Wolbachia is a maternally transmitted endosymbiotic bacterium with demonstrated potential for modulating vector competence and suppressing Plasmodium falciparum development in Anopheles mosquitoes. While naturally occurring Wolbachia infections have been reported in Anopheles gambiae sensu lato in Burkina Faso, the extent of its distribution among other key malaria vectors, particularly within the Anopheles funestus complex remains unclear. This study aimed to assess the presence and prevalence of natural Wolbachia infections in wild An. funestus complex populations from western Burkina Faso. Adult females were collected from Soumousso and screened for Wolbachia using a quantitative PCR assay targeting the 16S rRNA gene (W16S-qPCR). Molecular species identification was conducted on a subsample to resolve intra-group composition. Of 329 individuals identified, An. funestus sensu stricto accounted for 50.2% of the sample, with An. rivulorum-like (23.4%) and An. leesoni (5.8%) also present. A notable proportion of specimens exhibited mixed molecular profiles, indicating possible limitations in marker resolution or interspecific hybridization. Out of 510 specimens tested by qPCR, Wolbachia DNA was detected in 178 individuals, yielding an overall infection prevalence of 34.9%. Stratified by species, An. funestussensu stricto exhibited the highest prevalence (36.4%), followed by An. leesoni and An. rivulorum-like. These findings provide the first molecular evidence of natural Wolbachia infections in An. funestus complex mosquitoes in Burkina Faso. The observed infection rates, particularly in An. funestus s.s., a major malaria vector, underscore the potential epidemiological relevance of this symbiosis. Further genomic and functional characterization of the detected Wolbachia strains is essential to elucidate their phylogenetic origins, tissue tropism, and potential influence on Plasmodium development. Such insights will be critical for evaluating the suitability of Wolbachia-based biocontrol strategies in African vector populations where An. funestus plays a dominant role in residual malaria transmission.
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