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Article
the selection statistics—integrated Haplotype Score (his)^20 and
XP-EHH (Cross Population Extended Haplotype Homozygosity)^21 —using
1,142 wild-caught A. gambiae^19 for the region in which the CSP cluster
is found on chromosome 3R (Fig. 3b). Evidence for a selective sweep at
this locus was observed in A. gambiae from Guinea and Burkina Faso.
The swept haplotype is present at a low frequency but there is evidence
of haplotype sharing between Guinea, Burkina Faso and Cameroon.
We next identified single-nucleotide polymorphisms (SNPs) that are
diagnostic of the derived haplotype in this selective sweep (Fig. 3b) and
sequenced this region in individual mosquitoes that were collected in
the Banfora region of Burkina Faso from 2011 to 2018. This haplotype
was stable in frequency in A. gambiae sensu stricto (s.s.), indicating
that this sweep occurred before the collections of mosquitoes by the
Anopheles gambiae 1000 Genomes Project^19 in 2012 and pre-dating
our collection dates (Fig. 3c and Supplementary Table 1). Conversely,
Anopheles coluzzii samples collected from 2011 to 2018 showed a large
increase in frequency of the SNPs associated with the sweep (Fig. 3c and
Supplementary Table 1), and this corresponded with a sharp increase
in the prevalence of pyrethroid resistance that occurred during this
time period (Extended Data Fig. 8).
Discussion
Our results show that SAP2, a chemosensory protein with no previous
known function in insecticide resistance, has a key role in conferring
pyrethroid resistance in the A. gambiae species complex through the
binding of insecticides at the first point of mosquito contact with
bed nets. When SAP2 was overexpressed in an otherwise-susceptible
background, the transgenic line was more resistant to pyrethroids,
but the phenotype was less marked than the phenotypes found in the
SAP2 knockdown lines, perhaps indicating that SAP2 acts in conjunc-
tion with other resistance mechanism(s) to provide an additive effect.
Given its strong binding to pyrethroid insecticides, it is possible that
SAP2 acts by sequestering the insecticide directly, thus either prevent-
ing the function of the insecticide on the nervous system or facilitating
its detoxification. Notably, longitudinal sequencing of field samples
and available transcriptomic data from wild collections show that this
mechanism is being selected for in multiple countries in West Africa,
highlighting its relevance in field settings. Nationwide distribution of
LLINs has not affected malaria transmission in Burkina Faso, where
cases continue to rise annually^22. Our finding of a potent mechanism
that has rapidly swept across anopheline populations in this region
will help to address the contribution of insecticide resistance to the
persistence of malaria, and the identification of the corresponding
SNPs will facilitate tracking its spread. Finally, the identification of
this previously undescribed insecticide sequestration mechanism
offers the concrete possibility to restore the effectiveness of pyre-
throid insecticides in natural mosquito populations through the
identification of new targets for inhibitors that can be incorporated
into bed nets, in an analogous manner to the incorporation of PBO
into nets—this may prove to be critical for the elimination of malaria
across Africa.
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