title: Characterization by deep sequencing of divergent plum bark necrosis stem pitting-associated virus (PBNSPaV) isolates and development of a broad-spectrum PBNSPaV detection assay.
abstract: 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.
authors: Armelle
authors: A
authors: Marais
authors: Chantal
authors: C
authors: Faure
authors: Carole
authors: C
authors: Couture
authors: Bernard
authors: B
authors: Bergey
authors: Pascal
authors: P
authors: Gentit
authors: Thierry
authors: T
authors: Candresse
mesh_terms: D001483:Base Sequence; D029381:Closteroviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D018515:Plant Leaves / Q000821:virology; D027861:Prunus / Q000821:virology*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013045:Species Specificity
chemical_list: D012367:RNA, Viral