Cucumber mosaic virus subgroup IA frequently occurs in the northwest Iran.

To monitor genetic variation between Cucumber mosaic virus (CMV) isolates of northwest Iran, samples of cucurbitaceous plants expressing symptoms similar to those caused by CMV were collected. The samples were first screened by ELISA to detect CMV and to determine its subgroup. All detected CMV isolates appeared to be subgroup I (S-I). When total RNA from the samples was subjected to RT-PCR with a pair of primers corresponding to the CMV coat protein (CP) flanking regions, the expected ~870 bp DNA fragment was amplified at 18 samples of 34 tested. MspI restriction analysis of 18 amplified products produced two DNA fragments with sizes about 530 and 330 bp corresponding to MspI profile of CMV S-I. The amplification products of four representative samples were cloned and nucleotide sequences of 1-5 clones from each isolate were determined. The clones from each isolate were over 99% identical and also the isolates themselves were only up to 2% divergent. These isolates clustered in subgroup IA clade on a consensus phylogenetic tree and formed a distinct subclade suggesting that the isolates have originated from a common source.