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Genetic diversity of Plum pox virus: strains, disease and related challenges for control

Abstract Plum pox virus (PPV), a member of the genus Potyvirus, family Potyviridae, is a positive-sense single-stranded RNA virus. RNA viruses tend to be genetically diverse because the viral RNA-dependent RNA polymerase responsible for virus replication lacks proofreading capacity. Consequently, PPV is genetically diverse, and nine strains of the virus (D, M, EA, C, Rec, W, T, CR, and An) have been identified to date. At least two of these strains (Rec, T) are the direct products of recombination events, a contributor to genetic diversity and a common occurrence in the genus Potyvirus. The strains are genetically distinct and can be identified using phylogenetic analysis of the whole genome, the PIPO gene, the polymerase region, and the coat protein (CP) region. The unique genetic characteristics of each strain have facilitated the development of nucleic-acid-based and protein-based tools that allow strain identification. The strains are usually defined also by distinct biological properties that may include differences in host range, aphid transmissibility, disease symptomatology, and/or geographic distribution. There is genetic diversity within strains that affects these biological properties, and these differences may overlap with, and sometimes blur, the biological distinction between strains.