Geographical variation drives adaptive equilibrium of the P. falciparum sickle-associated mutations

Python, A.; Forster, A. J.; Todd, P.; Niare, K.; Conrad, M.; Ishengoma, D. S.; Amenga-Etego, L. N.; Lian, J.; Liu, B.; Yan, Y.; Liang, J.; Khan, M. M.; Zheng, J.; Bailey, J.; Conway, D. J.; Mentzer, A. J.; Amambua-Ngwa, A.; Leffler, E. M.; Williams, T. N.; Band, G.

doi:10.1101/2025.08.31.672853

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bioRxiv · 10.1101/2025.08.31.672853

Geographical variation drives adaptive equilibrium of the P. falciparum sickle-associated mutations

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Abstract

The recent discovery of genetic mutations in Plasmodium falciparum--the most lethal malaria parasite--that enable it to overcome the protective effects of sickle cell trait, raises fundamental questions about the underlying biological and evolutionary interactions. Here we develop a geostatistical model to compare sickle haemoglobin genotype frequencies to the Plasmodium falciparum sickle-associated alleles across global populations, and find a robust association at multiple geographical scales, implying that sickle drives positive selection for these parasite mutations. A model of parasite evolution and an analysis of local haplotype patterns suggest that key features of these mutations - that they are polymorphic in all African populations and are mutually correlated despite lying in different genome regions - are caused by geographical variation in selection pressure, and that the alleles may have been maintained by balancing selection over timescales comparable to the age of the sickle mutation itself. The predicted impact of this host-parasite interaction on disease outcomes varies widely across populations, and functional data are needed to discover the biological mechanisms involved.

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Python, A., Forster, A. J., Todd, P., Niare, K., Conrad, M., Ishengoma, D. S., Amenga-Etego, L. N., Lian, J., Liu, B., Yan, Y., Liang, J., Khan, M. M., Zheng, J., Bailey, J., Conway, D. J., Mentzer, A. J., Amambua-Ngwa, A., Leffler, E. M., Williams, T. N., Band, G.. 2025-09-04. Geographical variation drives adaptive equilibrium of the P. falciparum sickle-associated mutations. https://doi.org/10.1101/2025.08.31.672853

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