Cotton leaf curl disease in resistant cotton is associated with a single begomovirus that lacks an intact transcriptional activator protein

Cotton leaf curl disease (CLCuD) is the major limitation to cotton production across Pakistan and northwestern India. The disease first appeared in epidemic form in the 1980s and was shown to be caused by monopartite begomoviruses (seven distinct species have thus far been shown to be involved), frequently as multiple infections. Additionally, the viruses are associated with a specific satellite, the CLCuD betasatellite Cotton leaf curl Multan betasatellite (CLCuMB), which is responsible for the distinctive disease symptoms, and a satellite-like molecule (termed an alphasatellite), the function of which is unclear. During the late 1990s, cotton varieties with conventional resistance were introduced, alleviating losses to cotton production. However, during 2001 a resistance breaking strain of CLCuD (known as the “Burewala” strain) appeared which spread across most cotton producing areas of Pakistan. We have conducted an analysis of the Burewala strain and show that, contrary to the earlier (Multan) strain, it consists of a single begomovirus. The virus is associated with a recombinant betasatellite, derived from the Multan strain, but we were unable to detect the presence of an alphasatellite. Sequence comparisons show the virus to be a new recombinant species, consisting of sequences derived from two of the viruses associated with the first epidemic, for which we propose the name Cotton leaf curl Burewala virus (CLCuBuV). Surprisingly the virus lacks an intact C2 gene, encoding the transcriptional activator protein, which is invariably present in begomoviruses. The possible mechanisms for the selection of a “defective” begomovirus are discussed.