A new tomato leaf curl virus from the Seychelles archipelago

In July 2004, a survey of plants with virus disease symptoms was conducted in the Seychelles archipelago on Mahé Island, located north of Madagascar. A small number of leaf samples showing curling symptoms were collected from bean (Phaseolus vulgaris), pepper (Capsicum annuum) and tomato (Lycopersicon esculentum). Leaf extracts were tested for the presence of begomoviruses by polymerase chain reaction (PCR), using two sets of degenerate primers designed to amplify portions of the coat protein (CP) gene of the DNA A component. The first primer set (AV494 and AC1048) amplified the core region of the CP gene (approximately 550bp) (Wyatt & Brown, 1996). The second primer set (VD360 and CD1266) amplified another fragment representing more than 90% of the CP gene (approximately 900 bp) (Delatte et al., 2005). No PCR products were obtained from pepper or bean leaf extracts. For two tomato samples, PCR products of the expected size were obtained with both sets of primers. One product, obtained with the primer set VD360-CD1266 (924bp), was cloned and sequenced (EMBL accession No. AM259286). No PCR products were obtained using degenerate primers designed for begomovirus DNA B or DNA β (Delatte et al., 2005). The most significant nucleotide sequence identities (NCBI BLASTn) were 88% with Tomato leaf curl Mayotte virus from Dembeni (ToLCYTV-[Dem]; AJ865341) and 83% with Pepper yellow vein virus from Mali (AY502935), Tomato leaf curl Madagascar virus isolates (AJ865339 and AJ865338) and a South African cassava mosaic virus isolate (AF155806). Analysis (DNAMAN, Lynnon BioSoft) using the 522bp core CP sequences, previously used to provide provisional identification of begomoviruses (Brown et al., 2001), showed between 88% and 89% nucleotide sequence identity with ToLCYTV isolates (AJ865339 and AJ865340) and between 85 and 86% identity with Tomato yellow leaf curl virus isolates from Réunion Island (TYLCV-[RE], AM234066; and TYLCV-Mld[RE], AJ865337). These results suggest the presence of a new tomato begomovirus in the Seychelles archipelago; genetically related to the ToLCYTV isolates and so to the African tomato monopartite begomoviruses previously identified in the South West Islands of the Indian Ocean (Delatte et al., 2005). The new virus is tentatively named Tomato leaf curl Seychelles virus (ToLCSCV).