The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii

Abstract

AbstractResistance to pyrethroid insecticides is a major concern for malaria vector control, because these are the compounds used in almost all insecticide-treated bed-nets (ITNs), and are also widely used for indoor residual spraying (IRS). Pyrethroids target the voltage-gated sodium channel (VGSC), an essential component of the mosquito nervous system, but substitutions in the amino acid sequence can disrupt the activity of these insecticides, inducing a resistance phenotype. Here we use Illumina whole-genome sequence data from phase 1 of the Anopheles gambiae 1000 Genomes Project (Ag1000G) to provide a comprehensive account of genetic variation in the Vgsc gene in mosquito populations from eight African countries. In addition to the three known resistance alleles, we describe 20 non-synonymous nucleotide substitutions at appreciable frequency in one or more populations that are previously unknown in Anopheles mosquitoes. Thirteen of these novel alleles were found to occur almost exclusively on haplotypes carrying the known L995F resistance allele (L1014F in Musca domesticus codon numbering), and may enhance or compensate for the L995F resistance pheno-type. A novel mutation I1527T, which is adjacent to a predicted pyrethroid binding site, was found in tight linkage with either of two alleles causing a V402L substitution, similar to a combination of substitutions found to cause pyrethroid resistance in several other insect species. We analyse the genetic backgrounds on which non-synonymous alleles are found, to determine which alleles have experienced recent positive selection, and to refine our understanding of the spread of resistance between species and geographical locations. We describe twelve distinct haplotype groups with evidence of recent positive selection, five of which carry the known L995F resistance allele, five of which carry the known L995S resistance allele, one of which carries the novel I1527T allele, and one of which carries a novel M490I allele. Seven of these groups are localised to a single geographical location, and five comprise haplotypes from different countries, in one case separated by over 3000 km, providing new information about the geographical distribution and spread of resistance. We also find evidence for multiple introgression events transmitting resistance alleles between An. gambiae and An. coluzzii. We identify markers that could be used to design high-throughput, low-cost genetic assays for improved surveillance of pyrethroid resistance in the field. Our results demonstrate that the molecular basis of target-site pyrethroid resistance in malaria vectors is more complex than previously appreciated, and provide a foundation for the development of new genetic tools to track the spread insecticide resistance and improve the design of strategies for insecticide resistance management.