Molecular characterization of a novel emaravrius infecting Actinidia spp. in China

•A novel emaravirus was discovered in Actinidia spp. grown in China.•The virus had the closest phylogenetic relationships to FMV and PPSMV-2.•It was the second emaravirus infecting Actinidia trees.•Virus detection showed the presence of virus in three Actinidia species in China. Viruses in the genus Emaravirus contain 5–8 negative genomic RNAs and cause severe diseases of plants. In this study, a novel emaravirus, provisionally named Actinidia emaravirus 2 (AcEV-2), was identified from a kiwifruit tree showing leaf mottle and chlorosis symptoms. The genome of AcEV-2 consisted of at least six RNAs (RNAs 1–6) with sizes of 7079, 2252, 1387, 1514, 1744 and 1233 nucleotides (nts), respectively. Proteins encoded by RNAs1–4 of AcEV-2 shared the highest amino acid (aa) sequence identities of 62.2%–77.3% with the corresponding proteins of fig mosaic emaravirues (FMV) and pigeonpea sterility mosaic emaravirus 2 (PPSMV-2). Whilst, the P5 and P6 encoded by AcEV-2 exhibited the highest identities of 44.2% and 39.2% with the corresponding proteins of PPSMV-2. It was the second emaravirus infecting Actinidia trees in China. Preliminary virus detection disclosed the presence of AcEV-2 in three Actinidia species grown in three provinces in the central and southern China.