Discovery of a novel emaravirus and an alphacytorhabdovirus infecting Spiraea in the USA

Spiraea plants showing symptoms of virus infection were investigated using high-throughput sequencing which resulted in the identification of two novel viruses: an emaravirus named Spiraea chlorotic leaf spot distortion virus (SCLSDV), and an alphacytorhabdovirus named Spiraea alphacytorhabdovirus 1 (SpCRV-1). The complete genome of SCLSDV comprises four RNA segments, each encoding a distinct protein: RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid protein, and movement protein, respectively. SCLSDV shares 33.99–71.78% amino acid identity with pear chlorotic leaf spot-associated virus. Virus purification and electron microscopy confirmed pleomorphic, enveloped particles (80–100 nm) matching the morphology of members of the genus Emaravirus . The alphacytorhabdovirus shares 70% of nucleotide identity with Actinidia virus D and encodes eight putative proteins. Both novel viruses were detected in a mixed infection with Spiraea yellow leaf spot virus. Additionally, SCLSDV was consistently detected in a single infection in 50 out of 77 plant samples exhibiting yellow spot disease, characterized by chlorotic lesions, leaf distortion, and necrosis. These findings suggest that strong yellow spot symptoms and leaf distortion are likely associated with SCLSDV infection. Furthermore, eriophyid mites were collected from symptomatic plants and identified morphologically as Calepitrimerus sp. Given the known role of eriophyid mites in emaravirus transmission, their presence suggests it could be a potential vector for SCLSDV.