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Characterization by Deep Sequencing of Divergent Plum bark necrosis stem pitting-associated virus (PBNSPaV) Isolates and Development of a Broad-Spectrum PBNSPaV Detection Assay

June 2014 , Volume 104 , Number  6
Pages  660 - 666

Armelle Marais , Chantal Faure , Carole Couture , Bernard Bergey , Pascal Gentit , and Thierry Candresse

First, second, third, fourth, and sixth authors: INRA and Université de Bordeaux, UMR 1332 BFP, CS20032, 33882 Villenave d'Ornon Cedex, France; and fifth author: Laboratoire de Virologie, CTIFL, 28 route des Nebouts, Centre de Lanxade, 24130 Prigonrieux, France.

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Accepted for publication 5 December 2013.

Plum bark necrosis stem pitting-associated virus (PBNSPaV), the causal agent of plum bark necrosis stem pitting disease, belongs to the genus Ampelovirus in the family Closteroviridae. The complete genome sequence of PBNSPaV isolates from four Prunus sources was determined by pyrosequencing. All isolates showed the same genomic organization as the PBNSPaV reference isolate. The least divergent isolate, found in a peach tree from China, showed an overall 91.8% of nucleotide identity with the type isolate. Two closely related isolates, defining a second cluster of diversity, were found in two Japanese plum lines from France and showed only 82.8% identity with the type isolate. On the other hand, they were highly homologous with two recently described PBNSPaV divergent isolates from China. The fourth and most divergent isolate, from a Chinese peach, showed only 71.2% identity to other PBNSPaV isolates and was not detected by currently available PBNSPaV reverse-transcription polymerase chain reaction detection assays. Complete sequencing of the divergent isolates allowed the development of a more broad-spectrum detection test targeting a conserved region in the P61 gene. Taken together, these results indicate a much broader diversity of PBNSPaV than previously thought and provide for a more robust detection of this still poorly characterized pathogen.

This article is in the public domain and not copyrightable. It may be freely reprinted with customary crediting of the source. The American Phytopathological Society, 2014.