Multi-omics analysis identifies a CYP9K1 haplotype conferring pyrethroid resistance in the malaria vector Anopheles funestus in East Africa

Jack Hearn*, Carlos S Djoko Tagne, Sulaiman S Ibrahim, Billy Tene-Fossog, Leon M J Mugenzi, Helen Irving, Jacob M Riveron, Gareth D Weedall, Charles S Wondji

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Metabolic resistance to pyrethroids is a menace to the continued effectiveness of malaria vector controls. Its molecular basis is complex and varies geographically across Africa. Here, we used a multi-omics approach, followed-up with functional validation to show that a directionally selected haplotype of a cytochrome P450, CYP9K1 is a major driver of resistance in Anopheles funestus. A PoolSeq GWAS using mosquitoes alive and dead after permethrin exposure, from Malawi and Cameroon, detected candidate genomic regions, but lacked consistency across replicates. Targeted sequencing of candidate resistance genes detected several SNPs associated with known pyrethroid resistance QTLs. The most significant SNPs were in the cytochrome P450 CYP304B1 (Cameroon), CYP315A1 (Uganda) and the ABC transporter gene ABCG4 (Malawi). However, when comparing field resistant mosquitoes to laboratory susceptible, the pyrethroid resistance locus rp1 and SNPs around the ABC transporter ABCG4 were consistently significant, except for Uganda where SNPs in the P450 CYP9K1 was markedly significant. In vitro heterologous metabolism assays with recombinant CYP9K1 revealed that it metabolises type II pyrethroid (deltamethrin; 64% depletion) but not type I (permethrin; 0%), while moderately metabolising DDT (17%). CYP9K1 exhibited reduced genetic diversity in Uganda underlying an extensive selective sweep. Furthermore, a glycine to alanine (G454A) amino acid change in CYP9K1 was fixed in Ugandan mosquitoes but not in other An. funestus populations. This study sheds further light on the evolution of metabolic resistance in a major malaria vector by implicating more genes and variants that can be used to design field-applicable markers to better track resistance Africa-wide.

Original languageEnglish
Pages (from-to)3642-3657
Number of pages16
JournalMolecular Ecology
Issue number13
Early online date24 May 2022
Publication statusPrint publication - Jul 2022
Externally publishedYes

Bibliographical note

© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.


  • ATP-Binding Cassette Transporters/genetics
  • Animals
  • Anopheles/genetics
  • Cytochrome P-450 Enzyme System/genetics
  • Haplotypes/genetics
  • Insecticide Resistance/genetics
  • Insecticides/pharmacology
  • Malaria/genetics
  • Mosquito Vectors/genetics
  • Permethrin/metabolism
  • Pyrethrins/pharmacology
  • Uganda
  • multi-omics
  • pyrethroid


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