Genetic surveillance of target site mutations and copy number variants associated with the escalating insecticide resistance in Anopheles gambiae (s.l.) in Ghana

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.