Molecular characterization of three Faba bean necrotic yellows virus (FBNYV) isolates, originated from chickpea in Iran

Yellowing is one of the most prevalent symptoms in chickpea fields, worldwide and Iran. Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae) is associated with the yellowing symptoms in the chickpea fields. During the survey of the Lorestan and Kermanshah provinces in May 2015-2016, chickpea plants showing yellowing symptoms were collected and total DNAs were extracted. The samples were checked for nanovirus infection by PCR, using nanovirus-specific degenerate primers. Total DNA preparations from the nanovirus-positive samples were used for RCA, using φ29 polymerase and restriction endonuclease Aat II digests yielding products of ~1kb corresponding to linearized nanovirus DNA components. FBNYV genomic components were amplified using RCA products and specific primers of eight different U1, M, N, C, S, R, U2, and U4 components. The amplified fragments were purified and sequenced. Nucleotide sequences of the eight different components of three Iranian isolates of FBNYV (Lor-28, Lor-1, and Ker-21) were compared with FBNYV sequences in GenBank. Sequence comparison indicated that Iranian isolates of FBNYV are most similar to Azerbaijan isolates of FBNYV: FBNYV-[AZ; 12], and FBNYV-[AZ; 13.5]. Phylogenetic analyses of nucleotide and deduced amino acid sequences of DNA-S, C, and U1 revealed that Iranian FBNYV isolates clustered with Azerbaijan isolate FBNYV-[AZ;12 ](group II), while DNA-R, DNA-M, DNA-N, DNA-U2, and DNA-U4 clustered with FBNYV-[AZ; 13.5], (group I). Considering the genomic differences between two Azerbaijan isolates, which can be expected among Iranian isolates. These results may provide evidence of the reassortment occurrence among Iranian and Azerbaijan FBNYV isolates.