Identification and genomic characterization of a novel tomato leaf curl virus infecting Alternanthera ficoidea in Tamil Nadu, India

Begomoviruses are single-stranded DNA viruses that cause significant yield losses in economically important crops and are transmitted mainly by the whitefly, Bemisia tabaci. Weeds frequently serve as alternate reservoirs for viruses when major crop hosts are not available, thereby promoting virus persistence and spread. During a survey in 2024 in tomato-growing regions of Coimbatore, Tamil Nadu, Alternanthera ficoidea plants exhibiting yellow-green mosaic and yellow vein mosaic symptoms were observed. PCR amplification using begomovirus specific primers PARIv772/PALIc1960 confirmed the presence of begomoviruses in all symptomatic samples, whereas healthy plants showed no amplification. The remaining sequence of the DNA-A genome was amplified using primer pairs GKToLCV-F/GKToLCV-R and PAL1v1978/PAR1c715. BLASTn analysis of the consensus sequence (2764 bp) revealed a 95.12 % nucleotide identity with tomato leaf curl Kerala virus (ToLCKeV) isolate OQ128343. Subsequent investigation of the ToLCKeV isolate found in this study (GenBank accession no: PQ901324) showed significant genetic variation and recombination, with the potential recombination parents being tomato leaf curl Sri Lanka virus (PP935251) and tomato leaf curl New Delhi virus (MK883715). This study provides the first report of ToLCKeV infecting A. ficoidea, suggesting its role as an alternative host and potential reservoir during off seasons, contributing to the persistence and spread of this virus. These findings underscore the importance of weed management in integrated approaches to manage leaf curl diseases caused by begomoviruses.