South West Indian Ocean islands tomato begomovirus populations represent a new major monopartite begomovirus group.

Biological and molecular properties of Tomato leaf curl Madagascar virus isolates from Morondova and Toliary (ToLCMGV-[Tol], -[Mor]), Tomato leaf curl Mayotte virus isolates from Dembeni and Kahani (ToLCYTV-[Dem], -[Kah]) and a Tomato yellow leaf curl virus isolate from Reunion (TYLCV-Mld[RE]) were determined. Full-length DNA components of the five isolates from Madagascar, Mayotte and Reunion were cloned and sequenced and, with the exception of ToLCMGV-[Tol], were shown to be both infectious in tomato and transmissible by Bemisia tabaci. Sequence analysis revealed that these viruses had genome organizations of monopartite begomoviruses and that both ToLCMGV and ToLCYTV belong to the African begomoviruses but represent a distinct monophyletic group that we have tentatively named the South West islands of the Indian Ocean (SWIO). All of the SWIO isolates examined were apparently complex recombinants. None of the sequences within the recombinant regions closely resembled that of any known non-SWIO begomovirus, suggesting an isolation of these virus populations.