A novel assay for tracking carboxylesterase gene amplifications conferring organophosphate resistance in the mosquito Aedes aegypti: from experimental evolution to field application

Abstract By altering gene expression and offering a hold for selection by creating paralogs, genomic duplications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene duplications causing an increased expression of detoxification enzymes, supporting their usefulness for monitoring the dynamics of resistance alleles in the field. In this context, the present study aimed at characterising a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and developing a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos confirmed the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a large gene amplification at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number variations among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-colour multiplex TaqMan assay allowing the rapid detection and copy number quantification of this duplication event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay shall improve resistance tracking in this major arbovirus vector.