Abstract
Double stranded RNAs from Prunus samples gathered from various surveys were analyzed by a deep-sequencing approach. Contig annotations revealed the presence of a potential new viral species in an Azerbaijani almond tree (Prunus amygdalus) and its genome sequence was completed. Its genomic organization is similar to that of the recently described Apricot vein clearing associated virus (AVCaV) for which two new isolates were also characterized, in a similar fashion, from two Japanese plums (Prunus salicina) from a French germplasm collection. The amino acid identity values between the four proteins encoded by the genome of the new virus have identity levels with those of AVCaV which fall clearly outside the species demarcation criteria. The new virus should therefore be considered as a new species for which the name of Caucasus prunus virus (CPrV) has been proposed. Phylogenetic relationships and nucleotide comparisons suggested that together with AVCaV, CPrV could define a new genus (proposed name: Prunevirus) in the family Betaflexiviridae. A molecular test targeting both members of the new genus was developed, allowing the detection of additional AVCaV isolates, and therefore extending the known geographical distribution and the host range of AVCaV. Moreover, the phylogenetic trees reconstructed with the amino acid sequences of replicase, movement and coat proteins of representative Betaflexiviridae members suggest that Citrus leaf blotch virus (CLBV, type member of the genus Citrivirus) may have evolved from a recombination event involving a Prunevirus, further highlighting the importance of recombination as a driving force in Betaflexiviridae evolution. The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers KM507061-KM504070.
Highlights
The family Betaflexiviridae is composed of plant viruses with particles of flexuous morphology
A novel Tepovirus infecting Prunus species, tentatively named Prunus virus T, was recently characterized following a pyrosequencing analysis of Double-stranded RNAs (dsRNAs) recovered from plum and cherry trees, but it was not possible to associate this new agent with specific symptoms because of its presence in co-infection with common fruit tree viruses [20]
Illumina sequencing of dsRNAs obtained from an apricot tree with vein clearing symptoms recently allowed the identification of a novel unclassified Betaflexiviridae member named Apricot vein clearing associated virus (AVCaV); its co-infection with Plum bark necrosis stem pitting associated virus (PBNSPaV) hampered the establishment of a causal relationship between AVCaV and the vein clearing symptoms [21]
Summary
The family Betaflexiviridae is composed of plant viruses with particles of flexuous morphology. Fruit tree materials have been subjected to a systematic NGS screening of viral infections, in particular to elucidate diseases of still unknown etiology [18]. In this context, the failure to detect viral sequence other than Little cherry virus 1 (LChV1) in sour cherry sources of the Shirofungen stunt disease led to the suggestion that LChV1 may be responsible for this syndrome [19]. A novel Tepovirus infecting Prunus species, tentatively named Prunus virus T, was recently characterized following a pyrosequencing analysis of dsRNAs recovered from plum and cherry trees, but it was not possible to associate this new agent with specific symptoms because of its presence in co-infection with common fruit tree viruses [20]. Illumina sequencing of dsRNAs obtained from an apricot tree with vein clearing symptoms recently allowed the identification of a novel unclassified Betaflexiviridae member named Apricot vein clearing associated virus (AVCaV); its co-infection with Plum bark necrosis stem pitting associated virus (PBNSPaV) hampered the establishment of a causal relationship between AVCaV and the vein clearing symptoms [21]
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