Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5'UTR

• Published in: Archives of virology Vol. 155; no. 12; pp. 1997 - 2006
• Main Authors: JOOSTE, A. E. C, MAREE, H. J, BELLSTEDT, D. U, GOSZCZYNSKI, D. E, PIETERSEN, G, BURGER, J. T
• Format: Journal Article
• Language: English
• Published: Wien Springer 01.12.2010; Springer Nature B.V
• Subjects: 5' Untranslated Regions; Biological and medical sciences; Closteroviridae - classification; Closteroviridae - genetics; Closteroviridae - isolation & purification; Cluster Analysis; DNA Fingerprinting; Flowers & plants; Fundamental and applied biological sciences. Psychology; Genetics; Genomes; Genotype; Grapevine leafroll-associated virus 3; Infections; Microbiology; Miscellaneous; Molecular Sequence Data; Phylogenetics; Phylogeny; Phytopathology. Animal pests. Plant and forest protection; Plant viruses and viroids; Polymorphism; Polymorphism, Genetic; Polymorphism, Single-Stranded Conformational; RNA, Viral - genetics; Sequence Alignment; Sequence Analysis, DNA; South Africa; Virology; Viruses; Vitis - virology; Wineries & vineyards; South Africa; Ampelovirus; Virus; Grapevine leafroll-associated virus 3; Plant pathogen; Closteroviridae; Non coding sequence; Genetics
• ISSN: 0304-8608; 1432-8798
• DOI: 10.1007/s00705-010-0793-y

Three genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) were identified in vineyards of the Western Cape, South Africa. The GLRaV-3 variants were identified by single-strand conformation polymorphism (SSCP) profiles generated from a region amplified in ORF5. ORF5 sequence data confirmed the three genetic variant groups, and a specific SSCP profile was assigned to each variant group. The results of SSCP analysis of this region in ORF5 showed that this method gives a fast and reliable indication of the GLRaV-3 variant status of a plant, which in many instances showed mixed infections. The full genome sequence of one representative of each variant group i.e. isolates 621 (group I), 623 (group II) and PL-20 (group III), was determined by sequencing overlapping cloned fragments of these isolates. The sequences of genomic 5' ends of these isolates were determined by RLM-RACE. Sequence alignment of the 5'UTRs indicated significant sequence and length variation in this region between the three South African variant groups. Alignment of the Hsp70h and CP gene regions of these isolates with those of isolates from elsewhere in the world, followed by phylogenetic analysis, further supported the presence of three variants of GLRaV-3 in South Africa and the presence of two or three additional variant groups elsewhere in the world.