Investigation of viruses infecting rice in southern China using a multiplex RT-PCR assay

Rice black streaked dwarf virus (RBSDV), southern rice black streaked dwarf virus (SRBSDV), rice ragged stunt virus (RRSV) and rice gall dwarf virus (RGDV) are common pathogens that affect rice in eastern and southeastern Asia. They are transmitted by the white-backed planthopper, brown planthopper, leafhopper and small brown planthopper, respectively, and require different control strategies. Although rice plants develop characteristic symptoms when infected by each virus, infected plants may also exhibit similar symptoms, which can hinder accurate symptom-based diagnoses. Thus, a one-step multiplex reverse transcription-PCR assay was developed for the simultaneous detection of the four viruses. The amplification products in singly or co-infected plants were easily distinguished during agarose gel electrophoresis. The optimized multiplex reverse transcription-PCR method was used to analyze 582 field samples collected from southern China between 2013 and 2015. RGDV was the most common virus, detected in ∼36.1% of the samples, while RRSV, SRBSDV, and RBSDV were detected in ∼34.0%, ∼30.1%, and ∼0.5% of the samples, respectively. There were also differences in the geographical distributions of the four viruses. RRSV mostly occurred in southern Hainan, RGDV was mainly distributed in southwestern and northeastern Guangdong, SRBSDV was detected across southern China, and RBSDV was detected only in the northern parts of southern China.