Molecular Detection and Determination of Phylogenetic Position of Watermelon Chlorotic Stunt Virus Khouzestan Isolate Based on Coat Protein Gene

Watermelon chlorotic stunt virus (WmCSV) is a destructive Begomovirus from the family of Geminiviridae with a bipartite genome including similar-sized circular, single-stranded DNA (DNA-A and DNA-B) which has recently developed dangerously in many countries in the Middle East. WmCSV is transmitted by the whitefly Bemisia tabaci in a persistent and circulative manner. In order to detect this virus, in the summer of 2023, samples of watermelon with symptoms of yellowing and severe leaf curl, leathery and blistering of the young leaves surface, chlorotic spots, and dwarf were collected from watermelon fields in the north of Khouzestan province (Dezful, Shoush, and Andimeshk). PCR was performed using two primer pairs of Begomovirus related to AV1 and also AV2 genomic region. The sequencing results confirmed WmCSV infection in the samples. In the phylogenetic tree drawn based on the coat protein gene (AV1), Khouzestan isolates were placed in a group next to other Iranian isolates and they had most similarities to Noorabad isolate from Fars province. Also, results of two by two comparisons of nucleotide sequences of the AV1 genomic region using SDT v1.2 software showed the sequences of three Khouzestan isolates are highly similar (99.40%) and had the most identity (99.60%) with Noorabad Mamassani isolate from Fars province and the greatest genetic distance with Saudi Arabia isolates (95.80%) and Lebanon isolate (96.50%). This is the first report of WmCSV occurrence in Khouzestan province’s watermelon fields. WmCSV is rapidly advancing on their host crops in Iran, especially in the southern regions of the country.