High-Throughput Virome Surveillance Reveals Emerging Viral Threats to Cucumber Production in Taiwan

Cucumber (Cucumis sativus L.) production in Taiwan is increasingly threatened by insect-transmitted viral diseases and complex mixed infections. In this study, symptomatic cucumber plants from a commercial net-house production system in Xizhou Township, Changhua County, Taiwan, were investigated using Illumina-based high-throughput sequencing (HTS) and virus-specific reverse transcription–polymerase chain reaction. A virome analysis conducted in 2022 identified five previously detected viruses, namely cucumber mosaic virus, cucumber Bulgarian latent virus, cucurbit chlorotic yellows virus (CCYV), melon yellow spot virus (MYSV), and watermelon silver mottle virus (WSMoV), and two emerging viruses, including a known virus, cucurbit chlorotic virus (CuCV), and an uncharacterized virus, tentatively designated cucumber tymovirus (CTyV). The complete genome of CuCV isolate XZ-C-1 was determined, and its sequence was closely related to previously reported CuCV isolates. A 5394-nt sequence of CTyV was also obtained and showed substantial divergence from its closest known viral relative. Importantly, comparative virus detection revealed a marked increase in the detection rates of several viruses between 2022 (n = 34) and 2025 (n = 30). MYSV remained highly prevalent (100.0% to 90.0%), whereas WSMoV increased dramatically from 2.9% to 96.7% and CCYV from 11.8% to 83.3%. The detection rates of CuCV and CTyV also increased from 20.6% to 53.3% and from 8.8% to 40.0%, respectively. In addition, all samples collected in 2025 harbored two to five viruses, indicating extensive mixed infections. These results reveal a dynamic and increasingly complex viral community in Taiwanese cucumber production systems and highlight the importance of continuous virome-based surveillance for early detection of emerging viruses and development of integrated disease-management strategies.