Molecular characterization of two divergent variants of sugarcane bacilliform viruses infecting sugarcane in China

Sugarcane bacilliform viruses (SCBV; genus Badnavirus, family Caulimoviridae) are considered economically important pathogens of sugarcane, limiting the exchange of its germplasm worldwide. Similar to other badnaviruses, SCBV are genetically diverse and highly complex, hence the need for a thorough analysis of its genetic structure and diversity. In the present study, we report the molecular characterization of two new SCBV isolates (SCBV-CHN1 and SCBV-CHN2) from China and their genetic variation and phylogenetic relationship with 10 global SCBV isolates. The complete genomes of SCBV-CHN1 and SCBV-CHN2 were determined to be 7764 and 7629 nucleotides (nt) in size, respectively. Both isolates displayed a typical Badnavirus genome organization with three open reading frames (ORFs) but differed in their predicted sizes and putative scanning model for P2 (ORF2-encoded) and P3 (ORF3-encoded) protein translation. Phylogenetic analysis revealed the segregation of complete genomes, individual ORFs, and the RT/RNase H region of the 12 SCBV isolates (two from this study and 10 from the GenBank) into nine phylogroups. SCBV-CHN1 was more closely aligned with SCBV-BB in the SCBV-H clade with both isolates sharing 83 % nt sequence identity and low genetic distance (0.19), based on analysis of the RT/RNase H region. In contrast, SCBV-CHN2 clustered with SCBV-BT into a distinct clade designated as SCBV-G. Recombination analysis identified SCBV-CHN1 and SCBV-CHN2 as putative new recombinant variants arising from putative inter- and intra-specific recombination events. Our findings provide evidence for the presence of distinct genotypic variants of SCBV affecting sugarcane in China and contribute to the understanding of genetic diversity and evolution of sugarcane badnaviruses.