Identification and molecular characterization of Faba bean necrotic stunt virus, a new nanovirus in legume fields in Iran

Viruses inducing yellowing and stunting syndrome in legumes including nanoviruses cause losses in several species particularly broad bean in Iran. One of the most damaging nanoviruses in legumes is Faba bean necrotic yellows virus (FBNYV). To detect nanoviruses in infected fields, symptomatic plants including broad bean and common bean were collected from Fars and Khuzestan provinces, respectively, in 2014-2015. DNA was extracted and subjected to PCR, cloning and sequencing using specific nanovirus primers. Four fragments of a nanovirus genome including DNA-R, DNA-M, DNA-U1 and DNA-U2 were amplified and sequenced. The results of sequencing showed that these fragments belong to Faba bean necrotic stunt virus (FBNSV). This is the first report of this virus in Iran. Sequence comparison of aforementioned genomic fragments with corresponding DNA fragments of FBNSV isolates and other nanoviruses for which nucleotide sequence information was available in GenBank indicated that both Iranian isolates of FBNSV are most similar to Azerbaijani isolates of this virus. Phylogenetic analysis showed that FBNSV is closer to FBNYV and Milk vetch dwarf virus (MDV) than to subterranean clover stunt virus. Dendrograms obtained by phylogenetic analyses of DNA-R and DNA-U2 sequences indicated that FBNSV was closest to FBNYV while in those obtained for DNA-M and DNA-U1, FBNSV was closer to MDV and Faba bean yellow leaf virus than to other nanoviruses. For all DNAs characterized in this study, FBNSV isolates from Azerbaijan, Ethiopia, Morocco and Iran formed a separate group distinct from FBNYV isolates. It seems that FBNSV and FBNYV are distinct nanovirus species.