A novel emaravirus comprising five RNA segments is associated with ringspot disease in oak

Abstract

We report the complete nucleotide sequence of the genome of a novel virus in ringspot-diseased common oak (Quercus robur L.). The newly identified pathogen is associated with leaf symptoms such as mottle, chlorotic spots and ringspots on diseased trees. High-throughput sequencing (HTS, Illumina RNASeq) was used to explore the virome of a ringspot-diseased oak that had chlorotic ringspots of suspected viral origin on leaves for several years. Bioinformatic analysis of the HTS dataset followed by RT-PCR enabled us to determine complete sequences of four RNA genome segments of a novel virus. These sequences showed high similarity to members of the genus Emaravirus, which includes segmented negative-stranded RNA viruses of economic importance. To verify the ends of each RNA, we conducted rapid amplification of cDNA ends (RACE). We identified an additional genome segment (RNA 5) by RT-PCR using a genus-specific primer (PDAP213) to the conserved 3´ and 5´termini in order to amplify full-length genome segments. RNA 5 encodes a 21-kDa protein that is homologous to the silencing suppressor P8 of High Plains wheat mosaic virus. The five viral RNAs were consistently detected by RT-PCR in ringspot-diseased oaks in Germany, Sweden, and Norway. We conclude that the virus represents a new member of the genus Emaravirus affecting oaks in Germany and in Scandinavia, and we propose the name “common oak ringspot-associated emaravirus” (CORaV).

Characterisation and Distribution of Karaka Ōkahu Purepure Virus—A Novel Emaravirus Likely to Be Endemic to New Zealand

“…Amino acid sequence analysis of the putative RdRp of known emaraviruses showed the emaraviruses comprise three major clades (clades I, II and III), with the largest clade (clade I) split into three subclades (subclades a, b and c). The observed branching pattern conforms to previous reports [ 52 , 53 , 54 , 55 ]. The earliest identified emaraviruses belong to Clade I, while more recent discoveries have expanded our understanding of emaravirus evolution with the identification of clades II and III.…”

Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

“…Among these, three virus genera are overwhelmingly represented. These are the genus Emaravirus with four species to date (aspen mosaic-associated virus [ 42 ], common oak ringspot-associated virus [ 56 , 57 ], maple mottle-associated virus [ 74 ] and European mountain ash ringspot-associated virus [ 16 ]), the genus Badnavirus with two species (birch leafroll-associated virus [ 15 ] and chestnut mosaic virus [ 55 ]) and the genus Carlavirus with eight species (birch carlavirus [ 14 ], blueberry scorch virus [ 43 , 44 ], elderberry carlaviruses A, B, C, D, E [ 59 , 60 ] and elm carlavirus [ 61 , 62 , 63 ]). All the novel emara- and badnaviruses are found to be associated with the corresponding symptoms and are, consequently, plant pathogenic, while the role of carlaviruses is not yet clarified.…”

Towards the Forest Virome: Next-Generation-Sequencing Drastically Expands our Understanding on Virosphere in Temperate Forest Ecosystems

“…Among these, three virus genera are overwhelmingly represented. These are the genus Emaravirus with up to now four species (aspen mosaic-associated virus [26]; common oak ringspot-associated virus [27,28]; maple mottle-associated virus [29]; European mountain ash ringspot-associated virus [9]), the genus Badnavirus with two species (birch leafroll-associated virus [15]; chestnut mosaic virus [30]) and the genus Carlavirus with eight species (birch carlavirus [14]; blueberry scorch virus [31]; elderberry carlaviruses A, B, C, D, E [32][33]; elm carlavirus [34]). All the novel emara-and badnaviruses are found to be associated with the corresponding symptoms and are, consequently, plant pathogenic, while the role of the carlaviruses is not yet clarified.…”

“…The disease was also found to affect 11-19% of oak seedling in propagation stations, threatening with wider spread of the disease through the infected oak propagation material [3]. Due to the employment of NGS strategies the causal agent of the disease could very lately be identified; the common oak ringspot-associated virus (CORaV) [27,28] represents a new member of the genus Emaravirus comprising five RNA segments. For one more time, metagenomic analysis provided the diagnostic answer to a problem remaining unsolved for long time.…”