Phylogenetic analysis of two Iranian grapevine virus A isolates using coat protein gene sequence

Abstract

Symptomatic grapevine samples were collected from vineyards in Zanjan province to detect Grapevine virus A. Total RNA was extracted from symptomatic leaf samples and subjected to cDNA synthesis using random hexamer primers. Then, a DNA fragment around 800 bp including the complete coat protein (CP) gene was amplified from nine out of 57 samples by polymerase chain reaction (PCR) using specific primers. The infection rate of GAV in vineyards was around 4%, 6%, 2%, and 6% in Zanjan, Abhar, Tarom, and Khoramdareh, respectively. Two DNA fragments corresponding to samples Abhar (p25) and Zanjan (p26), were purified and sequenced. The CP-nucleotide sequence identity between two Iranian isolates was 97.3%. However, sequence identity with previously reported isolates were 76 to 95% and 82 to 98% at the nt and amino acid levels, respectively. CP-based phylogenetic trees showed three main groups (I, II, III) in which p25 (MG977013) and p26 (MG977013) isolates were placed in the group I together with isolates from different geographical regions including Palestine (Israel), Italy, Czech Republic, Jordan, USA and South Africa. To our knowledge, this is the first report of detection and phylogenetic analysis of GVA isolates from Iranian vineyards based on the complete CP gene. Positive selection value was observed on codon 25 indicating the role of this position probably in virus survival and flexibility against evolutionary forces.