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Molecular characterization of a new Prunus-infecting cheravirus and complete genome sequence of stocky prune virus

M. Khalili, T. Candresse, Y. Brans, C. Faure, JM. Audergon, V. Decroocq, A. Marais. 2022 Viruses 14:2325. doi: 10.3390/v14112325. High-throughput sequencing allowed to identify three variants of a novel cheravirus, Alpine wild Prunus virus (AWPV), in three Prunus species, P. armeniaca (apricot), P. brigantina (wild apricot) and P. mahaleb (mahaleb or St Lucie cherry). A potential association of AWPV with symptoms could not be established so far due to mixed viral infections in the sampled trees. Moreover, the genome of stocky prune virus (StPV), a poorly known Prunus-infecting cheravirus, was determined. Phylogenetic analyses showed StPV and AWPV form a distinct cluster, away from other cheraviruses.

As part of a virome characterization of Prunus species, a novel cheravirus was discovered in two wild species, Prunus brigantina and P. mahaleb, and in an apricot (P. armeniaca) accession. The sequence of the two genomic RNAs was completed for two isolates. The Pro-Pol conserved region showed 86% amino acid (aa) identity with the corresponding region of Trillium govanianum cheravirus (TgCV), a tentative Cheravirus member, whereas the combined coat proteins (CPs) shared only 40% aa identity with TgCV CPs, well below the species demarcation threshold for the genus. This suggests the new virus should be considered as a new species for which the name Alpine wild prunus virus (AWPV) is proposed. In parallel, the complete-genome sequence of stocky prune virus (StPV), a poorly known cheravirus for which only partial sequences were available, was determined. A phylogenetic analysis showed AWPV, TgCV and StPV form a distinct cluster, away from other cheraviruses.

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