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Saffron (Crocus sativus L.), a highly valuable crop famous for the unique taste, aroma, colour and medicinal properties of the stigmas, is widely cultivated in Iran. During 2011–2016, a total of 965 samples were randomly collected from six important saffron growing provinces of Iran to test for the presence of viruses. Assays revealed the presence of a distinct species of the genus Potyvirus, which has been tentatively named saffron latent virus (SaLV). Phylogenetic analysis of the SaLV complete genome sequence, 9,693 nucleotides (nt) excluding poly(A) tail, revealed that this virus grouped into Bean common mosaic virus subgroup in the genus Potyvirus with the closest relative being Bean common mosaic necrosis virus. A number of distinct plant species were evaluated for the host range of SaLV; Chenopodium amaranticolor and Chenopodium quinoa were found to be systemic hosts of SaLV. There were no nucleotide sites that indicated any recombination events, and the analysis of the coat protein (CP) sequence of 50 samples, collected from different geographical origins, did not show spatially structured diversity. Overall, our data shows strong negative selection pressure in CP, estimated by nucleotide sequences. The relevance of SaLV for saffron production in Iran remains to be established.

Iris belongs to the Iridaceae family. It is one of the most important pharmaceutical and ornamental plants in the world. To assess the potyvirus incidence in natural resources of iris plants in Iran, Antigen Coated-Plate ELISA (ACP-ELISA) was performed on 490 symptomatic rhizomatous iris leaf samples, which detected the potyvirus in 36.7% of the samples. Genomic 3' end of one mechanically non-transmitted potyvirus isolate, comprising a 3' untranslated region (390 bp) and C-terminus of the coat protein (CP) gene (459 bp), was amplified by reverse transcription polymerase chain reaction (RT-PCR), which was ligated into pTG19-T vector.The nucleotide sequence of amplicons was compared with related sequences, using Blastn software available at NCBI GenBank, and showed the highest similarity with Iris severe mosaic virus (ISMV) isolates. The nucleotide and deduced amino acid sequence of the CP C-terminus region was more than 83% identical with other ISMV isolates, therefore this isolate was designated as ISMV-Ir. This new ISMV isolate is closely related to the Chinese ISMV-PHz in phylogenetic analysis, based on the partial nucleotide and deduced amino acid sequence of the CP region. This is the first report of ISMV occurrence on Iris spp. in Iran.