Emergence of new variant of chilli leaf curl virus in North India

The DNA from four leaf samples of Chilli Leaf Curl Virus (ChiLCV) symptomatic chilli plants collected from Varanasi, Mirzapur, Gorakhpur and Mahrajganj districts of Uttar Pradesh, India were isolated. Using coat protein gene (CP) specific primers, highly conserved coat protein regions of four isolates were amplified, sequenced and compared with 25 similar begomovirus sequences obtained from National Centre for Biotechnology Information (NCBD. The CP sequence identity of Varanasi isolate was 86% with Gorakhpur and Mirzapur isolates and 87% with Mahrajganj isolate. Phylogenetic relationships based on CP sequence similarity index grouped 29 sequences into three major clusters. The Gorakhpur, Mahrajganj and Mirzapur isolates were clustered together with tomato leaf curl Joydebpur virus-[Kalyani] isolated from chilli, whereas Varanasi isolate clustered with chilli leaf curl virus-[Amritsar:Papaya] in a separate cluster. Thus, based on very low CP sequence identity between Varanasi isolate (ChILCV-VNS) and other three isolates from Gorakhpur(Ch1LCV-GKP), Mahrajganj (ChiLCV-MAH) and Mirzapur (Ch1LCV-MZP), it is concluded that there is existence of a new variants of begomovirus, ChiLCV, infecting chilli crop in North India.