Genetic Variability of Natural Populations of Grapevine leafroll-associated virus 2 in Pacific Northwest Vineyards

• Published in: Phytopathology 2010-07, Vol.100 (7), p.698-707
• Main Authors: Jarugula, Sridhar, Alabi, Olufemi J, Martin, Robert R, Naidu, Rayapati A
• Format: Article
• Language: English
• Subjects: accuracy; Biological and medical sciences; Capsid Proteins - genetics; Closteroviridae - genetics; coat proteins; diagnostic techniques; disease diagnosis; enzyme-linked immunosorbent assay; fruit crops; Fundamental and applied biological sciences. Psychology; Genetic Variation; grapes; Grapevine leafroll-associated virus; Grapevine leafroll-associated virus 2; heat shock proteins; microbial genetics; molecular sequence data; natural selection; nucleotide sequences; Phytopathology. Animal pests. Plant and forest protection; plant diseases and disorders; plant viruses; Plant viruses and viroids; restriction fragment length polymorphism; Reverse Transcriptase Polymerase Chain Reaction; Selection, Genetic; Sequence Alignment; sequence analysis; strain differences; Vitis - virology; Vitis vinifera; Washington
• ISSN: 0031-949X; 1943-7684
• DOI: 10.1094/PHYTO-100-7-0698

Genetic variability of field populations of Grapevine leafroll-associated virus 2 (GLRaV-2) in Pacific Northwest (PNW) vineyards was characterized by sequencing the entire coat protein (CP) and a portion of the heat-shock protein-70 homolog (HSP70h) genes. Phylogenetic analysis of CP and HSP70h nucleotide sequences obtained in this study and corresponding sequences from GenBank revealed segregation of GLRaV-2 isolates into six lineages with virus isolates from PNW distributed in 'PN', 'H4', and 'RG' lineages. An estimation of the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated that different selection pressures may be acting on the two genomic regions encoding proteins with distinct functions. Multiple alignments of CP amino acid sequences showed lineage-specific differences. Enzyme-linked immunosorbent assay results indicated that GLRaV-2-specific antibodies from a commercial source are unable to reliably detect GLRaV-2 isolates in the RG lineage, thereby limiting antibody-based diagnosis of all GLRaV-2 isolates currently found in PNW vineyards. A protocol based on reverse-transcription polymerase chain reaction and restriction fragment length polymorphism analysis was developed for differentiating GLRaV-2 isolates belonging to the three lineages present in the region. The taxonomic status of GLRaV-2 is discussed in light of the current knowledge of global genetic diversity of the virus.