Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates

Hibiscus chlorotic ringspot virus (HCRSV), genus Betacarmovirus, family Tombusviridae, is a common pathogen of hibiscus plants in tropical and subtropical regions. During 2020-2021, leaf samples of Chinese hibiscus Hibiscus rosa-sinensis L. with mottling and chlorotic ring spot symptoms were collected from Ahvaz and Molasani Khuzestan province, southwestern Iran. Total RNA extracted from symptomatic samples was subjected to RT-PCR analysis to amplify the sequence of the coat protein gene (CP) (p38) of HCRSV. Complete (1038 bp) and partial (932 bp) p38 sequences were determined and deposited in the GenBank database. The consensus sequences obtained from CP were compared with those of known isolates using the nBLAST program and phylogenetic analysis. The phylogenetic tree constructed based on the p38 sequences showed different ancestors for Iranian isolates of HCRSV. Additionally, the isolates studied were grouped into clades regardless of their geographic distribution, suggesting that there is no differentiation of population based on location and that populations are interconnected. Recombination analysis based on p38 sequences predicted at least two acceptable recombinant isolates, Ahvaz (Iran) and Israel. In silico prediction of CP structures of isolates involved in recombination events showed low sequence to structure identity between HCRSV isolates. In addition to reporting two new HCRSV isolates from Iran, our work demonstrated that HCRSV exhibits a high genetic variation through recombination and that the classification criterion could be changed from low nucleotide sequence identity to a higher value, along with the structural analysis of betacarmovirus proteins.