Abstract
The spread of insecticide resistance in malaria vectors poses a major challenge to control programs. As insecticide-based interventions intensify, selection for resistance alleles increases, making it essential to understand the genetic mechanisms underlying resistance in local Anopheles populations. This study characterized target-site resistance mutations and copy number variants (CNVs) in Anopheles gambiae s.l. from nine sites with different malaria vector interventions and ecological contexts. WHO bioassays revealed moderate-to-high pyrethroid resistance (4–65%) at all sites, while Obuasi (IRS) showed markedly elevated organophosphate resistance (1.7%) compared to other locations. The L995F kdr mutation was strongly associated with pyrethroid resistance (P < 0.05) and occurred at high frequencies in IRS and standard LLIN sites (0.82–1.0). Additional kdr variants (L995S, N1570Y, I1527T, V402L) appeared at variable frequencies (0–0.59). The Ace-1 G280S mutation was significantly associated with pirimiphos-methyl resistance (OR=2.20, P<0.001). Ace-1 gene duplications occurred in 22.8% of mosquitoes, predominantly in individuals carrying the G280S resistance allele (P<0.001). Carboxylesterase CNVs were also identified, with Coeaxf_Dup1 (30.4%) significantly associated with pirimiphos-methyl resistance (OR = 1.68, P = 0.02). These findings demonstrate the widespread, multifaceted resistance mechanisms in An. gambiae s.l. across Ghana and highlight the need for locally tailored vector control strategies.