Simultaneous identification of Cucumber mosaic virus and Tomato spotted wilt virus from tomato fields and their phylogenetic analysis

Cucumber mosaic virus (CMV) and Tomato spotted wilt virus (TSWV) are important viruses in tomato fields. In this research, 36 tomato plant samples showing viral symptoms were collected from fields in various regions of west and northwest of Iran. To detect CMV and TSWV, cDNAs were prepared using Random Hexamer primer and total RNAs extracted from the collected samples. The prepared cDNAs and specific primers for CMV-coat protein (CP) gene and TSWV-nucleocapsid (N) gene were used to amplify a part of each virus genome by Polymerase Chain Reaction (PCR), separately. The results revealed that a 654 bp fragment from the CMV-CP and a 777 bp fragment from TSWV-N were amplified from six and three samples, respectively. To detect mixed infection of CMV and TSWV in tomato plants simultaneously, we used their specific primers in a single PCR assay. DNA fragments from both viruses were amplified from two samples. In these plants more severe symptoms such as deformation, mosaic, chlorosis and necrosis on the leaves were observed and compared to the specific symptoms in plants infected by either CMV or TSWV. Phylogenetic tree of mixed isolates based on nucleic acid and amino acids showed that the isolate of CMV in this research were grouped with isolates from Iran and India whereas TSWV isolate were grouped with isolates from different country such as Turkey, Italy and Montenegro.