Phylogenomics of Schistosoma haematobium in Nigeria: Unravelling Population Structure, Hybridisation, and Transmission Dynamics

The phylogenomics of Schistosoma haematobium in Nigeria is complicated by documented hybridisation with the livestock-infecting S. bovis, with implications for transmission dynamics, intermediate host compatibility, and praziquantel treatment efficacy that remain poorly resolved. This doctoral study applied phylogenomic approaches to characterise S. haematobium population structure, hybridisation frequency, and transmission dynamics across Nigeria. Adult worm pairs and cercariae were recovered from infected Bulinus intermediate host snails collected from 20 endemic sites across six states. Complete mitochondrial genomes from 180 individual specimens were sequenced on the Illumina platform. Phylogenetic analysis used maximum likelihood and Bayesian inference methods, while STRUCTURE and ADMIXTURE software assessed hybridisation signatures. S. haematobium-S. bovis hybrid genotypes were detected at frequencies ranging from 3.1 to 18.7 percent across sites, with highest rates in Kebbi and Zamfara states where cattle grazing and human water contact overlap extensively. Phylogeographic analysis identified three distinct Nigerian S. haematobium lineages with different intermediate host snail affinities. Hybridisation frequencies correlated positively with grazing intensity and inversely with praziquantel coverage. These findings reveal that hybridisation constitutes a significant, geographically variable complication to S. haematobium transmission dynamics in Nigeria, with implications for intermediate host control, treatment protocols, and one-health schistosomiasis management strategies. Keywords: Schistosoma haematobium, phylogenomics, hybridisation, population structure, Nigeria.