Multi-omics analysis identifies loci associated with pyrethroid resistance across sister species in the Anopheles gambiae species complex

The Anopheles gambiae species complex includes An. gambiae, An. coluzzii, and An. arabiensis, three of the four major malaria vector species across Africa. Insecticide-based vector control remains the most critical tool in the fight against malaria, with a heavy reliance on pyrethroid insecticides. However, widespread pyrethroid resistance jeopardises the effectiveness of these methods. Currently, the number of diagnostic markers available to track pyrethroid resistance in endemic settings is limited, focusing mainly on changes at the insecticide target site. Genetic analysis of seven insecticide-resistant populations from West Africa, a region with intense insecticide resistance, reveals shared loci associated with pyrethroid resistance among the sister species of the An. gambiae complex including kdr, GSTE1-8 and the CYP6P region. Notably, a mutation in the voltage-gated sodium channel, I1527T, previously identified in An. coluzzii and An. gambiae, was detected in wild-caught An. arabiensis from Burkina Faso. Additionally, a mutation, L207I, in GSTE7 common to An. coluzzii and An. arabiensis, significantly increases survivorship to deltamethrin. With the additional integration of RNAseq and data from the Anopheles gambiae 1000 genomes project, we were able to identify putative eQTLs associated with the expression of major insecticide resistance-related transcripts, such as CYP6P3, CYP9K1 and CYP6AA1. This study reveals several potential diagnostic markers of resistance that can be implemented in endemic settings and identifies putative introgression between An. arabiensis and An. coluzzii in Burkina Faso.