Molecular Detection and Prevalence of Banana Streak Virus in Musa Germplasm Collections in South West Nigeria

Banana Streak Virus (BSV), caused by a complex of badnaviruses integrated into the Musa B genome as endogenous viral elements, poses a unique challenge to Musa germplasm management because integrated sequences can be activated into infectious episomal forms under abiotic stress. The prevalence of BSV in Musa germplasm collections and farmer fields in South West Nigeria has not been systematically documented, creating a phytosanitary blind spot for germplasm distribution programmes. This study used real-time polymerase chain reaction targeting the reverse transcriptase open reading frame to detect and quantify episomal BSV in 110 Musa accessions maintained at the Cocoa Research Institute of Nigeria and in 80 farmer plantain samples from Ogun, Ondo, and Osun States. Immunocapture reverse transcription polymerase chain reaction supplemented the molecular detection. Restriction fragment length polymorphism and sequencing of polymerase chain reaction products identified three BSV species, including BSV-OL, BSV-GF, and a tentatively novel badnavirus species. Episomal BSV was detected in 34 percent of germplasm collection accessions and 21 percent of farmer field samples, with hybrid accessions of AAAB genome constitution showing the highest activation rates. A subset of accessions carrying integrated sequences without detectable episomal virus were stress-challenged with polyethylene glycol-induced drought, which triggered viral activation in four of nine challenged accessions. These findings provide the first comprehensive BSV prevalence dataset for South West Nigeria and recommend mandatory pre-distribution BSV screening of Musa accessions and stress-avoidance protocols in germplasm management. Keywords: Banana Streak Virus, Musa, endogenous viral elements, molecular detection, South West Nigeria.