Phylogenetic and recombination analysis of the homing protein domain of grapevine fanleaf virus (GFLV) isolates associated with ‘yellow mosaic’ and ‘infectious malformation’ syndromes in grapevine

• Published in: Archives of virology Vol. 159; no. 10; pp. 2757 - 2764
• Main Authors: Elbeaino, Toufic, Kiyi, Hulusi, Boutarfa, Reza, Minafra, Angelantonio, Martelli, Giovanni Paolo, Digiaro, Michele
• Format: Journal Article
• Language: English
• Published: Vienna Springer-Verlag 01-10-2014; Springer Vienna; Springer Nature B.V
• Subjects: abnormal development; Amino Acid Sequence; Arabis mosaic virus; Base Sequence; Biomedical and Life Sciences; Biomedicine; Brief Report; genes; Genetic Variation; Genome, Viral - genetics; Genomes; Grapevine fanleaf virus; Infectious Diseases; Medical Microbiology; Nepovirus - classification; Nepovirus - genetics; Nepovirus - isolation & purification; Open Reading Frames; Phylogenetics; Phylogeny; Plant Diseases - virology; Polypeptides; Protein Structure, Tertiary; Proteins; Recombination, Genetic; RNA polymerase; RNA, Viral - genetics; Sequence Alignment; Sequence Analysis, RNA; Sequence Homology, Nucleic Acid; vines; Virology; Viruses; Vitaceae; Vitis - virology; Vitis vinifera; Italy; RDP3 Program; Vein Banding; Homing Protein; Grapevine Fanleaf Virus; Infected Grapevine
• ISSN: 0304-8608; 1432-8798
• DOI: 10.1007/s00705-014-2138-8

The RNA2 of seven grapevine fanleaf virus (GFLV) isolates from vines with yellow mosaic (YM) symptoms from different origin were sequenced. These sequences showed a high variability in the homing protein (2Aᴴᴾ) and, in five of them, a putative recombination with arabis mosaic virus (ArMV) was detected. To investigate recombination frequency, the partial sequences of the 2Aᴴᴾ of 28 additional GFLV isolates from nine different countries, showing either YM or infectious malformations (MF) symptoms, were obtained and compared with those of GFLV isolates from GenBank. The analysis confirmed the high level of sequence variability (up to 41 % at the nucleotide level) among isolates. In phylogenetic trees constructed using different approaches, the sequenced isolates always clustered in four conserved groups, three of which comprised YM strains (groups 1, 2 and 3), and one (group 4) the MF strains. Potential interspecific recombination sites between GFLV and ArMV were predicted in the 2Aᴴᴾ gene of several isolates, all of which were associated with YM symptoms.