Characterization of the Pepper Virome in Oklahoma Reveals Emerging RNA and DNA Viruses

Pepper (<i>Capsicum</i> spp.) is an economically valuable crop worldwide including in the United States due to its nutritional benefits in human health and widespread use as a spice or vegetable. Although numerous viruses have been reported infecting peppers in the USA, little is known about the diversity and distribution of pepper-infecting viruses in Oklahoma. To address this knowledge gap, we conducted a comprehensive pepper virome study to identify viruses infecting pepper and their incidence across six different counties in Oklahoma. A total of 310 plant samples including pepper and other potential hosts were collected during the 2021 and 2022 growing seasons. Samples were analyzed using high-throughput sequencing (HTS) and/or reverse transcription-polymerase chain reaction (RT-PCR) assays. Viral contigs identified via HTS were further validated through RT-PCR or PCR assays followed by Sanger sequencing. In total, 17 distinct viruses were detected, including 15 RNA and two DNA viruses, with several representing putatively novel findings. The most prevalent virus was beet curly top virus (BCTV), followed by tomato yellow leaf curl virus (TYLCV), potato yellow dwarf virus/constricta yellow dwarf virus (PYDV/CYDV), and pepper mild mottle virus (PMMoV). Virus incidence varied by season and location, with some surveys showing infection rates exceeding 80%. This study provides the first in-depth characterization of the pepper virome in Oklahoma and valuable insights into the prevalence and distribution of pepper-infecting viruses. These findings will support the development of informed, targeted strategies for virus detection and management in pepper production systems.