title: Grapevine leafroll-associated virus 1 occurs as genetically diverse populations.
abstract: The genetic diversity of 34 isolates of Grapevine leafroll-associated virus 1 (GLRaV-1) from different wine, table, and ornamental grape cultivars in California, New York, and Washington States in the United States was investigated. Segments of the heat-shock protein 70 homolog (HSP70h) gene, coat protein (CP) gene, coat protein duplicate 2 (CPd2) gene, and open reading frame 9 (p24) were amplified by reverse-transcription polymerase chain reaction, cloned, and sequenced. A pairwise comparison of nucleotide sequences revealed intra- and interisolate sequence diversity, with CPd2 and HSP70h being the most and the least divergent, respectively, among the four genomic regions studied. The normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated different purifying selection pressures acting on each of the four genomic regions, with the CP and CPd2 being subjected to the strongest and weakest functional constraints, respectively. A global phylogenetic analysis of sequences from the four genomic regions revealed segregation of GLRaV-1 isolates into three major clades and a lack of clearly defined clustering by geographical origin. In contrast, only two lineages were apparent when the CP and CPd2 gene sequences were used in phylogenetic analyses. Putative recombination events were revealed among the HSP70h, CP, and p24 sequences. The genetic landscape of GLRaV-1 populations presented in this study provides a foundation for better understanding of the epidemiology of grapevine leafroll disease across grape-growing regions in the United States. In addition, this study will benefit grape clean plant programs across the country in improving the sanitary status of planting materials provided to nurseries and grape growers.
authors.affiliation: Department of Plant Pathology, Washington State University, WA, USA.
authors.forename: Olufemi J
authors.initials: OJ
authors.lastname: Alabi
authors.forename: Maher
authors.initials: M
authors.lastname: Al Rwahnih
authors.forename: Gandhi
authors.initials: G
authors.lastname: Karthikeyan
authors.forename: Sudarsana
authors.initials: S
authors.lastname: Poojari
authors.forename: Marc
authors.initials: M
authors.lastname: Fuchs
authors.forename: Adib
authors.initials: A
authors.lastname: Rowhani
authors.forename: Rayapati A
authors.initials: RA
authors.lastname: Naidu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D002140:California; D036022:Capsid Proteins / Q000235:genetics; D029381:Closteroviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D009518:New York; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012526:Satellite Viruses / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics*; D027843:Vitis / Q000821:virology*; D014861:Washington
chemical_list: D036022:Capsid Proteins; D018840:HSP70 Heat-Shock Proteins; D014764:Viral Proteins