Genomic analysis reveals selection pressure and the emergence of molecular insecticide resistance in the malaria vector, Anopheles gambiae, from Western Ethiopia

Abstract Background Insecticide resistance poses a significant challenge to malaria control, driven by diverse molecular mechanisms, whose distribution remains poorly characterized in Ethiopia. This study presents the first results using whole-genome sequence data of Anopheles gambiae from Ethiopia, confirming its presence in the western region of the country and expanding its known geographical distribution. Methods Analysis of single-nucleotide polymorphisms and copy number variants focussed on key target-site insecticide resistance genes, including the voltage-gated sodium channel ( Vgsc ), acetylcholinesterase-1 ( Ace-1 ), the gamma-aminobutyric acid ( GABA )-gated chloride channel ( Rdl ) gene, as well as metabolic resistance loci such as cytochrome P450s ( Cyp6m2, Cyp6aa/p , Cyp9k1 ) and carboxylesterases ( Coeae2f , Coeae2–7g ). Results Genomic analysis revealed high frequencies of Vgsc -L995F (kdr-west) mutations, alongside amplifications at Cyp6aa/p , Cyp9k1 , and Gste2 . Notably, frequencies of Vgsc and Gste2 variants exhibited differences on a local scale, while Vgsc and Cyp9k1 variant frequencies also fluctuated seasonally. Findings highlight the need for site-specific monitoring on a fine temporal scale. Furthermore, genome-wide selection scans using phased haplotypes identified emerging signals of selection at loci with a potential link to insecticide resistance, including a signal spanning 2L:33,767,545–34,391,778, which expands the catalogue of candidate loci for functional validation. Conclusions Together, the presence of high frequencies of known insecticide resistance markers suggests that An . gambiae populations may be largely refractory to pyrethroids and moderately resistant to organophosphate (OPs) insecticides in western Ethiopia. Findings necessitate a better understanding of the An. gambiae geographical distribution in Ethiopia, accompanied by resistance-informed malaria control interventions targeting the vector.