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Characterization by Deep Sequencing of Prunus virus T, a Novel Tepovirus Infecting Prunus Species

First, second, and sixth authors: INRA and Université de Bordeaux, UMR 1332 BFP, CS20032, 33882 Villenave d'Ornon Cedex, France; third author: Genetic Resource Institute of the Azerbaijan National Academy of Sciences, Az-1106 Baku, Azerbaijan; and fourth and fifth authors: Università degli Studi di Napoli “Federico II”, Dipartimento di Agraria, I-80055 Portici, Italy.

Double-stranded RNAs purified from a cherry tree collected in Italy and a plum tree collected in Azerbaijan were submitted to deep sequencing. Contigs showing weak but significant identity with various members of the family Betaflexiviridae were reconstructed. Sequence comparisons led to the conclusion that the viral isolates identified in the analyzed Prunus plants belong to the same viral species. Their genome organization is similar to that of some members of the family Betaflexiviridae, with three overlapping open reading frames (RNA polymerase, movement protein, and capsid protein). Phylogenetic analyses of the deduced encoded proteins showed a clustering with the sole member of the genus Tepovirus, Potato virus T (PVT). Given these results, the name Prunus virus T (PrVT) is proposed for the new virus. It should be considered as a new member of the genus Tepovirus, even if the level of nucleotide identity with PVT is borderline with the genus demarcation criteria for the family Betaflexiviridae. A reverse-transcription polymerase chain reaction detection assay was developed and allowed the identification of two other PrVT isolates and an estimate of 1% prevalence in the large Prunus collection screened. Due to the mixed infection status of all hosts identified to date, it was not possible to correlate the presence of PrVT with specific symptoms.