Table 3.
Detection and virus genetic variability studies.
| Virus | Genus | Family | Host | Aim of the research & New Findings | Reference |
|---|---|---|---|---|---|
| Apple stem grooving virus | Capillovirus | Betaflexiviridae | apple | Differential expression of siRNAs in symptomless infections | Visser et al. [33] |
| Apple stem grooving virus | Capillovirus | Betaflexiviridae | Actinidia | First HTS-obtained ASGV genome in kiwi | Wang et al. [88] |
| Asian prunus virus 1 | Foveavirus | Betaflexiviridae | Prunus | Genome reconstruction of Asian prunus viruses from 5 samples: phylogenetic and recombination implications | Marais et al. [46] |
| Asian prunus virus 2 | Foveavirus | Betaflexiviridae | Marais et al. [46] | ||
| Asian prunus virus 3 | Foveavirus | Betaflexiviridae | Marais et al. [46] | ||
| cherry-associated luteovirus | Luteovirus | Luteoviridae | peach | Highly divergent isolate in a new host (peach) | Igori et al. [76] |
| Cherry necrotic rusty mottle virus | Robigovirus | Betaflexiviridae | cherry | One CNRMV and three CGRMV isolates sequenced from a collection survey | Špak et al. [106] |
| Cherry green ring mottle virus | Robigovirus | Betaflexiviridae | |||
| Cherry virus A | Capillovirus | Betaflexiviridae | apricot | First complete sequence by HTS (apricot isolate); Description in apricot on propagation material | Koinuma et al. [104]; Barath et al. [41] |
| Cherry virus A | Capillovirus | Betaflexiviridae | cherry | New isolate from China | Wang et al. [105] |
| Cherry virus A | Capillovirus | Betaflexiviridae | Coinfection of two divergent variants in a wild cherry tree | Glasa et al. [9] | |
| Cherry virus A | Capillovirus | Betaflexiviridae | HTS survey on 39 Prunus samples: 75 full genomes and phylogenetic implications | Kesanakurti et al. [50] | |
| Cherry virus F | Fabavirus | Secoviridae | sweet cherry, sour cherry | Virome of 9 samples: co-infection of different viruses and co-existence of multiple fabavirus variants | Koloniuk et al. [40] |
| Citrus sudden death virus | Marafivirus | Tymoviridae | Citrus | Virome analysis of CSD-affected plants: wide variability of genotypes and mixed infections with different viruses | Matsumura et al. [69] |
| Citrus tristeza virus | Closterovirus | Closteroviridae | Genotyping 3 cross-protecting CTV strains in grapefruit; CTV p33 amplicons sequencing on 92 field samples: high diversity between and within samples | Zablocki & Pietersen [92]; Read & Pietersen [93] | |
| Citrus tristeza virus | Closterovirus | Closteroviridae | siRNAs study: altered siRNAs pattern in CTV-infected plants, hot spot on CTV genome | Visser et al. [94] | |
| Citrus tristeza virus | Closterovirus | Closteroviridae | siRNAs analysis: mixed CTV genotypes in resistance-breaking isolates | Yokomi et al. [17] | |
| Citrus tristeza virus | Closterovirus | Closteroviridae | Phylogenetic analysis on 2 CTV populations on 225 samples for epidemiology and risk assessment | Licciardello et al. [96] | |
| Citrus tristeza virus | Closterovirus | Closteroviridae | siRNAs sequencing of an old lemon isolate of CTV | Varveri et al. [109] | |
| Citrus Yellow vein clearing virus | Mandarivirus | Alphaflexiviridae | siRNAs analysis and phylogeny of 10 isolates of CYVCV | Yu et al. [98] | |
| Citrus vein enation virus | Enamovirus | Luteoviridae | Characterization of 5 Japanese genomes of Citrus vein enation virus | Nakazono-Nakaoga et al. [97] | |
| Little cherry virus 1 | Velarivirus | Closteroviridae | peach | A new isolate sequenced from South Korea in alternate host (peach) | Lim et al. [102]; |
| Little cherry virus 1 | Velarivirus | Closteroviridae | sweet cherry | New isolate in China | Wang et al. [103] |
| Little cherry virus 1 | Velarivirus | Closteroviridae | cherry | Genetic diversity among isolates and co-infection of different variants | Katsiani et al. [110] |
| Little cherry virus 1 | Velarivirus | Closteroviridae | Prunus | First description in Hungary on apricot and in Spain on sweet cherry | Baràth et al. [41]; Ruiz-Garcia et al. [36] |
| Plum bark necrosis stem pitting-associated virus | Ampelovirus | Closteroviridae | Prunus | 4 full genomes sequenced from Prunus sources | Marais et al. [100] |
| Plum bark necrosis stem pitting-associated virus | Ampelovirus | Closteroviridae | cherry | One complete genome from sweet cherry | Wang et al. [101] |
| Prunus necrotic ringspot virus | Ilarvirus | Bromoviridae | Prunus | Ilarvirus RNA2 generic amplicons from 61 trees: new potential ilarviruses; 53 PNRSV-infected sources: genetic strains network designed; incidence and genotyping of Australian ApMV and PDV | Kinoti et al. [99]; Kinoti et al. [107]; Kinoti et al. [108] |
| Prune dwarf virus & Apple mosaic virus | Ilarvirus | Bromoviridae | |||
| Prunus virus F | Fabavirus | Secoviridae | sweet cherry, sour cherry | Virome of 9 samples: co-infection of different viruses and co-existence of multiple fabavirus variants | Koloniuk et al. [40] |
HTS: High-throughput sequencing; ASGV: Apple stem grooving virus; CNMRV: Cherry necrotic rusty mottle virus; CSD: Citrus sudden death; CTV: Citrus tristeza virus; CYVCV: Citrus yellow vein clearing virus; PNRSV: Prunus necrotic ringspot virus; ApMV: Apple mosaic virus; PDV: Prune dwarf virus.