Background Identification of variation in Ace-1 copy number and G119S mutation genotype from samples of Anopheles gambiae and Anopheles coluzzii across West Africa are important diagnostics of carbamate and organophosphate resistance at population and individual levels. The most widespread and economical method, PCR–RFLP, suffers from an inability to discriminate true heterozygotes from heterozygotes with duplication. MethodsIn addition to PCR–RFLP, in this study three different molecular techniques were applied on the same mosquito specimens: TaqMan qPCR, qRTPCR and ddPCR. To group heterozygous individuals recorded from the PCR–RFLP analysis into different assumptive genotypes K-means clustering was applied on the Z-scores of data obtained from both the TaqMan and ddPCR methods. The qRTPCR analysis was used for absolute quantification of copy number variation.ResultsThe results indicate that most heterozygotes are duplicated and that G119S mutation must now be regarded as a complex genotype ranging from primarily single-copy susceptible Glycine homozygotes to balanced and imbalanced heterozygotes, and multiply-amplified resistant Serine allele homozygotes. Whilst qRTPCR-based gene copy analysis suffers from some imprecision, it clearly illustrates differences in copy number among genotype groups identified by TaqMan or ddPCR. Based on TaqMan method properties, and by coupling TaqMan and ddPCR methods simultaneously on the same type of mosquito specimens, it demonstrated that the TaqMan genotype assays associated with the K-means clustering algorithm could provide a useful semi-quantitative estimate method to investigate the level of allele-specific duplication in mosquito populations.ConclusionsAce-1 gene duplication is evidently far more complex in An. gambiae and An. coluzzii than the better-studied mosquito Culex quinquefasciatus, which consequently can no longer be considered an appropriate model for prediction of phenotypic consequences. These require urgent further evaluation in Anopheles. To maintain the sustained effectiveness carbamates and organophosphates as alternative products to pyrethroids for malaria vector control, monitoring of duplicated resistant alleles in natural populations is essential to guide the rational use of these insecticides.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-015-1026-3) contains supplementary material, which is available to authorized users.

BackgroundThe use of long-lasting insecticidal nets (LLINs) is an effective malaria control strategy. However, there are challenges to achieve high coverage, such as distribution sustainability, and coverage keep-up. This study assessed the effect of LLINs coverage and contextual factors on entomological indicators of malaria in rural Côte d’Ivoire.MethodsThe study was carried out between July 2009 and May 2012 in three villages (Bozi, N’Dakonankro and Yoho) of central Côte d’Ivoire. In Bozi and Yoho, LLINs were distributed free of charge by the national malaria control programme in 2008. In Bozi, an additional distribution was carried out in May 2011. No specific interventions were done in N’Dakonankro. Entomological surveys were conducted in July 2009 and July 2010 (baseline), and in August and November 2011 and in February 2012. Frequency of circumsporozoite protein was determined using an enzyme-linked immunosorbent assay. Regression models were employed to assess the impact of LLINs and changing patterns of irrigated rice farming on entomological parameters, and to determine associations with LLINs coverage and other contextual factors.ResultsIn Bozi, high proportion of LLIN usage was observed (95-100%). After six months, 95% of LLINs were washed at least once and 79% were washed up to three times within one year. Anopheles gambiae was the predominant malaria vector (66.6% of all mosquitoes caught). From 2009 to 2012, in N’Dakonankro, the mean annual entomological inoculation rate (EIR) increased significantly from 116.8 infectious bites/human/year (ib/h/y) to 408.8 ib/h/y, while in the intervention villages, the EIR decreased significantly from 514.6 ib/h/y to 62.0 ib/h/y (Bozi) and from 83.9 ib/h/y to 25.5 ib/h/y (Yoho). The risk of an infectious bite over the three-year period was significantly lower in the intervention villages compared to the control village (p <0.001).ConclusionHigh coverage and sensitization of households to use LLINs through regular visits (particularly in Bozi) and abandoning irrigated rice farming (in Yoho) resulted in highly significant reductions of EIR. The national malaria control programme should consider household sensitization and education campaigns and other contextual factors to maximize the benefit of LLINs.