Virus Research 153 (2010) 161–165 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres Short communication Cotton leaf curl disease in Sindh province of Pakistan is associated with recombinant begomovirus components Luqman Amrao, Sohail Akhter, Muhammad Nouman Tahir, Imran Amin, Rob W. Briddon, Shahid Mansoor ∗ Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang Road, Faisalabad, Punjab 38000, Pakistan article info Article history: Received 27 October 2009 Received in revised form 14 June 2010 Accepted 4 July 2010 Available online 3 August 2010 Keywords: Geminiviruses Begomoviruses Recombination Cotton abstract Cotton leaf curl disease (CLCuD) is a devastating disease of cotton causing severe losses to cotton across the Punjab province of Pakistan and northeastern India. Although the disease has been reported as occurring sporadically in Sindh province, Pakistan, this has not caused significant losses. However, in the last few years the disease has become more significant in Sindh province. CLCuD is caused by begomoviruses in association with a disease-specific symptom determining satellite (Cotton leaf curl Multan betasaellite [CLCuMB]) and, in some cases, a non-essential alphasatellite (the function of which remains unclear). These components were cloned from six samples collected in Sindh. Analysis of the full-length sequences of six begomovirus clones showed one to be an isolate of Cotton leaf curl Kokhran virus (CLCuKV), a virus previously shown to be associated with CLCuD in the Punjab, whereas the other five clones showed less than ∼90% nucleotide sequence identity to several known begomoviruses associated with CLCuD. We take this to indicate that these are isolates of a newly identified begomovirus, for which we propose the name Cotton leaf curl Shahdadpur virus (CLCuShV). Closer inspection of the sequence of CLCuShV showed it to have a recombinant origin. For only two of the cotton samples was the presence of an alphasatellite detected. The sequences of clones of these alphasatellites indicate them to be newly identified species. A betasatellite was shown to be present in all six plants examined and sequence analysis of seven full- length clones indicated that two types of CLCuMB are present in Sindh and both are recombinant. These results indicate that the virus complex causing CLCuD in Sindh is distinct from that in the adjacent Punjab province. Possible reasons for these differences are discussed. © 2010 Elsevier B.V. All rights reserved. Cotton leaf curl disease (CLCuD) is a severe disease of cotton and several other malvaceous plant species that is transmitted by the whitefly (Bemisia tabaci Gennadius) and causes severe yield losses cotton in Pakistan and northwestern India (Mansoor et al., 2003a). CLCuD was first observed near the city of Multan, Pakistan, in 1967 (Hussain and Ali, 1975) and became epidemic in the late 1980s, causing an estimated 5 billion US Dollars worth of losses to the economy of Pakistan during the five years from 1992 to 1997 (Briddon and Markham, 2001). During the late 1990s the intro- duction of CLCuD resistant/tolerant cotton varieties in Pakistan, produced by conventional breeding/selection, reduced the losses due to the disease. However, in 2001 it became evident that the resistance had been broken, as previously resistant varieties were exhibiting symptoms of CLCuD (Mansoor et al., 2003c; Mahmood et al., 2003). While the epidemic of CLCuD during the 1990s caused heavy losses in the Punjab, the southern Sindh province remained largely ∗ Corresponding author. Tel.: +92 41 2651475; fax: +92 41 2651472. E-mail address: shahidmansoor7@gmail.com (S. Mansoor). unaffected. Although several distinct begomoviruses were reported from Sindh affecting various crops, ornamental plants and weeds, none were identified in cotton (Sanz et al., 2000). These bego- moviruses and associated whitefly biotypes identified were distinct from those occurring in the Punjab (Simón et al., 2003). The disease was reported from Sindh on cotton in 1997–1998, although losses were not significant in comparison to those experienced in the Pun- jab, and the etiology was not investigated (Mansoor et al., 1998). However, since 2003–2004 the disease has appeared in central and lower Sindh, causing substantial yield losses, and this coincided with introduction of cotton varieties not approved by the Govern- ment authorities for cultivation, since they are highly susceptible to CLCuD. CLCuD on the Indian subcontinent is caused by a complex of one or more monopartite begomoviruses (genus Begomovirus, family Geminiviridae), six of which have been identified so far, in associ- ation with an essential, disease-specific DNA satellite component, Cotton leaf curl Multan betasatellite (CLCuMB; Briddon et al., 2001; Briddon, 2003; Mansoor et al., 2003b). Betasatellites are a diverse group of recently identified, symptom modulating, single-stranded DNA satellite molecules that encode a dominant symptom deter- 0168-1702/$ – see front matter © 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.virusres.2010.07.003