Alfalfa mosaic virus (AMV) belongs to the genus Alfamovirus , in the family Bromoviridae , occurs worldwide. The virus can naturally infect many herbaceous and some woody plant hosts (150 species in 22 families) such as alfalfa, potato, bean, pepper, pea, soybean, basil and causes severe losses. Alfalfa mosaic virus is transmitted by aphids, pollen, seed and dodder. Since there are no available molecular data for AMV isolates in Iran. During a survey in 2011 and 2012, to detect and determine certain molecular properties of AMV, leaf samples showing viral symptoms were collected from alfalfa, potato, bean, soybean, pepperandbasil crops in IsfahanandCharmahalva bakhtiariprovinces. Total RNA was extracted from leaf samples and subjected to RT-PCR using specific primer pairs of AMV (AlMV-3pr/AlMV-5pr, AMV-F2/AMV-R2). Several samples amplified expected sizes of 901 bp and 669 bp in RT-PCR, respectively. The amplicons of 13 isolates including ADA4 (Daran-alfalfa), AK2 (Karkhane ghand-alfalfa), SMZ (Daran-potato), PSH (Shahrkord-potato), 13LM (Shahrkord-bean), PPF (Daran-pepper), 4 (Dorcheh-pepper), CLD (Dorcheh-clover), LPK (Kelishad-tomato), PKH (Khomeini shahr-pepper), TBN (Daran-cowpea), WD (Dastgerd-chenopodium) and WS (Dastgerd-weed) representing different hosts and regions were cloned and sequenced. The BLAST search revealed high homology between the Iranian isolates and other AMV isolates available at GenBank. Multiple alignment of coat protein amino acid sequence of Iranian isolates and those of AMV isolates available at GenBank revealed homology ranging from 97.7-100% between Iranian isolates. Nine isolates showed 100% homology and Shahrkord bean isolate showed the lowest homology with other isolates.All Iranian isolates showed highest homology ranging from 98.6-99.5% to American soybean isolate with accession number HQ185569 and China alfalfa isolate with accession number HQ316647 whereas they showed lowest homology ranging from 95.2-97.2% to Korean potato isolate with accession number AB126032 and New Zealand alfalfa isolate with accession number U12510. In phylogenetic analysis, Iranian isolates were placed in one cluster, and there is no separation based on hosts or geographical regions. For comparison of biological properties of isolates, potato and alfalfa isolates were mechanically inoculated on test plants including Chenopodium quinoa , Gomphrena globosa , Nicotiana rustica , Nicotiana glutinosa , Cucumis sativus, Vigna unguiculata and Solanum tuberosum . There are no differences in symptoms of test plants between Daran potato and Dastgerd alfalfa isolates. The infection of test plants to AMV was confirmed via RT-PCR. Key word : Alfalfa mosaic virus , RT-PCR, Coat protein gene, Alignment, Phylogenetic tree
