A nationwide survey and genetic analysis of rice stripe virus in South Korea during 2012–2013

Rice stripe virus (RSV) is a major rice-infecting virus in Korea that has caused a severe resurgence in the western provinces in 2007–2008. The outbreak of RSV in rice was caused by the small brown planthopper Laodelphax striatellus (an RSV vector), which overwinters in temperate climates. Mass immigration of its insect vector from China has been proposed as a critical risk factor in development of the disease. A nationwide survey was done in June and July 2012–2013 in 30 Korean provinces to confirm RSV sequence variation. The sequence of the nucleocapsid protein (NCP) gene and the intergenic region (IR) of RSV RNA3 was analyzed. A phylogenetic analysis of the NCP gene and the IR demonstrated that the 33 isolates were closely related to earlier reported isolates from Japan and China, but the secondary IR structure showed strong geographic clustering. This is the first report on a nationwide RSV survey of Korea. The results will provide information on the relationships among RSV isolates to understand the epidemiology of this rice disease and the effect of climate changes and insect migration.