Rapid selection of transposon-based resistance in malaria vectors with 4.3kb fixation in less than 5 years.
PoolSeq data analysis identified this 4.3kb insertion between theCYP6P5 and CYP6P9b loci on Chromosome 2 found only in Uganda and Cameroon samples of 2014 out of 8 countries assessed. This 4.3bk SV contains 2 open reading frames (a gag-like and reverse transcriptase-like proteins), which correspond to 2 (gag andpol ) out of the 3 open reading frames that characterised LTR- retrotransposons. The gagencodes capsid proteins, pol encodes enzymes regulating the transposition of a mobile element, while the missing env encodes a product responsible for the recognition of cell receptors and the penetration of a virus into a cell (L. N. Nefedova, Kuzmin, Makhnovskii, & Kim, 2014). The Drosophila melanogastergag-related gene (gagr), a homolog to the Gypsy group of LTR retroelements, is possibly associated with the origin of new functions and the involvement in stress response in Drosophila species (L. Nefedova, Gigin, & Kim, 2022). This SV was at a high frequency in Uganda and observed at a low frequency in Cameroon in 2014. Therefore, we hypothesised that this SV spread from Uganda to Cameroon as it is inserted in an identical position but does not rule out a de novoorigin in Cameroonian populations.
Interestingly population structure analyses using ddRADseq, Poolseq, and microsatellites have revealed a low level of divergence between Cameroon and Ugandan populations of An. funestus indicating that there is likely little barrier to gene flow and increased introgression of alleles between them (Barnes et al., 2017; Weedall et al., 2020). Temporal analysis of the changes in the allelic frequency of the 4.3kb SV in Cameroon collected across the years (2014-2021) revealed a rapid selection of this marker, with its frequency reaching fixation in less than 5 years. The such rapid selection indicates that this insertion will likely provide mosquitoes with an essential adaptive advantage. This is supported by the low nucleotide diversity and negative Tajima’s D values in the CYP6P5 to CYP6P9b intergenic region (Figure S1, Table S2). These high frequencies observed show a similar pattern to the 6.5 kb structural variant previously identified inAn. funestus populations from southern Africa in Malawi and Mozambique (Mugenzi et al., 2020) and was correlated with an increase in deltamethrin/permetrhin resistance observed in field populations. This 6.5kb SV was shown to increase in frequency from 5% in 2002 to about 90% in 2016 in Mozambique samples (Mugenzi et al., 2020). Similarly, inAn. gambiae , an upstream insertion of a partial Zanzibar-like transposable element (TE), was identified in association with two other mutations (nonsynonymous point mutation in CYP6P4 (I236M) and a duplication of the CYP6AA1 gene) in Uganda populations at high frequency and shown to have spread to Kenya, the Democratic Republic of Congo and Tanzania (Njoroge et al., 2022).
Genotyping of recently collected samples for the 4.3kb SV revealed its presence in West Africa in Ghana and Benin at low frequencies, suggesting that this resistance allele is migrating westward. Future works with up-to-date genomic data are needed to understand the origin of this structural variant which could be through adaptive gene flow from East to Central to West, or it could be occurring de novo.