Characterization of Capsicum chlorosis virus infecting chilli (Capsicum annuum. L) in southern India

During a field survey in Tamil Nadu (2014-16), chilli plants showing chlorotic and necrotic ring spots and necrotic streaks on leaves and stems were observed. Disease incidence ranged between 5 and 50% among five surveyed districts. RT-PCR assay using species specific primers detected 25% of samples infected with Capsicum chlorosis virus (CaCV) and 50% of samples infected with groundnut bud necrosis virus (GBNV). For simultaneous detection of CaCV and GBNV, duplex RT-PCR (dRT-PCR) has been validated. Complete nucleotide sequences of L-RNA, M-RNA, NSs and N genes of CaCV isolate (CaCV-TN-CBE) were determined.The L-RNA constitutes 8913 nt, M-RNA of 4848 nt, NSs gene of 1320 nt and the N gene of 828 nt. Sequence analysis showed that CaCV-TN-CBE isolate is closely related to China isolate based on L- and M- RNA whereas with Taiwan isolate based on S RNA. Also, based on nucleotide identity and phylogenetic analysis CaCV-TN-CBE isolate is different from the previously reported isolate from India. Further nucleotide sequences of L- and S- RNA have shown recombination events. This study suggested the isolate infecting chilli in Tamil Nadu might have evolved by undergoing recombination and reassortment evolutionary mechanisms.

Automated summary

The field survey in Tamil Nadu revealed the infection of chilli plants by CaCV and GBNV, with the CaCV-TN-CBE isolate showing potential evolution through recombination and reassortment mechanisms. The nucleotide sequences of CaCV-TN-CBE isolate were determined, demonstrating close relation with China and Taiwan isolates based on different RNA segments.