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Leaf curl disease of chilli (LCDC) is a major constraint in production of chilli in the Indian subcontinent. The objective of this study was to identify the begomovirus species occurring in chilli in Sri Lanka, where the LCDC was initially recorded in 1938. The virus samples were collected from the North Central Province, the major chilli growing region in Sri Lanka with a history of epidemic prevalence of LCDC. The virus could be readily transmitted by Bemisia tabaci to chilli, tomato and tobacco, where vein clearing followed by leaf curl developed. The genome analysis of two isolates obtained from two distantly located fields showing 100 % LCDC, revealed that the DNA-A genome (2754 nucleotides) shared 89.5 % sequence identity with each other and 68.80-84.40 % sequence identity with the other begomoviruses occurring in the Indian subcontinent. The closest identity (84.40 %) of the virus isolates was with Tomato leaf curl Sri Lanka virus (ToLCLKV). The results support that a new begomovirus species is affecting chilli in Sri Lanka and the name Chilli leaf curl Sri Lanka virus (ChiLCSLV) is proposed. Recombination analysis indicated that ChiLCSLV was a recombinant virus potentially originated from the begomoviruses prevailing in southern India and Sri Lanka. The genome of betasatellite associated with the two isolates consisted of 1366 and 1371 nucleotides and shared 95.2 % sequence identity with each other and 41.50-73.70 % sequence identity with the other betasatellite species. The results suggest that a new begomovirus betasatellite, Chilli leaf curl Sri Lanka betasatellite is associated with LCDC in Sri Lanka. This study demonstrates a new species of begomovirus and betasatellite complex is occurring in chilli in Sri Lanka and further shows that diverse begomovirus species are affecting chilli production in the Indian subcontinent.

Leaf curl disease is a serious constraint in tomato production throughout India. Several begomoviruses were reported from different parts of the country; however, identity of begomovirus associated with leaf curl disease in tomato in north-eastern states of India was obscured. In the present study, the complete genome of an isolate (To-Ag-1) of begomovirus was generated from a leaf curl sample collected from Tripura state. However, no DNA-B and betasatellite were detected in the field samples. The genome of To-Ag-1 isolate contained 2,755 nucleotides that shared 94.7 % sequence identity with Tobacco curly shoot virus (TbCSV) and 71.3-90.1 % sequence identity with the other tomato-infecting begomoviruses occurring in the Indian subcontinent. Several inter-specific recombination events among different tomato-infecting begomoviruses from India and intra-specific recombination among different isolates of TbCSV reported from China were observed in the genome of To-Ag-1 isolate. Agroinoculation of the virus alone produced leaf curl symptoms in tomato and Nicotiana benthamiana. However, co-inoculation with a non-cognate betasatellite, Croton yellow vein mosaic betasatellite (CroYVMB) with the TbCSV resulted in increased severity of the symptoms both in tomato and N. benthamiana. Systemic distribution of the TbCSV and CroYVMB was detected in the newly developed leaves of tobacco and tomato, which showed ability of TbCSV to trans-replicate CroYVMB. The present study for the first time provides evidence of occurrence of TbCSV in tomato in north-eastern region of India and showed increased virulence of TbCSV with a non-cognate betasatellite.

Large cardamom (Amomum subulatum), an important spice crop grown in eastern sub-Himalayan mountains of India, is affected by a viral disease commonly known as 'chirke', which is characterised by light and dark green streaks on the leaf lamina. Although chirke has been known to affect large cardamom for over 50 years, its distribution in large cardamom growing regions and aetiology have remained unaddressed. In this study for the first time, distribution of chirke in the major large cardamom growing regions in India has been determined. North Sikkim and eastern region of Darjeeling hills were endemic region with average disease incidence of 19.2-35%, whereas, Mirik region of Darjeeling hills were free from the disease. Suckers, the commonly used planting material, were the major source for spread of the disease. The virus was sap transmissible to the popular large cardamom cultivars Golsey, Ramsey, Swaney and Varlangey and vectored by Rhopalosiphum maidis and Myzus persicae in a non-persistent manner. Flexuous virus particles measuring 625-650 × 12.5 nm were observed consistently associated with the diseased samples. Polyclonal antiserum to the purified virus showed serological affinity with a macluravirus, cardamom mosaic virus (CdMV) associated with a similar disease known as katte disease of small cardamom (Elettaria cardamomum) occurring in southern India. The 3 terminal genome sequence (1776 nucleotides) of the virus was determined, which revealed a close sequence identity and phylogenetic relationships with the members of the genus Macluravirus. The deduced amino acid sequence of putative coat protein (CP) gene showed maximum similarity of 65.7% with the CdMV. Phylogenetic analysis based on CP and 3 UTR showed that the virus was closer to Alpinia mosaic virus, CdMV and Chinese yam necrotic mosaic virus subclade. The results suggest that the virus associated with the chirke disease of large cardamom is a new species under the genus Macluravirus in the family Potyviridae for which the name large cardamom chirke virus (LCCV) is proposed.