Several isolates of Banana bunchy top virus (BBTV) have been reported worldwide. They are members of either the Pacific Indian Ocean (PIO) or the South East Asian (SEA) group. However, there is only one completely sequenced isolate published from the northeastern part of India till date. Therefore, we obtained the complete sequences of all the six genomic components of a BBTV isolate from the northeastern Indian state of Assam. The isolate was named as BBTV-As-JOR, and its genome showed the presence of the reported conserved motifs. Nevertheless, like other Indian BBTV isolate, the major common regions in DNA-R and DNA-U3 of BBTV-As-JOR had deletions of 26 and 36 nucleotides, respectively. Phylogenetic analysis based on 312 sequences of BBTV DNA-R classified BBTV-As-JOR as a member of the PIO group; similar phylogenetic patterns were also found with the other genomic segments. Analysis with Recombination Detection Program revealed two intra-segment recombination events involving DNA-C of geographically distinct BBTV isolates. On the other hand, DNA-U3 and DNA-N were found to be involved in few inter-segment recombination events in BBTV-As-JOR. This is the first report of a BBTV isolate from Assam and also of another PIO isolate from the region (the other isolate, BBTV-Umiam, was much closer to the SEA group). The detected possible recombinants could emerge as a major future threat for the banana cultivations in the country considering the asexual nature of propagation of banana crop.
Keywords: BBTV; Banana bunchy top nanovirus; Pacific Indian Ocean; Recombination; South East Asian.