ORIGINAL ARTICLE A survey of geminiviruses and associated satellite DNAs in the cotton-growing areas of northwestern India Valerio Zaffalon • Sunil Kumar Mukherjee • Vanga Siva Reddy • Jeremy R. Thompson • Mark Tepfer Received: 3 August 2011 / Accepted: 17 November 2011 Ó Springer-Verlag 2011 Abstract Severe symptoms of cotton leaf curl disease (CLCuD) are caused by the association of a single-stranded circular DNA satellite (betasatellite) with a helper begomovirus. In this study, we analyzed 40 leaf samples (primarily cotton with CLCuD symptoms and other plants growing close by) from four sites between New Delhi and the Pakistan/India border, using rolling-circle amplification (RCA) and PCR. In total, the complete sequences of 12 different helper viruses, eight alphasatellites, and one betasatellite from five different plant species were obtained. A recombinant helper virus molecule found in okra and a novel alphasatellite-related DNA from croton are also described. This is the first report of the presence of both DNA components (helper virus and betasatellite) associated with resistance-breaking CLCuD in India, and it highlights the need for further work to combat its damage and spread. Introduction Geminiviruses and their associated satellites present mod- ern agriculture with important challenges, inducing a variety of diseases in tropical and subtropical regions [26, 31, 35]. Economic losses caused by the geminiviral cotton leaf curl disease (CLCuD) are some of the most significant caused by any plant virus. In the Indian subcontinent it was first identified around the Pakistani city of Multan in 1986 [17] and has since spread rapidly; in 1991 in the Pakistani Punjab, the disease affected 14,000 ha out of a total growing area of 2.5 million ha and two years later had spread to affect an overall area of 202,000 ha, resulting in a reduction in cotton yield of 29% [7]. In the following years, the disease continued to spread in the Punjab and to the surrounding Pakistani regions, and in 1993 it was first reported across the border in India, in Sriganganagar, Rajasthan [20]. Between 1992 and 1997, the economic loss due to CLCuD in Pakistan was calculated to be about 5 billion US dollars [7]. The establishment of the disease was assumed to be principally due to the introduction of high- yielding, highly CLCuD-susceptible varieties of cotton (Gossypium hirsutum) in place of the native, resistant cotton species G. arboreum, a problem only temporarily addressed by the development of new tolerant/resistant Electronic supplementary material The online version of this article (doi:10.1007/s00705-011-1201-y) contains supplementary material, which is available to authorized users. V. Zaffalon  J. R. Thompson  M. Tepfer Plant Virology Group, ICGEB Biosafety Outstation, Via Piovega 23, 31056 Ca’ Tron di Roncade, Italy V. Zaffalon Department of Environmental Agronomy and Crop Science, University of Padova, Viale dell’Universita ` 16, 35020 Legnaro, Padova, Italy S. K. Mukherjee  V. S. Reddy Plant Biology Group, ICGEB Campus, Aruna Asaf Ali Marg, 110 067 New Delhi, India J. R. Thompson (&) Department of Plant Pathology and Plant-Microbe Biology, Plant Science 334, Cornell University, Ithaca, NY 14853, USA e-mail: jrt36@cornell.edu M. Tepfer Institut Jean-Pierre Bourgin UMR1318, INRA-Versailles, 78026 Versailles Cedex, France M. Tepfer (&) INRA, UR407 Pathologie Ve ´ge ´tale, 84140 Montfavet cedex, France e-mail: Mark.Tepfer@versailles.inra.fr 123 Arch Virol DOI 10.1007/s00705-011-1201-y