Population genetic dynamics of southern tomato virus from Turkey

Southern tomato virus (STV) has been reported from many countries. However, the infection status and population structure of STV in Turkey are unknown. In this study, the presence of STV was investigated in eight provinces across three different geographical regions of Turkey, including the Mediterranean, Aegean, and Marmara regions during the 2019 year vegetation period. Samples from 127 symptomatic and 9 asymptomatic plants from tomato production areas in three different geographical regions of Turkey were tested for a range of tomato infecting viruses using conventional molecular assays. Over 54% of the tomato plants sampled were found to be infected with STV. Also, single, double, and triple infections caused by STV, CMV, a potyvirus, and 16SrXII-A 'Candidatus Phytoplasma Solani' subgroup were detected. The genetic diversity of STV was investigated using the complete coat protein (CP) and RNA-dependent RNA polymerases (RdRp) gene regions of 15 randomly selected STV variants from different geographical regions of Turkey, and global variants accessions from GenBank. Variants from Turkey and other countries showed more than 99% homology with each other. According to the complete CP and RdRp gene regions, phylogenetic analyses revealed two lineages independent of geographical origin and host, and it was observed that all Turkish STV variants clustered in Clade I. Based on the complete CP and RdRP genes of STV, genetic parameters for Turkish and other international variants demonstrated high haplotype diversity and low nucleotide diversity. Negative (purifying) selection, a mechanism that constrains genetic variation, was determined on either CP and RdRp genes of STV. Moreover, based on our best knowledge this study is the first report of STV in Turkey.