Appearance of Cotton leaf curl disease begomovirus avirulent strains associated with a lower disease incidence in Delhi

A survey of cotton leaf curl disease (CLCuD) in cotton fields of ICAR-IARI, New Delhi was made to study the disease incidence and determine the causal agents of CLCuD-begomovirus species or variants. The CLCuD incidence was estimated to 20.7% in the year 2018 and 26.3% in 2019 and it was observed lower than in the previous years. Five CLCuD-begomovirus isolates collected from infected fields were characterized based on sequence analysis of complete CP gene. The present isolates shared 99–100% nt identity among them, and 71–91% identity among the other CLCuD begomoviruses. Based on phylogenetic analysis, three isolates were members of Cotton leaf curl Multan virus-Rajasthan (CLCuMuV-Ra) and two were Cotton leaf curl Kokhran virus-Burewala (CLCuKoV) strains. Of five CLCuD isolates, four were detected as recombinants showing a common break point at 759-52nt (P=1.768 × 10⁻¹). Thus, the occurrence of present lower degree of CLCuD may be due to the appearance of putative recombinant and avirulent CLCuMuV and CLCuKoV stains.