Abstract
Plant viruses are major constraints to chili (Capsicum annuum L.) production, with chili leaf curl disease (ChiLCD) representing one of the most destructive viral diseases in South and Southeast Asia. ChiLCD is primarily caused by begomoviruses (family Geminiviridae) and their associated betasatellites, whose evolution is strongly shaped by recombination and mixed infections. In this study, chili plants exhibiting typical leaf curl symptoms were collected from the Kottayam district of Kerala, India, and subjected to detailed molecular characterization. Rolling circle amplification (RCA), cloning, and sequencing revealed the presence of chili leaf curl Vellanad virus (ChiLCVeV) in association with tomato leaf curl Joydebpur betasatellite (ToLCJoB). Comprehensive sequence analysis confirmed conserved geminiviral features, while phylogenetic reconstruction validated the taxonomic placement of both components. Importantly, recombination analyses identified multiple recombinant regions in both ChiLCVeV and ToLCJoB, indicating independent and dynamic evolutionary histories of the helper virus and its associated satellite. To the best of our knowledge, this study provides the first evidence of a natural association between ChiLCVeV and ToLCJoB, and demonstrates that recombination-driven evolution contributes to the emergence of novel begomovirus-betasatellite complexes infecting chili. These findings highlight the role of recombination in shaping begomovirus diversity and underscore the potential of such recombinant complexes to drive disease emergence and spread in chili-growing regions of India. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13337-026-00954-0.