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Viral Detection in Phalaenopsis Orchids Using High-Throughput Sequencing and One-Step Multiplex RT-PCR
Jing Huang1, Ying Chen2, Xiao Zhu2
1College of Food and Biological Engineering, Zhangzhou Institute of Technology, Zhangzhou 363000, China.
Plant Disease
|April 9, 2025
Summary
High-throughput sequencing identified six viruses in Phalaenopsis orchids, including four new to the genus. A novel multiplex RT-PCR method offers efficient detection for improved disease management and cultivation.
Area of Science:
- Plant Virology
- Molecular Biology
- Orchid Cultivation
Background:
- Phalaenopsis orchids are economically important but vulnerable to viral infections.
- Existing virus detection methods lack efficiency and broad scope.
- Viral diseases significantly reduce the commercial value of orchids.
Purpose of the Study:
- To identify viruses infecting Phalaenopsis orchids using high-throughput sequencing (HTS).
- To develop and validate a rapid, efficient detection method for identified viruses.
- To enhance understanding of the Phalaenopsis virome and inform disease management strategies.
Main Methods:
- High-throughput sequencing (HTS) of 82 Phalaenopsis samples from three cultivars.
- Identification and characterization of RNA viruses.
- Design and optimization of a one-step multiplex reverse transcription polymerase chain reaction (mRT-PCR) assay.
Main Results:
- Six positive-sense single-stranded RNA (+ssRNA) viruses were identified: Odontoglossum ringspot virus (ORSV), Tobacco mosaic virus (TMV), Tomato mottle mosaic virus (ToMMV), Pepper mild mottle virus (PMMoV), Plum pox virus (PPV), and Tobacco etch virus (TEV).
- ORSV (86.59%) and TMV (34.15%) were most prevalent; ToMMV, PMMoV, PPV, and TEV were detected for the first time in Phalaenopsis.
- Co-infection was common (37.80%), and a specific mRT-PCR assay was developed for simultaneous detection.
Conclusions:
- This study expands the known virome of Phalaenopsis orchids, revealing new viral threats.
- The developed mRT-PCR provides a practical tool for early and accurate diagnosis of multiple viral infections.
- Findings support improved quarantine, disease management, and cultivation practices for Phalaenopsis.
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