Chilli leaf curl Palampur virus is a distinct begomovirus species associated with a betasatellite




Capsicum frutescens (chilli) plants exhibiting leaf curl symptoms, collected from Palampur, Himachal Pradesh region of India, were found associated with a begomovirus and a betasatellite-like molecule. Viral DNA was amplified, cloned and sequenced. The begomoviral genome and the betasatellite consisted of 2775 and 1376 nucleotides respectively. The virus appeared to be monopartite. The genome sequence had <87·9% identity with all other begomovirus sequences, below the threshold for species demarcation, suggesting that the isolate represents a distinct species for which the name Chilli leaf curl Palampur virus (ChiLCPaV) is proposed. Infectious clones consisting of partial tandem repeats of the viral genome (1·9-mer) and the betasatellite (1·7-mer) were constructed in the binary vector pCAMBIA-1300 and agroinoculated to chilli and Nicotiana benthamiana. The viral clone did not produce leaf curl symptoms when inoculated alone but the plants were stunted compared to controls. Typical leaf curling and stunting symptoms were observed when the viral clone was inoculated with the betasatellite. In a phylogenetic analysis with other closely related begomoviruses, the new sequence grouped with an isolate of Papaya leaf curl virus-[Pakistan:2008] from Rhynchosia capitata and Tomato leaf curl New Delhi virus-[India:2006] from tomato. The betasatellite showed most identity (94%) with an isolate of Chilli leaf curl betasatellite from Pakistan. Using the rdp3 recombination detection program, a recombination event involving Croton yellow vein mosaic virus-[India:2007] as a major parent and Tomato leaf curl Karnataka virus-[India:2007] as a minor parent was detected in the ChiLCPaV sequence. No significant recombination event was detected in the betasatellite sequence.