Geographically distant isolates of the persistent southern tomato virus (STV) show very low genetic diversity in the putative coat protein gene

Abstract

Southern tomato virus (STV) from genus Amalgavirus (Family Amalgaviridae) is a persistent virus infecting tomato crops worldwide. Information on genetic diversity and evolutionary mechanisms for plant persistent viruses are very scarce in comparison with plant acute viruses. In this work, the putative coat protein gene of worldwide STV isolates was analyzed showing very low nucleotide diversity (< 0.0100). Phylogenetic analysis separated STV isolates into two clades, but no correlation was found between genetic and geographic distances. Also, no recombination events among STV isolates were detected. Comparison of synonymous and nonsynonymous substitutions indicated negative selection at the amino acid level.