First report of Tomato leaf curl Joydebpur virus infecting chilli in India

Symptoms of mild yellowing, severe leaf curling, leaf distortion, stunting and blistering (Fig. 1) were observed in June, 2004 in chilli (Capsicum annuum) fields in Ludhiana, Punjab State, India. DNA was extracted from 3 such symptomatic plants and tested for the presence of begomoviral DNA-A, DNA-B and associated satellite DNA by polymerase chain reaction (PCR) using previously described primer pairs (Shih et al., 2003). In all 3 samples, the expected 1.4kb DNA-A fragment for begomovirus was obtained and DNA-beta of 1.3 kb was detected using the Beta01/Beta02 primers (Briddon et al., 2002). DNA-B was not detected.

Based on the sequence of the 1.4 kb DNA-A product, specific primers were designed to complete the DNA-A sequence. The DNA-A consisted of 2767 nucleotides (DQ673859) and was found to contain the geminiviral conserved nanosequence TAATATTAC in the intergenic region. BLAST analysis was conducted with geminivirus sequences available in the GenBank database and MegAlign software (DNASTAR, Madison, WI) was used for further comparisons. Highest full length DNA-A sequence identity of 90.8% was found with a recently described tomato begomovirus from India (DQ629103). However, the genome organization of the chilli begomovirus from Punjab is similar to that of Tomato leaf curl Joydebpur virus (ToLCJV, AJ875159) from Bangladesh (Maruthi et al., 2006), with which it shares 90.3% sequence identity. Both of these viruses contain the V1, V2, C1, C2, C3 and C4 predicted opening reading frames (ORFs), and an additional predicted ORF C5 of 849 nt (282 amino acids) on the complementary strand which is absent in DQ629103. Only low sequence identities (ranging from 73-80%) were obtained with other incompletely sequenced (771-1087 nt) Indian chilli begomoviruses reported from Lucknow, Bahraich and Kanpur (DQ119573, AY883570, DQ431845, DQ431846, DQ431844 and DQ141676), which are all tentative strains of Tomato leaf curl New Delhi virus(ToLCNDV).

On the basis of DNA-A sequence analysis, the ICTV species demarcation of 89% sequence identity and genome organization, the Punjab chilli begomovirus is a provisional strain of ToLCJV described from tomato in Bangladesh. To our knowledge, this is the first report of ToLCJV naturally occurring on chilli in India. Besides the two chilli infecting begomoviruses mentioned above, there seems to be at least one more distinct begomovirus in India. This partially-sequenced (995 nt, DQ445255) begomovirus (Senanayake et al., 2006) is considered a tentative strain of the Chilli leaf curl virus from Pakistan (AF336806) and shares only 82% sequence identity with chilli begomovirus from Punjab. The presence of 3 distinct chilli begomoviruses needs to be considered for developing stable begomovirus virus resistant chilli cultivars for India.