Wisterias host a diverse range of viruses, including badnaviruses (family Caulimoviridae). To date, only one complete genome of a badnavirus, wisteria badnavirus 1 (WBV1, species Badnavirus wisteriae), has been characterized worldwide. In this study, a new badnavirus, tentatively named wisteria badnavirus 3 (WBV3), was identified in Iran from Wisteria sinensis affected by wisteria mosaic disease. The virus was discovered through high-throughput sequencing and confirmed by polymerase chain reaction and Sanger sequencing. Its genome, which follows a typical badnavirus organization, is 6,016 nucleotides long. Among its open reading frames (ORFs), two major ORFs (ORF3 and ORF4) were sequenced, with ORF4 overlapping the end of ORF3. ORF3 encodes a 1,909-amino acid polyprotein and contains putative movement protein, capsid protein, zinc finger domain, pepsin-like aspartate protease, reverse transcriptase, and RNase H conserved motifs. ORF4 encodes a 152-amino acid protein that shares 72.5% nucleotide and 74.3% amino acid sequence identity with WBV1 ORF4. BLAST results showed that WBV3 shares the highest nucleotide (69–74%) and amino acid (73–79%) identity with WBV1 and pagoda yellow mosaic associated virus (PYMaV, species Badnavirus tessellostyphnolobii), among extant badnaviruses. These values are below the 80% nucleotide sequence identity threshold proposed by ICTV for species demarcation in the genus Badnavirus, suggesting that WBV3 represents a novel species. Phylogenetic trees based on RT/RNase H and ORF3 sequences placed WBV3 within the genus Badnavirus, clustering it in a clade with WBV1 and PYMaV, but forming a distinct sub-branch. Notably, all WBV3-positive samples were also co-infected with wisteria vein mosaic virus (WVMV), suggesting a potential association between the two viruses. This study reports the identification and partial genome characterization of WBV3, providing a basis for future research on its molecular evolution, interaction with WVMV, and potential relevance to diagnostics and disease management.

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