Genetic structure and phylogenetic analysis of grapevine leafroll-associated virus-1 ( Ampelovirus univitis ) in different grape-producing regions of Iran

ABSTRACT Grapevine leafroll-associated virus 1 (GLRaV-1) is a major viral pathogen within the genus Ampelovirus and a key contributor to grapevine leafroll disease, posing significant threats to viticulture worldwide. Despite its importance, the genetic structure and diversity of GLRaV-1 in Iran have remained largely unexplored. In this study, a total of 325 symptomatic grapevine samples were collected from 5 major grape-producing provinces of Iran and screened using immunoassay and reverse transcription-PCR (RT-PCR) for GLRaV-1. Nine positive samples were subjected to sequencing of the coat protein (CP) gene. Phylogenetic analyses of CP gene sequences and publicly available full-genome sequences, performed using MEGA 11, revealed three distinct phylogenetic clades among Iranian isolates. Recombinant sequences were identified and excluded to avoid phylogenetic bias. Population genetic analyses indicated high haplotype diversity and strong purifying selection across the genome. Significant population structure and restricted gene flow were observed, consistent with geographic isolation of viral populations. Molecular clock analysis suggested recent divergence of GLRaV-1 lineages within Iran. These findings provide new insights into the evolutionary dynamics of GLRaV-1 and its population structure in Iranian vineyards, with implications for virus spread, surveillance, and disease management. IMPORTANCE Grapevine leafroll-associated virus 1 (GLRaV-1) is a widespread and economically important virus affecting grapevines. This study is the first to investigate the genetic diversity and population structure of GLRaV-1 across major grape-growing regions of Iran. We discovered a high level of genetic variation and geographically structured virus populations, which may reflect localized transmission and limited movement of infected material. Understanding this diversity is crucial for improving diagnostic strategies and managing the spread of grapevine leafroll disease. Our findings support the need for region-specific disease control efforts and contribute to the global understanding of Ampelovirus evolution.