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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 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.

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 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.

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.