.020, respectively. A single nucleotide polymorphism, SNP (G → A) at position 608 was observed, which resulted in a change of the amino acid cysteine at position 203 to tyrosine. Haplotype and nucleotide diversities were 0.318 ± 0.016 and 0.0046 ± 0.0001 while inter-population genetic differentiation ranged from 0.007 to 0.037. Five polypeptide variants were identified, the most frequent being KTKYH with a frequency of 51.3%. One B-cell epitope, 151 major histocompatibility complex (MHC) class II T-cell epitopes, four intrinsically unstructured regions (IURs) and six MHC class I T-cell epitopes were observed in the study. Phylogenetic analysis of the sequences showed clustering and evidence of evolutionary relationship with 3D7, PAS-2 and FCB-2 RH5 sequences. Conclusions This study has revealed low level of genetic polymorphisms in PfRH5 antigen with B- and T-cell epitopes in intrinsically unstructured regions along the PfRH5 gene in Lagos, Nigeria. A broader investigation is however required in other parts of the country to support the possible inclusion of PfRH5 in a cross-protective multi-component vaccine.

Background The devastating public health impact of malaria has prompted the need for effective interventions. Malaria control gained traction after the introduction of artemisinin-based combination therapy (ACT). However, the emergence of artemisinin (ART) partial resistance in Southeast Asia and emerging reports of delayed parasite sensitivity to ACT in African parasites signal a gradual trend towards treatment failure. Monitoring the prevalence of mutations associated with artemisinin resistance in African populations is necessary to stop resistance in its tracks. Mutations in Plasmodium falciparum genes pfk13, pfcoronin and pfatpase6 have been linked with ART partial resistance. Methods Findings from published research articles on the prevalence of pfk13, pfcoronin and pfatpase6 polymorphisms in Africa were collated. PubMed, Embase and Google Scholar were searched for relevant articles reporting polymorphisms in these genes across Africa from 2014 to August 2021, for pfk13 and pfcoronin. For pfatpase6, relevant articles between 2003 and August 2021 were retrieved. Results Eighty-seven studies passed the inclusion criteria for this analysis and reported 742 single nucleotide polymorphisms in 37,864 P. falciparum isolates from 29 African countries. Five validated-pfk13 partial resistance markers were identified in Africa: R561H in Rwanda and Tanzania, M476I in Tanzania, F446I in Mali, C580Y in Ghana, and P553L in an Angolan isolate. In Tanzania, three (L263E, E431K, S769N) of the four mutations (L263E, E431K, A623E, S769N) in pfatpase6 gene associated with high in vitro IC50 were reported. pfcoronin polymorphisms were reported in Senegal, Gabon, Ghana, Kenya, and Congo, with P76S being the most prevalent mutation. Conclusions This meta-analysis provides an overview of the prevalence and widespread distribution of pfk13, pfcoronin and pfatpase6 mutations in Africa. Understanding the phenotypic consequences of these mutations can provide information on the efficacy status of artemisinin-based treatment of malaria across the continent. Graphical Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Background The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions. Methods We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima’s D) and integrated haplotype score (iHS) to identify genes under selection. Results Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima’s D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively. Conclusion We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known genomic signatures of selection from drug pressure and host immunity. This is evidence that P. falciparum populations explore common adaptive strategies that can be targeted for the development of new interventions. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2260-z) contains supplementary material, which is available to authorized users.

