Multi-locus investigation of Anopheles-mediated selective pressure on Plasmodium falciparum in Africa

Background: The high burden of malaria in Africa is largely due to the presence of competent and adapted Anopheles vector species. With invasive Anopheles stephensi implicated in malaria outbreaks in Africa, understanding the genomic basis of vector-parasite compatibility is essential for assessing the risk of future outbreaks due to this mosquito. Vector compatibility with P. falciparum arises from ancient coevolution and involves genes like Pfs47 in P. falciparum and P47Rec in Anopheles . Questions remain about whether sub-continental vector variation is a selective pressure on current Plasmodium populations or not. Methods: We analyzed the genetic diversity in parasite-vector interaction genes in P. falciparum and An. gambiae from 9 and 15 countries in Africa, respectively. Specifically, we looked for evidence of malaria vector-mediated selection within three P. falciparum genes (Pfs47, Pfs16, Pfs37) and conducted association analyses with occurrence probabilities of prominent malaria vectors (VOP). Results: Higher protein haplotype diversities of Pfs47 and Pfs16 were associated with the probability of occurrence of An. arabiensis and An. funestus together. Only Pfs16 carried a signature of positive selection consistently (average Tajima’s D = -2.96) which was associated with the probability of occurrence of An. funestus . These findings support vector-mediated selection based on vector species diversity may be occurring within Africa. We also employed phylogenetic analyses of An. gambiae interaction genes ( P47Rec , APN1 , HPX15 ) to identify significant subspecies diversity as a prerequisite to vector-population-mediated selection. An. gambiae HPX15 revealed significant sub-species differentiation (multiple branches bootstrap >70) compared to absence of variation in P47Rec, suggesting further investigation into sub-species mediated selection based on HPX15 is needed. Finally, we observed five amino acid changes at P47Rec in invasive An. stephensi compared to dominant African Anopheles species, calling for further investigation of the impact these distinct P47Rec variants would have on local African P. falciparum Pfs47 diversity. Conclusion: Overall, these findings support the notion that vector variation within Africa could influence P. falciparum diversity and lay a genomic framework for future investigation of invasive An. stephensi's impact on African malaria.