The full-length genome characterization and diversity of faba bean necrotic stunt virus in Iran

Faba bean necrotic stunt virus (FBNSV) (genus Nanovirus; family Nanoviridae) is a multipartite virus comprising eight circular single-stranded DNA components, each about 1 kb in length. Also, two alphasatellites have often been reported to be associated with FBNSV infection. The only full-length genome sequence of an Iranian FBNSV isolate, FBNSV-[IR;Ka:FB], so far reported is one infecting faba bean (Vicia faba L.). To obtain more information about Iranian isolates of FBNSV (FBNSV-IRs) and their diversity, the full-length genome of four FBNSV isolates and associated alphasatellites obtained from faba bean (two isolates), common bean (Phaseolus vulgaris L., one isolate) and chickpea (Cicer arietinum L., one isolate) were characterized. All genomic components except U4 had the expected size in accordance with the FBNSV genomic sequences published in the GenBank. The component U4 had an additional stretch of 16 nucleotides (nts 765–780) in its non-coding region (NCR). Alphasatellites of the aforementioned isolates showed 98–100% sequence identity. Intra-component sequence analyses of FBNSV-IRs indicated a range of 98 to 100% nt identity between each single FBNSV-IRs component or between their associated alphasatellites. DNA-M and DNA-U2 exhibited the highest value of diversity, sharing 98–99% identity. Phylogenetic analyses indicated that FBNSV-IRs were clustered with a Moroccan isolate and some Azerbaijani isolates of FBNSV forming a clade distinct from Ethiopian isolates. Inter-component sequence analyses of NCRs revealed the DNA-S and DNA-U4 subgrouped together in all FBNSV-IRs isolates except the chickpea isolate in which NCRs of DNA-S and DNA–U4 formed separate subgroups.