Genetic diversity ofPlum 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.Résumé: Le virus de la sharka du prunier (PPV), appartenant au genre Potyvirus de la famille des Potyviridae, est un virus à ARN simple brin à polarité positive. Les virus à ARN tendent à être différents génétiquement parce que l'ARN-polymérase sous la dépendance de l'ARN viral responsable de la réplication du virus ne possède pas la capacité de corriger les épreuves. En conséquence, le PPV est différent génétiquement et neuf souches du virus (D, M, EA, C, Ree, W, T, CR, et An) ont été identifiées à ce jour. Au moins deux de ces souches (Rec et T) sont les produits directs d'évènements de recombinaison, évènements qui contribuent à la diversité génétique et qui sont chose courante chez le genre Potyvirus. Les souches sont différentes génétiquement et elles peuvent être identifiées par analyse phylogénétique du génome entier, du gène PIPO, de la région de la polymérase et de la région de la capside. Les caractéristiques uniques propres à chaque souche ont facilité le développement d'outils basés sur les acides nucléiques et les protéines, outils qui permettent l'identification des souches. Celles-ci sont également habituellement définies par des propriétés biologiques qui peuvent comporter des différences quant à la gamme d'hôtes, à la transmissibilité par les pucerons, à la symptomatologie des maladies ou à la distribution géographique. Il y a des différences génétiques au sein des souches qui influencent ces propriétés biologiques et ces différences peuvent se superposer aux différences biologiques qui existent entre les souches, voire les brouiller à l'occasion.

Detection and Identification of Plum Pox Virus on Prunus Species in Crimea

“…These results indicate that all the isolates tested belong to the PPV-D strain. The PPV-D strain is widespread in Europe and probably is the most distributed in the world (Maejima et al, 2011;James et al, 2013;Garcia et al, 2014). The origin of the PPV-D isolates in Crimea as well as their phylogenetic relationships has to be elucidated yet.…”

Intra‐strain biological and epidemiological characterization of plum pox virus

“…Because some strains possess distinct biological properties, such as host preference, aphid transmissibility, disease symptomatology, and geographic distribution (James et al , ; Rimbaud et al , ; Sihelská et al ., ), strain typing has been the sole approach to the characterization of PPV isolates or populations of interest (EPPO, ; IPPC, ). Meanwhile, biological variation among isolates or populations in a single strain has been recognized as another important but unsolved aspect of PPV epidemiology (Candresse and Cambra, ; James et al , ; García et al , ; Rimbaud et al , ). Several studies have revealed intra‐strain variation in biological properties, such as host preference (Maiss et al , ; Dallot et al , ), aphid transmissibility (Deborre et al ., ; Glasa et al , ; Schneider et al , ), and competitiveness (Glasa et al , ), among PPV isolates.…”

Genetic Diversity and Population Structure

“…Phylogenetic analysis indicates the common ancestor for W, C and СR strains, and this branch further evolved, mainly or exclusively, in the territory of contemporary Russia. Assumptions of East-Europe ancestry of W and С strains have been reported [13,40,53]. A presumable ancestor could appear in Russia or be introduced from Front and Middle Asia with infected plants.…”

“…These are Dideron (D), Marcus (M), Recombinant (Rec), Cherry (С), Cherry Russian (CR), El Amar (EA), Winona (W), Turkish (T) and Ancestral (An) [9,13], clustered into monophylic groups of closely related isolates. Recombination plays important role in the PPV evolution together with spot mutations.…”

“…However, the An, T, Rec and М distinguishes are mainly located in the genome 5´-end. Besides, even single nucleotide or amino acid replacement may result in incorrectness of strain identification [13]. Therefore, several methods should be used, of which the phylogenetic analysis of full genome sequences is deemed the most reliable.…”