Molecular Characterization and Genetic Diversity of Broad Bean Wilt Virus 2 (BBWV-2) from Catharanthus roseus

Small RNA deep sequencing (sRNA-seq) is a powerful tool for detecting known and novel plant viruses by analyzing virus-derived small RNAs (vsRNAs). In this study, the complete genome of Broad Bean Wilt Virus 2 (BBWV-2) was recovered from Catharanthus roseus leaf samples using sRNA-seq, followed by bioinformatics analysis. The Genome Detective Tool, an online bioinformatics platform, identified both RNA1 (5.952 kb) and RNA2 (3.509 kb) of the BBWV-2 form raw data. RNA1 and RNA2 showed 78.8% and 78.1% nucleotide identity, and 88.2% and 87.4% amino acid identity, respectively, with their corresponding reference sequences. Comparative sequence analysis identified multiple mutations, comprising 8 and 6 indels distributed across the full-length sequences of RNA1 and RNA2, respectively, along with 1027 and 690 single-nucleotide substitutions localized within their coding regions. Analysis of the 5' untranslated regions (UTRs) identified five distinct motifs from both RNAs. Structural modeling suggested that RNA2 exhibits greater flexibility than RNA1, which may influence its biological functions. Phylogenetic analysis placed the Indian isolate within Group I, clustering with isolates from South Korea, China, the USA, and Germany, without clear host or geographic clustering. This study provides the first complete sequences of BBWV-2 RNA1 and RNA2 from India and represents the first global report of its occurrence in C. roseus. Further, these findings enhance our understanding of the molecular diversity and evolutionary dynamics of BBWV-2.