Prevalence of Viruses and Viroids and Seasonal Dynamics of Prunus Necrotic Ringspot Virus and Prune Dwarf Virus in Peach Orchards in South Carolina

Prunus species are susceptible to plant viruses, which can cause significant losses to growers. Peach (Prunus persica [L.] Batsch) is an essential economic crop grown in the southeastern United States, specifically South Carolina and Georgia. Viruses have various mechanisms for spreading from plant to plant, including through insect vectors, pollen, pruning, seeds, and the movement of infected propagative material. Virus detection and characterization are critical to decrease virus prevalence in peach orchards. Excluding infected material is the best practice to mitigate the spread of the virus in peach orchards. Reducing virus spread is also achieved using virus-tested propagative material in conjunction with routine testing of budwood trees. Virus testing programs require updated knowledge of important viruses in the region. Also, these programs rely on the development and optimization of effective virus detection methods. Some viruses can fluctuate in titer in different tissues throughout the season. Sampling suboptimal tissues or at a suboptimal time could result in false negative results. It is, therefore, important to understand the dynamics of viruses within peach trees to optimize virus diagnostics. Using high throughput sequencing of pooled peach tree samples, we surveyed 20 peach orchards to detect known and unknown viruses and viroids. We characterized six complete virus genomes and one viroid. Prunus necrotic ringspot virus (PNRSV), peach latent mosaic viroid (PLMVd), and prune dwarf virus (PDV) were among the most prevalent viruses and viroid. Additionally, seasonal virus dynamics of two common peach viruses, PDV and PNRSV, were quantified to better understand virus fluctuations. Our study showed that these viruses were detectable at any time of the year in flowers, leaves, stems, and roots. We revealed that flower and leaf tissue are suitable for virus detection in the spring while stems were optimal for virus detection at any point of the year. Roots were not optimal for virus detection due to challenges in nucleic acid extraction and a high number of failed PCRs. These results will better inform virus diagnostics and help decrease the prevalence of viruses in peach orchards in the southeastern United States.