The global phylogeny of Plum pox virus is emerging

Abstract

The 206 complete genomic sequences of Plum pox virus in GenBank (January 2019) were downloaded. Their main open reading frames (ORF)s were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the PPV-Rec and PPV-T strain ORFs were all recombinants, whereas most of those in the PPV-C, PPV-CR, PPV-CV, PPV-D, PPV-EA, PPV-M and PPV-W strain clusters were not. The strain clusters ranged in size from 2 (PPV-CV and PPV-EA) to 74 (PPV-D). The isolates of eight of the nine strains came solely from Europe and the Levant (with an exception resulting from a quarantine breach), but many PPV-D strain isolates also came from east and south Asia and the Americas. The estimated time to the most recent common ancestor (TMRCA) of all 134 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain PPV-W was the oldest. Eurasia is clearly the 'centre of emergence' of PPV and the several PPV-D strain populations found elsewhere only show evidence of gene flow with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected pipo gene of the recently migrant populations. The possible ancient origins of PPV are discussed.

Intra‐strain biological and epidemiological characterization of plum pox virus

“…Thus far, there is minimal evidence and there have been no prospective studies of positive selection acting on PPV; however, Glasa et al reported weak positive selection at two codon sites in the C‐terminal region of P3 protein based on comparison of three PPV strains (Glasa et al , ), and Hajizadeh et al . recently reported four positively selected codon sites in the PIPO of the PPV‐D strain (Hajizadeh et al , ). In this study, comparative genomic analysis of 257 PPV‐D isolates detected significant positive selection, in at least three of the four tested methods, at five codon sites: three (amino acid positions 2,855, 2,872, and 2,873) resided in the N‐terminal region of CP, and two (amino acid positions 2,303 and 2,635) resided in NIb.…”

“…AL11pl, a PPV-Ancestor Marcus (An) isolate, was employed as an outgroup instead of PPV-M for the same reason, that is, because the PPV-Marcus (M) strain was suggested as a recombinant strain between PPV-D and PPV-An (García et al, 2014). Although a recent report has suggested that recombination events occurred in the PPV-An isolate, it remains reasonable to use the isolate as an outgroup in our analysis because PPV-D was not involved in the recombination (Hajizadeh et al, 2019).…”

Common and Strain-Specific Post-Translational Modifications of the Potyvirus Plum pox virus Coat Protein in Different Hosts

“…PPV is a virus with high intra-species variability. At least nine PPV strains have been identified so far [43,69], with the largest divergence affecting the coding sequence of the N-terminal region of CP, where all O-GlcNAcylation and most of the phosphorylation targets are focused. Thus, we wondered if PTMs widely analyzed in an isolate (PPV-R) of the strain D would similarly affect other PPV strains.…”

“…Former studies concerning O-GlcNAcylation and phosphorylation of PPV CP focused on the isolate PPV-R, belonging to strain D. To assess whether these PTMs affect the CP of other PPV strains, virions from isolates PPV-BOR-3 (strain Rec) and PPV-SwCM (strain C) were analyzed. Rec was selected because signs of phosphorylation and O-GlcNAcylation had been previously reported for isolates of this strain [29], and strain C was selected because it is one of the most distant from strain D [43].…”

“…All studies about O-GlcNAcylation and phosphorylation affecting PPV CP have been narrowed to infections in herbaceous hosts, mainly in Nicotiana spp., and no data concerning PTMs of CP during infections in natural woody hosts are available. On the other hand, up to 10 different PPV strains have been described [42,43]. Although earlier assays, done with isolates belonging to strains D, M, and Rec, suggested that O-GlcNAcylation and phosphorylation affecting CP may be a common attribute of PPV species [28,29,44], thorough proteomic analyses of PTMs have only been conducted for the CP of the PPV R isolate, belonging to strain D.…”