Background Asymptomatic malaria parasites are significant sources of infections for onward malaria transmission. Conventional tools for malaria diagnosis such as microscopy and rapid diagnostic test kits (RDT) have relatively low sensitivity, hence the need for alternative tools for active screening of such low-density infections. Methods This study tested var acidic terminal sequence-based (varATS) quantitative polymerase chain reaction (qPCR) for screening asymptomatic Plasmodium falciparum infections among dwellers of a sub-urban community in Lagos, Nigeria. Clinically healthy participants were screened for malaria using microscopy, RDT and varATS qPCR techniques. Participants were stratified into three age groups: 1–5, 6–14 and > 14 years old. Results Of the 316 participants screened for asymptomatic malaria infection, 78 (24.68%) were positive by microscopy, 99 (31.33%) were positive by RDT and 112 (35.44%) by varATS qPCR. Participants aged 6–14 years had the highest prevalence of asymptomatic malaria, with geometric means of ~ 116 parasites/µL and ~ 6689 parasites/µL as detected by microscopy and varATS, respectively. Conclusion This study has revealed high prevalence of asymptomatic malaria in the study population, with varATS detecting additional sub-microscopic infections. The highest concentration of asymptomatic malaria was observed among school-age children between 6 and 14 years old. A large-scale screening to identify other potential hotspots of asymptomatic parasites in the country is recommended.

Plasmodium vivax and P. falciparum are the most important human malaria species. P. falciparum is considered the most virulent and widespread species in sub-Saharan Africa. Hence, control efforts have focused on reducing the morbidity and mortality associated with falciparum malaria. However, with improved malaria diagnostics, there is more evidence of high vivax burden in Africa. As P. vivax is capable of dormancy in the liver, it is suspected that artemisinin-based combination treatment widely use across Africa to combat falciparum malaria may be favouring adaptive selection for P. vivax. Additionally, a better understanding of the mechanism of erythrocytes invasion in Duffy-negative individuals who were previously believed to be protected against P. vivax is needed. Therefore, this review discusses the epidemiological implications of P. vivax and P. falciparum co-endemicity in Africa. We also examine available tools for diagnosis of vivax malaria. We conclude by recommending specific interventions against P. vivax that can impact current malaria elimination strategies.

Introduction: Extensive genetic diversity of malaria parasites is a major draw back to ongoing control efforts. Population-specific investigation of genetic structure of the parasite is important for effective malaria intervention in endemic populations such as Nigeria where about one-third of the global burden of the disease is borne. This study describes the genetic diversity of Plasmodium falciparum isolates in the Niger River basins, North-Central Nigeria. Methodology: Parasite DNA w as extracted fr om finger -prick blood samples collected from eighty P. falciparum positive individuals. Polymerase Chain Reaction (PCR) genotyping was carried out to target K1, MAD20 and R033 allelic families of Merozoite Surface Protein (MSP) -1 gene and FC27 and 3D7 allelic families of MSP-2 gene. Results: Proportion of isolates with K1 family w as 28(70%) with two alleles in Idah and 16(40%) with two alleles in Ibaji. Proportion of isolates with MAD20 family was 8 (20%) and a total of two alleles were observed in Idah and 4(10%) with two alleles in Ibaji. RO33 proportion was 16 (40%) in Idah one allele and 8(20%) in Ibaji where the allelic family was also observed to be monomorphic. K1 was the most predominant MSP1 allele in the two parasite populations and the frequency of FC27 genotype was higher than 3D7 in both populations. Multiplicity of infection (Mol) with MSP-1 loci was higher in Ibaji (1.30) than Idah (1.05) while MoI with MSP-2 loci was lower in Ibaji (2.00) than Idah (2.13). However, there is no significant difference in the mean Mol between Idah and Ibaji (P > 0.05). The expected heterozygosity (HE) value was 0.56 for MSP-1 and 0.84 for MSP-2. Conclusion: Our findings revealed high levels of monoclonal infections with P. falciparum, suggesting low parasite diversity. This may be a pointer to a reduction in malaria transmission in the river basins.

