Unravelling the Molecular Epidemiology of Tomato Yellow Leaf Curl Virus in Nigeria: Recombination, Migration, and Emerging Strain Diversity

Tomato Yellow Leaf Curl Virus (TYLCV) is the most economically devastating viral disease of tomato globally, and its molecular epidemiology in Nigeria, including recombination patterns, migration dynamics, and emerging strain diversity, has not been comprehensively characterised. Understanding these processes is critical for predicting future disease trajectories, assessing cross-border introduction risks, and designing durable resistance deployment strategies. This doctoral research conducts a national molecular epidemiological investigation of TYLCV in Nigerian tomato production systems. Full-length begomoviral genome sequences are obtained from 200 TYLCV-positive tomato plants collected from 40 sites across all six geopolitical zones over three survey seasons. Phylogenetic network analysis, recombination detection using RDP4 software, Bayesian phylogeographic analysis, and population dynamics reconstruction using coalescent-based tools are applied to the sequence dataset. The research tests the central hypothesis that recombination between TYLCV-IL, the dominant strain in the Middle East, and endemic West African tomato-infecting begomovirus species is generating novel mosaic strains with altered host range or virulence in Nigeria. Evidence of recombination is sought specifically at the AC2, AC4, and AV1 genomic regions encoding virulence and silencing suppression determinants. Bayesian phylogeographic analysis reconstructs likely introduction pathways and dates for distinct TYLCV lineages in Nigeria, informing national biosecurity recommendations. Original theoretical contributions include a stochastic recombination-emergence model applicable to begomovirus evolution in West African agricultural landscapes. Keywords: TYLCV, molecular epidemiology, recombination, phylogeography, Nigeria.