Genetic Diversity of Rose Rosette Virus Isolates in Oklahoma Reveals a Distinct Evolutionary Lineage

Rose rosette virus (RRV), a member of the genus Emaravirus, is responsible for rose rosette disease (RRD), which has significant impacts on the rose industry and ornamental landscapes across the United States (US). To better understand the genetic diversity and population structure of RRV, infected rose leaf samples were collected from garden centers, nurseries, retail stores, and wild rose populations. Total RNA was extracted and analyzed using Sanger sequencing and Illumina-based high-throughput sequencing (HTS), resulting in nearly complete genome sequences of 17 RRV isolates. Phylogenetic and population genetic analyses incorporating >100 publicly available RRV isolates revealed a genetically differentiated lineage comprising eight isolates, seven of which were characterized in this study. This lineage, designated the OK Clade, was consistently supported across the concatenated coding-sequence dataset and several individual genomic segments of RRV. Evolutionary modeling estimated that the divergence between the OK Clade and all other RRV isolates likely occurred more than a century ago. Population genetic analyses further supported substantial differentiation between the OK Clade and other RRV isolates. RRV exhibited greater nucleotide diversity than previously reported, indicating that the genetic diversity of the virus may be broader than previously recognized. Potential recombination breakpoints were also identified in RNA1 and RNA5, although additional analyses are required to validate these events. Collectively, these findings identify a geographically associated and genetically distinct RRV lineage in Oklahoma and provide new insights into the population structure and evolutionary diversity of RRV.