In-depth CIDER-Seq profiling reveals a novel alphasatellite associated with Banana bunchy top virus from Vietnam

BEJERMAN, NICOLÁS; GOLYAEV, VICTOR; SYED SHAN-E-ALI ZAIDI; HA VIET CUONG; SWENNEN, RONY; VANDERSCHUREN, HERVE

Congreso; International Symposium on ssDNA Viruses; 2022

Banana bunchy top virus (BBTV, genus Babuvirus, family Nanoviridae) is a multipartite virus composed of 6 circular single-stranded DNA components. BBTV is the most damaging viral agent of bananas and plantains. Satellite molecules, named as alphasatellites are commonly found associated to BBTV, and four species of alphasatellites associated to this virus have so far been identified. Satellites are usually able to replicate themselves but rely on the associated virus for movement, encapsidation and plant-to-plant transmission. Despite their regular presence in cultivated and wild bananas, the role of alphasatellites in BBTV infection remains to be characterized. We took advantage of the recently developed circular DNA enrichment sequencing (CIDER-Seq) method to profile BBTV genomes and associated molecules in three samples collected in three different geographical regions from Vietnam. Our methodology allows a rapid and cost-effective generation of full genomes from circular DNA viruses. Our approach was instrumental to generate multiple complete genomic sequences of BBTV in samples contrasting for virus symptoms (two samples from banana plants displaying severe symptoms (samples #3 and #5) and one from banana plants with mild symptoms (sample #4)). Bioinformatic analysis revealed the presence of the six core components as well as two previously reported BBTV alphasatellites species, BBTV alphasatellite 2 and 3 which belong to the genus Muscarsatellite, subfamily Petromoalphasatellitinae. Those alphasatellites were present in all tree samples. Additionally, a novel alphasatellite was identifed in samples #4 and #5. Phylogenetic analysis revealed that the novel alphasatellite clusters with a recently discovered alphasatellite associated to BBTV in samples from DR Congo. The later belongs to a novel genus, proposed to be named as Banaphisatellite, within the subfamily Nanoalphasatellitinae of the family Alphasatellitidae. Interestingly, the novel alphasatellite detected in the samples from Vietnam is well distant from BBTV alphasatellites previously identified in Asia and is related to a BBTV alphasatellite identified in Africa. CIDER-Seq allowed us to obtain for each sample plenty of full-length highly accurate BBTV core components and alphasatellites which allowed an in-depth analysis of their diversity both within each sample and between the three samples. Taken together our finding shows that CIDER-Seq is a powerful method to profile the diversity of circular DNA viruses and their associated circular DNA molecules as well as to facilitate their taxonomy classification and evolutionary studies.