Figure 1.
Genomic structure of prunus virus I (PrVI). (A) Schematic representation of PrVI genome organization. White boxes show positions of different open reading frames (ORFs), black lines depict untranslated genomic regions (UTRs) and green, vertical lines indicate conserved motifs in ilarviruses’ genomes. Red lines indicate the locations of contigs. (B) Length and conserved nucleotide sequences detected at the 5′ and 3′ termini of the three genomic RNA segments of PrVI. Conserved nucleotides are presented with black capital letters, whereas mismatches are highlighted with grey letters. Abbreviations: MET = methyltransferase, HEL = helicase, MP = movement protein, CP = capsid protein.
Figure 1.
Genomic structure of prunus virus I (PrVI). (A) Schematic representation of PrVI genome organization. White boxes show positions of different open reading frames (ORFs), black lines depict untranslated genomic regions (UTRs) and green, vertical lines indicate conserved motifs in ilarviruses’ genomes. Red lines indicate the locations of contigs. (B) Length and conserved nucleotide sequences detected at the 5′ and 3′ termini of the three genomic RNA segments of PrVI. Conserved nucleotides are presented with black capital letters, whereas mismatches are highlighted with grey letters. Abbreviations: MET = methyltransferase, HEL = helicase, MP = movement protein, CP = capsid protein.
Figure 2.
Multiple alignment of the putative amino acid motifs and signatures detected in PrVI and other relative ilarviruses/bromoviruses. Amino acids conserved among all viruses are indicated with green/bold letters, whereas amino acids conserved in all ilarviruses are highlighted with black, bold letters. Grey letters indicate amino acid mismatches with PrVI residues.
Figure 3.
Multiple alignment of the 5′ and 3′ terminal nucleotide sequences of PrVI and other subgroup 1 ilarviruses. Conserved nucleotides are highlighted in bold.
Figure 4.
Phylogenetic analysis of the amino acid sequences of (A) 1a, (B) 2a, (C) MP and (D) CP of PrVI and other ilarviruses. The trees were constructed using the best fit model for each alignment. The phylogenetic trees were constructed using the Maximum Likelihood method and the statistical significance of branches was evaluated by bootstrap analysis (500 replicates). Bootstrap values above 60% are indicated on the branches. The acronyms are used as follows: ageratum latent virus, AgLV (NC_022127-29); American plum line pattern virus, APLPV (LC496469-71); apple mosaic virus, ApMV (KY965060, KY965062, KY971020); asparagus virus 2, AV-2 (NC_011807-9); blackberry chlorotic ringspot virus, BCRV (KX834010-12); blueberry shock virus, BlShV (NC_022250-52); citrus leaf rugose virus, CLRV (NC_003546-8); citrus variegation virus, CVV (NC_009536-8); elm mottle virus, EMoV (NC_003568-70); fragaria chiloensis latent virus, FClLV (NC_006566-8); humulus japonicas latent virus, HJLV (NC_006064-6); lilac leaf chlorosis virus, LLCV (KU947033-5); lilac ring mottle virus, LiRMoV (NC_038776-7); parietaria mottle virus, PMoV (KT005243-5); privet ringspot virus, PrRSV (KT290039-41); prune dwarf virus, PDV (MK522387-88, MK563042); prunus necrotic ringspot virus, PNRSV (JN416771-3); spinach latent virus, SpLV (NC_003808-10); strawberry necrotic shock virus, SNSV (NC_008706-8); tobacco streak virus, TSV (FJ403375-7); tomato necrotic streak virus, TomNSV (NC_039074-6); tulare apple mosaic virus, TAMV (AF226160-2). Cucumber mosaic virus, CMV (NC_00234-5, NC001440) was used as outgroup. Scale refers to amino acid substitutions per site.
Figure 4.
Phylogenetic analysis of the amino acid sequences of (A) 1a, (B) 2a, (C) MP and (D) CP of PrVI and other ilarviruses. The trees were constructed using the best fit model for each alignment. The phylogenetic trees were constructed using the Maximum Likelihood method and the statistical significance of branches was evaluated by bootstrap analysis (500 replicates). Bootstrap values above 60% are indicated on the branches. The acronyms are used as follows: ageratum latent virus, AgLV (NC_022127-29); American plum line pattern virus, APLPV (LC496469-71); apple mosaic virus, ApMV (KY965060, KY965062, KY971020); asparagus virus 2, AV-2 (NC_011807-9); blackberry chlorotic ringspot virus, BCRV (KX834010-12); blueberry shock virus, BlShV (NC_022250-52); citrus leaf rugose virus, CLRV (NC_003546-8); citrus variegation virus, CVV (NC_009536-8); elm mottle virus, EMoV (NC_003568-70); fragaria chiloensis latent virus, FClLV (NC_006566-8); humulus japonicas latent virus, HJLV (NC_006064-6); lilac leaf chlorosis virus, LLCV (KU947033-5); lilac ring mottle virus, LiRMoV (NC_038776-7); parietaria mottle virus, PMoV (KT005243-5); privet ringspot virus, PrRSV (KT290039-41); prune dwarf virus, PDV (MK522387-88, MK563042); prunus necrotic ringspot virus, PNRSV (JN416771-3); spinach latent virus, SpLV (NC_003808-10); strawberry necrotic shock virus, SNSV (NC_008706-8); tobacco streak virus, TSV (FJ403375-7); tomato necrotic streak virus, TomNSV (NC_039074-6); tulare apple mosaic virus, TAMV (AF226160-2). Cucumber mosaic virus, CMV (NC_00234-5, NC001440) was used as outgroup. Scale refers to amino acid substitutions per site.

Table 1.
Presence of PrVI in Greek Prunus spp. orchards.
Prunus spp. | Collection Date | Geographic County | Total Number of Samples | Number of Samples Positive to PrVI | Accession Numbers |
---|
P. avium | 2009 | Imathia | 12 | 1 | MW591551 |
| 2014 | | | | MW591550 |
| | Imathia | 10 | 2 | |
| | | | | MW591552 |
| 2019 | Imathia | 31 | 1 | MW591554 |
| 2020 | Imathia | 15 | 0 | - 1 |
P. persica | 2013 | Arta | 12 | 0 | - |
| 2014 | Imathia | 11 | 0 | - |
| 2019 | Imathia | 6 | 1 | MW591553 |
| 2020 | Imathia | 29 | 0 | - |
P. domestica | 2020 | Imathia | 12 | 0 | - |
SUM | 138 | 5 | |