Study of genetic variability and emerging strains of Okra enation leaf curl virus: increasing risks to okra production in India

Abstract

Okra enation leaf curl disease (OELCuD), caused by Okra enation leaf curl virus (OELCuV) and transmitted by whiteflies (Bemisia tabaci), significantly threatens okra cultivation in India. This study conducted a comprehensive survey (2020-2022) across seven Indian states, recording disease incidence ranging from 14.03% to 67.57%. Polymerase chain reaction (PCR) using coat protein gene-specific primers confirmed the presence of OELCuV in symptomatic plants, amplifying a ~ 750 bp fragment. Full-genome characterization of five isolates from different geographic regions using rolling circle amplification (RCA) revealed high genetic variability, with nucleotide identities ranging from 92.2% to 96.5% compared to existing OELCuV DNA-A sequences. Two novel strains were identified in Meerut (Uttar Pradesh) and Viluppuram (Tamil Nadu), meeting the International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria. Phylogenetic and recombination analyses demonstrated that these strains form a unique cluster with recombinant features, particularly in the AC1 coding region, which is under purifying selection. The findings underscore the urgent need to monitor the genetic variability and spread of OELCuV to protect okra cultivation from evolving viral threats.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-025-01578-2.

Keywords: Begomovirus; DNA-A; Genetic diversity; Okra; Okra enation leaf curl virus; RCA.