First report of tomato chlorosis virus (ToCV) and detection of other viruses in field-grown tomatoes in North-Western region of India.

Tomato crop is known to be infected by large number of viruses across the globe causing severe losses in its yield. Accurate information on the distribution and incidence of different viruses is essential to implement virus control strategies. This study provides information on prevalence and distribution of different viruses infecting tomato crop in North-western region of India. Leaf samples of 76 symptomatic tomato and 30 symptomatic and asymptomatic plants of Chenopodium sp. (weed) were collected from eight villages. DAS-ELISA and/or RT-PCR/PCR were used to detect occurrence of nineteen viruses and one viroid in tomatoes. Nine viruses viz. cucumber mosaic virus, groundnut bud necrosis virus, potato virus M, potato virus S, potato virus X, potato virus Y, tomato chlorosis virus, tomato leaf curl New Delhi virus and tomato mosaic virus were detected in 58 of 76 tomato samples. Detection of viruses was confirmed by cloning of specific amplicons followed by sequencing and submission of sequences to the GenBank database. None of the targeted pathogens were found in collected weed samples. Tomato leaf curl New Delhi virus (ToLCNDV) was the most prevalent virus (64.47%) followed by potato virus Y (PVY) (23.68%). Double, triple, quadruple and quintuple infections were also noticed. Phylogenetic analysis of nucleotide sequences was also carried out. Nine viruses infecting tomato crop from North-western region of India were detected. ToLCNDV was most prevalent with highest incidence. To the best of our knowledge, this is the first report of ToCV on tomato from India.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-022-00801-y.