Background The decline in the efficacy of artemisinin-based combination treatment (ACT) in some endemic regions threatens the progress towards global elimination of malaria. Molecular surveillance of drug resistance in malaria-endemic regions is vital to detect the emergence and spread of mutant strains. Methods We observed 89 malaria patients for the efficacy of artemether-lumefantrine for the treatment of uncomplicated Plasmodium falciparum infections in Lagos, Nigeria and determined the prevalence of drug resistant strains in the population. Parasite clearance rates were determined by microscopy and the highly sensitive var gene acidic terminal sequence (varATS) polymerase chain reaction for 65 patients with samples on days 0, 1, 3, 7, 14, 21 and 28 after commencement of treatment. The genomic finger print of parasite DNA from pre- and post-treatment samples were determined using 24 nuclear single nucleotide polymorphisms (SNP) barcode for P. falciparum. Drug resistance associated alleles in chloroquine resistance transporter gene (crt-76), multidrug resistance genes (mdr1–86 and mdr1–184), dihydropteroate synthase (dhps-540), dihydrofolate reductase (dhfr-108) and kelch domain (K-13580) were genotyped by high resolution melt analysis of polymerase chain reaction (PCR) fragments. Results By varATS qPCR, 12 (18.5%) of the participants had detectable parasite DNA in their blood three days after treatment, while eight (12.3%) individuals presented with genotypable day 28 parasitaemia. Complexity of infection (CoI) was 1.30 on day 0 and 1.34 on day 28, the mean expected heterozygosity (HE) values across all barcodes were 0.50 ± 0.05 and 0.56 ± 0.05 on days 0 and 28 respectively. Barcode (π) pairwise comparisons showed high genetic relatedness of day 0 and day 28 parasite isolates in three (37.5%) of the eight individuals who presented with re-appearing infections. Crt-76 mutant allele was present in 38 (58.5%) isolates. The mdr1–86 mutant allele was found in 56 (86.2%) isolates. No mutation in the K-13580 was observed. Conclusions Persistence of DNA-detectable parasitaemia in more than 18% of cases after treatment and indications of genetic relatedness between pre- and post-treatment infections warrants further investigation of a larger population for signs of reduced ACT efficacy in Nigeria. Electronic supplementary material The online version of this article (10.1186/s12879-018-3314-3) contains supplementary material, which is available to authorized users.

Background: There are emerging reports of poor efficacy of artemisinin-based combination treatment (ACT). However, mutations on the Kelch-13 gene marking delayed parasite clearance have no clinically defined relationship with ACT resistance across Africa. With increasing malaria control efforts, declining acquired immunity could be responsible for varying drug response profiles that may be dependent on levels of exposure to infections. To examine antibody responses against malaria and the influence on the efficacy of artemether-lumefantrine (AL), plasma samples were collected, prior to treatment, from individuals presenting with uncomplicated malaria. Methods: Participants were stratified into two groups: early (within 24 hours, N = 20) and late (between 48 – 72 hours, N = 30) parasite clearance after treatment, as determined by var gene acidic terminal sequence (varATS) polymerase chain reaction. Magnetic bead-based luminex assay was used to profile antibody responses specific to a panel of 21 Plasmodium falciparum sporozoite, merozoite and An. gambiae salivary antigens. Results: Median fluorescence intensity (MFI) of the antibodies was highest against glutamate-rich protein (GLURP-R0) and lowest against merozoite surface protein (MSP2) antigen. Analysis showed a positive correlation between expression of immunity and age of individuals (P = 0.023). However, there was no association between parasite density and antibody responses, except a significant positive relationship with reticulocyte binding protein-like homologue 5 (Rh5), P = 0.047; Plasmodium exported protein (Hyp2), P = 0.037 and merozoite surface protein 11 (H103), P = 0.038. Though higher levels of antibodies against erythrocyte binding antigens (EBA 140 and 175), MSP1.19, GLURP, circumsporozoite protein (CSP) and Rh4.2 were observed in individuals who recorded early parasite clearance, there was no significant difference in antibody responses in the early and late parasitological response groups. Conclusions: Characterization of additional markers in larger populations is required to reveal potential immunological correlates of drug efficacy.

Background In malaria endemic regions, malnutrition has also been reported to be a public health problem. Considering that the pattern of host cytokines-mediated innate immunity is critical in determining malaria outcomes-understanding the impact of malnutrition on innate immune response in Plasmodium falciparum (Pf)-infected patients may be helpful for malaria control. This study aims to determine nutritional status and evaluate the influence of malnutrition on the immune response of infected patients in Lagos, Nigeria.