5.1 Genotyping of field samples reveals a correlation between the 4.3kb SV and pyrethroid resistance.
Gounougou samples obtained from the deltamethrin 0.05% WHO tube bioassays in 2018 (when the 4.3kb structural variant was not yet fixed) were genotyped to determine any association between the 4.3kb SV and deltamethrin resistance phenotype. The mortality rate for deltamethrin was 49.8±11.6%. Genotyping of 77 mosquitoes exposed to deltamethrin (35 alive and 42 dead) revealed a strong association (χ2=33.8; P<0.00001) between this structural variant and the deltamethrin resistant phenotype, with 91.4% (32/35) of the survivors 24 hours post-exposure being homozygous for the structural variant (SV+/SV+), 5.7% (2/35) of the survivors being heterozygous (SV+/SV-) and only 2.9% (1/35) being homozygous without this SV (SV-/SV-) (Figure 3A; Table 1). Among the dead, the distribution of the genotypes was as follows 26.2% (SV+/SV+), 16.7% (SV+/SV-) and 57.1% (SV-/SV-). The odds ratio confirmed the positive association between the 4.3kb SV genotype and the ability to survive exposure to deltamethrin, with SV+/SV+ having a higher association with survival than the SV+/SV- [OR: 10.2; CI: 1.8-56.5; P = 0.0080] and SV-/SV- [OR: 69.8; CI: 8.4-578.5; P = 0.0001]. The higher odds ratio obtained when comparing the SV+/SV+ genotype to the SV+/SV- genotype (10.18) indicates an additive effect of each 4.3 kb structural variant allele. Also, at the allelic frequency, we observed that 94.3% of the alive had the SV+ allele against 5.7% lacking the 4.3kb SV allele showing that this structural variant is strongly associated with the deltamethrin resistance phenotype (OR: 29; CI: 11.6-73.2 ; P< 0.0001). Of the dead, 65.5% lacked the 4.3kb SV (SV-), and 34.5% had the 4.3kb SV (SV+), revealing a lower likelihood for the individuals with the 4.3kb SV to be dead compared to those without (Figure 3B; Table 1).