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Citrus yellow vein clearing virus (CYVCV) is an emerging virus that causes serious economic damage to the lemon industry worldwide. The coat protein (CP) of CYVCV is a strong RNA silencing suppressor and is associated with the severity of symptoms in citrus, yet the interaction between CP and host factors remains unknown. In this study, the 40S ribosomal subunit protein S9‐2 (ClRPS9‐2) was identified as a CP‐binding partner using the yeast two‐hybrid system from a lemon (cv. Eureka) cDNA library, and the interaction between CP and ClRPS9‐2 was demonstrated by in vivo methods. The results suggest that the N‐terminal 8–108 amino acid sequence of ClRPS9‐2 is crucial for its interaction with CP and may be associated with the nuclear localization of ClRPS9‐2. The accumulation and silencing suppressor activity of CP were reduced by transient expression of ClRPS9‐2 in Nicotiana benthamiana. Reverse transcription‐quantitative PCR analysis showed that the content of CYVCV in ClRPS9‐2 transgenic Eureka lemon plants was approximately 50% of that in CYVCV‐infected wild‐type plants 1 month after inoculation, and mild yellowing and vein clearing symptoms were observed in the transgenic plants. These findings demonstrate that ClRPS9‐2 plays a role in host defensive reactions, and the enhanced resistance of transgenic plants to CYVCV may be associated with the up‐regulation of salicylic acid‐related and R genes. [ABSTRACT FROM AUTHOR]