Evolution and spread of malaria parasite Plasmodium falciparum capable of evading antimalarials are the prime concern to malaria control. The currently effective drug, artemisinin (ART), is under threat due to detection of ART-resistant P. falciparum parasites in the Southeast Asian countries. It has been shown that amino acid (AA) mutations at the P. falciparum Kelch13 (Pfk13) gene provide resistance to ART. Nigeria, a part of the Sub-Saharan Africa, is highly endemic to malaria, contributing quite significantly to malaria, and resistance to chloroquine (CQ) and sulfadoxine-pyrimethamine (SP) combination drugs has already been reported. Since artemisinin combined therapy (ACT) is the first-line drug for treatment of uncomplicated malaria in Nigeria and five amino acid mutations have been validated in the Pfk13 gene alongside with candidate mutations for ART resistance, we performed molecular surveillance for mutations (following PCR and DNA sequence analyses) in this gene from two southwestern states of Nigeria. Statistical analyses of DNA sequences were also performed following different evolutionary models. None of the different validated and candidate AA mutations of Pfk13 gene conferring resistance to ART could be detected in P. falciparum sampled in the two southwestern states of Nigeria. In addition, DNA sequencing and sequence analyses indicated neither evolutionary selection pressure on the Pfk13 gene nor association of mutations in Pfk13 gene with mutations of other three genes conferring resistance to CQ and SP. Therefore, based on the monomorphism at the Pfk13 gene and nonassociation of mutations of this gene with mutations in three other drug-resistant genes in malaria parasite P. falciparum, it can be proposed that malaria public health is not under immediate threat in southwestern Nigeria concerning ART resistance.

Widespread of insecticide resistance amongst the species of the Anopheles gambiae complex continues to threaten vector control in Senegal. In this study, we investigated the presence and evolution of the Ace-1 and Gste2 resistance genes in natural populations of Anopheles gambiae s.l., the main malaria vector in Senegal. Using historical samples collected from ten sentinel health districts, this study focused on three different years (2013, 2017, and 2018) marking the periods of shift between the main public health insecticides families (pyrethroids, carbamates, organophosphates) used in IRS to track back the evolutionary history of the resistance mutations on the Ace-1 and Gste2 loci. The results revealed the presence of four members of the Anopheles gambiae complex, with the predominance of An. arabiensis followed by An. gambiae, An. coluzzii, and An. gambiae–coluzzii hybrids. The Ace-1 mutation was only detected in An. gambiae and An. gambiae–coluzzii hybrids at low frequencies varying between 0.006 and 0.02, while the Gste2 mutation was found in all the species with a frequency ranging between 0.02 and 0.25. The Ace-1 and Gste2 genes were highly diversified with twenty-two and thirty-one different haplotypes, respectively. The neutrality tests on each gene indicated a negative Tajima’s D, suggesting the abundance of rare alleles. The presence and spread of the Ace-1 and Gste2 resistance mutations represent a serious threat to of the effectiveness and the sustainability of IRS-based interventions using carbamates or organophosphates to manage the widespread pyrethroids resistance in Senegal. These data are of the highest importance to support the NMCP for evidence-based vector control interventions selection and targeting.

Duffy antigen receptor for chemokines (DARC) is a transmembrane receptor (glycoprotein) expressed on human red blood cells. Sub-Saharan Africa (sSA) individuals, who suffer the most of the global malaria burden, predominantly carry a Duffy negative phenotype. Expression of this gene (found among Duffy-positive individuals) is known to be essential for P. vivax invasion of RBCs. While P. falciparum is the predominant Plasmodium in sSA, the upward trend in P. vivax infection is a major threat to the malaria eradication programme in the region. Since Duffy null individuals (homozygous negative) lack DARC expression, we investigated the DARC gene dynamics in relation to the emerging presence of P. vivax infections in a previously predominant P. falciparum endemic region. A total of 223 DARC genes were retrieved from the NCBI database across various countries, Nigeria, Cameroon, Ethiopia, Madagascar and South Africa and were used for population dynamic analysis using different population genetic metrics. Among these sSA countries, South Africa showed the most haplotype and nucleotide diversity compared to other parts of sSA. Various selection pressures were observed in Western Africa and the Central African Republic. Population structure analysis revealed DARC population clustering of Cameroon, Nigeria and Ethiopia (despite Ethiopia's geographic distance), suggestive of shared ancestry and minimal DARC locus divergence. Conversely, South Africa and Madagascar showed a distinct genetic lineage reflecting differences in evolutionary pressures. Our analysis suggests minimal genetic diversity within sSA with evidence of selection potentially attributed to the recent emergence of P. vivax infections. However, greater diversity was observed in South Africa. Evidence of selection of this gene and detection of P. vivax among Duffy-null individuals in the other regions is truly a public health concern.

Background: Large-scale deployment of artemisinin-based combination therapies (ACTs) has profoundly altered the evolutionary landscape of Plasmodium falciparum. Although resistance-associated loci have been extensively studied in Southeast Asia, the long-term spatiotemporal dynamics of candidate drug resistance genes in West African parasite populations remain incompletely understood. Methods: We analysed longitudinal genomic data from 1,969 P. falciparum isolates collected across multiple regions of The Gambia spanning the pre-ACT and post-ACT eras. Mixed-effects logistic regression models were used to estimate temporal selection coefficients for candidate resistance-associated variants, accounting for regional structure. Complementary analyses compared allele-frequency trajectories before and after ACT introduction and evaluated region-specific temporal slopes to identify spatial heterogeneity in selection responses. Findings: Substantial temporal restructuring of parasite populations was observed following ACT introduction. Multiple variants demonstrated significant declines over time, particularly within genes associated with transport, ubiquitination, membrane homeostasis, and phosphoinositide signalling, including MRP2, UBP1, PI4K, NHE, tetQ, and NFS1. Spatial analyses revealed marked regional heterogeneity in evolutionary trajectories. The Western Coast Region showed the strongest concentration of declining variants, whereas several variants (e.g. MRP2 T353M, PANK1 Y470H, and NHE N146S) exhibited region-specific expansion within the Upper River Region. Several loci displayed opposing regional trajectories, suggesting localised selective pressures rather than uniform nationwide adaptation. Additionally, multiple de novo (emergent post-ACT) variants absent before 2014 were also identified. Interpretation: P. falciparum populations in The Gambia have undergone substantial spatially heterogeneous evolutionary restructuring following ACT deployment. The observed patterns suggest that antimalarial selection pressures operate within complex regional transmission and genetic backgrounds, shaping adaptive responses across multiple functional pathways. Continued genomic surveillance integrating spatial and temporal modelling is essential for early detection of emerging adaptive lineages and for understanding the evolutionary consequences of sustained ACT use in Africa.