High-Throughput Sequencing-Based Detection and Characterisation of a Putative Emaravirus Infecting Scaevola taccada

Scaevola taccada is an important perennial evergreen shrubby seaside plant that can be used to prevent coastal erosion and to protect cultivated plants against salt spray. In January 2022, a virus-like disease, tentatively named yellow blotch disease (YBD), that severely affected the growth of S. taccada was detected in Sansha City, Hainan Province, China. To identify the pathogen responsible for this disease, we examined the virome profile of a symptomatic S. taccada using ribosomal RNA-depleted total RNA sequencing. Sequence assembly and analysis revealed the presence of eleven viral genome segments in the symptomatic sample encoding a putative RNA-dependent RNA polymerase (RNA1a and RNA1b), glycoprotein precursor (RNA2a and RNA 2b), nucleocapsid protein (RNA3a and RNA3b), movement protein (RNA4a and RNA4b) and P5 (RNA5) and P6 proteins (RNA6a and RNA6b) of unknown function, respectively. Molecular signatures in the viral RNAs, sequence comparisons, and phylogenetic analysis collectively indicate the presence of a novel virus in the symptomatic S. taccada sample, tentatively named Scaevola yellow blotch virus (ScYBV). This virus belongs to a new species in the genus Emaravirus of family Fimoviridae, tentatively designated as Emaravirus scaevolae. This marks the first report of an emaravirus infecting S. taccada plants. Bioassays showed that ScYBV is not mechanically transmissible to Nicotiana benthamiana plants. Molecular screening of leaves from 52 symptomatic and 20 asymptomatic individual S. taccada plants suggested a strong relationship between yellow blotch and the presence of ScYBV. These findings provide a basis for effective control of YBD and contribute to a greater understanding of the genetic diversity of emaraviruses.