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Viruses
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Fruit Tree Viruses and Viroids
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Fruit Tree Viruses and Viroids

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (1 December 2018) | Viewed by 62364

Special Issue Editors

Dr. Varvara I. Maliogka

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Guest Editor
Aristotle University of Thessaloniki, School of Agriculture, Faculty of Agriculture, Forestry and Natural Enivonment, Plant Pathology Laboratory, 54 124 Thessaloniki, Greece
Interests: Interests: fruit tree virus characterization, ; molecular diagnostics, ; next generation sequencing
Prof. Dr. Nikolaos I. Katis

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Guest Editor
Aristotle University of Thessaloniki, School of Agriculture, Faculty of Agriculture, Forestry and Natural Enivonment, Plant Pathology Laboratory, 54 124 Thessaloniki, Greece
Interests: fruit tree virus characterization, ; molecular diagnostics, ; next generation sequencing

Special Issue Information

Dear Colleagues,

Fruit trees constitute a very important part of agricultural economy worldwide. They are propagated vegetatively and they are also grafted on rootstocks. As a result, they are susceptible to many plant viruses with some of them causing severe diseases, crop losses and reducing the productive life of their fruit trees host plants. The movement of propagative material across the borders has facilitated the spread of fruit tree viruses and their insect vectors worldwide. The last few years the use of next generation sequencing (NGS) technology has increased the number of virus species detected and in some cases these viruses were identified as the causal agents of known diseases having previously unknown etiology. The NGS technology has also increased the number of virus sequences deposited in the data bases and this also helped to improve their molecular diagnostic tools and studies on their genetic diversity.

In this Special Issue of Viruses, we would like to include both research and review papers, providing an insight into the latest research on Fruit Tree Viruses and Viroids and to highlight key outcomes.

Dr. Varvara I. Maliogka
Prof. Nikolaos I. Katis
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fruit tree virus diseases

  • viroids

  • stone-fruits, pome-fruits

  • detection methods

  • NGS

  • genetic diversity

  • evolution and phylogeny

  • transmission and vectors

  • epidemiology

  • plant-virus interactions

  • management and control

  • small fruits

Published Papers (12 papers)

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Research

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18 pages, 6012 KiB  
Article
Strawberry Vein Banding Virus P6 Protein Is a Translation Trans-Activator and Its Activity Can be Suppressed by FveIF3g
by Shuai Li, Yahui Hu, Lei Jiang, Penghuan Rui, Qingqing Zhao, Jiying Feng, Dengpan Zuo, Xueping Zhou and Tong Jiang
Viruses 2018, 10(12), 717; https://0-doi-org.brum.beds.ac.uk/10.3390/v10120717 - 15 Dec 2018
Cited by 8 | Viewed by 3605
Abstract
The strawberry vein banding virus (SVBV) open reading frame (ORF) VI encodes a P6 protein known as the RNA silencing suppressor. This protein is known to form inclusion like granules of various sizes and accumulate in both the nuclei and the cytoplasm of [...] Read more.
The strawberry vein banding virus (SVBV) open reading frame (ORF) VI encodes a P6 protein known as the RNA silencing suppressor. This protein is known to form inclusion like granules of various sizes and accumulate in both the nuclei and the cytoplasm of SVBV-infected plant cells. In this study, we have determined that the P6 protein is the only trans-activator (TAV) encoded by SVBV, and can efficiently trans-activate the translation of downstream gfp mRNA in a bicistron derived from the SVBV. Furthermore, the P6 protein can trans-activate the expression of different bicistrons expressed by different caulimovirus promoters. The P6 protein encoded by SVBV from an infectious clone can also trans-activate the expression of bicistron. Through protein-protein interaction assays, we determined that the P6 protein could interact with the cell translation initiation factor FveIF3g of Fragaria vesca and co-localize with it in the nuclei of Nicotiana benthamiana cells. This interaction reduced the formation of P6 granules in cells and its trans-activation activity on translation. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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10 pages, 1454 KiB  
Article
A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales
by Thanuja Thekke-Veetil, Thien Ho, Joseph D. Postman, Robert R. Martin and Ioannis E. Tzanetakis
Viruses 2018, 10(8), 406; https://0-doi-org.brum.beds.ac.uk/10.3390/v10080406 - 03 Aug 2018
Cited by 6 | Viewed by 4313
Abstract
A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome [...] Read more.
A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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14 pages, 5846 KiB  
Article
High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics
by Asimina Katsiani, Varvara I. Maliogka, Nikolaos Katis, Laurence Svanella-Dumas, Antonio Olmos, Ana B. Ruiz-García, Armelle Marais, Chantal Faure, Sébastien Theil, Leonidas Lotos and Thierry Candresse
Viruses 2018, 10(7), 385; https://0-doi-org.brum.beds.ac.uk/10.3390/v10070385 - 21 Jul 2018
Cited by 19 | Viewed by 5064
Abstract
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have [...] Read more.
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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11 pages, 2357 KiB  
Article
Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species
by Igor Koloniuk, Thanuja Thekke-Veetil, Jean-Sébastien Reynard, Irena Mavrič Pleško, Jaroslava Přibylová, Justine Brodard, Isabelle Kellenberger, Tatiana Sarkisova, Josef Špak, Janja Lamovšek, Sebastien Massart, Thien Ho, Joseph D. Postman and Ioannis E. Tzanetakis
Viruses 2018, 10(7), 369; https://0-doi-org.brum.beds.ac.uk/10.3390/v10070369 - 12 Jul 2018
Cited by 11 | Viewed by 5408
Abstract
Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, [...] Read more.
Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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9 pages, 506 KiB  
Article
High Risk Blueberry Viruses by Region in North America; Implications for Certification, Nurseries, and Fruit Production
by Robert R. Martin and Ioannis E. Tzanetakis
Viruses 2018, 10(7), 342; https://0-doi-org.brum.beds.ac.uk/10.3390/v10070342 - 26 Jun 2018
Cited by 12 | Viewed by 4628
Abstract
There is limited information on the distribution of blueberry viruses in the U.S. or around the world other than where the viruses were first discovered and characterized. A survey for blueberry viruses was carried out in the U.S. in 2015–2017. Most blueberry viruses [...] Read more.
There is limited information on the distribution of blueberry viruses in the U.S. or around the world other than where the viruses were first discovered and characterized. A survey for blueberry viruses was carried out in the U.S. in 2015–2017. Most blueberry viruses have been characterized to the point that sensitive diagnostic assays have been developed. These assays are based on ELISA or variations of PCR, which were employed here to determine the presence of blueberry viruses in major blueberry production and nursery areas of the U.S. The viruses included in this study were: blueberry fruit drop (BFDaV), blueberry latent (BlLV), blueberry leaf mottle (BLMoV), blueberry mosaic (BlMaV), blueberry red ringspot (BRRV), blueberry scorch (BlScV), blueberry shock (BlShV), blueberry shoestring (BlSSV), blueberry virus A (BVA), peach rosette mosaic (PRMV), tobacco ringspot (TRSV), and tomato ringspot (ToRSV). In the Pacific Northwest BlShV was the most widespread virus, with BlScV and ToRSV detected in a limited number of fields in Oregon and Washington, but BlScV was widespread in British Columbia. In the upper midwest, the nematode-borne (ToRSV, TRSV), aphid-transmitted (BlSSV and BVA) and pollen-borne (BLMoV) viruses were most widespread. In the northeast, TRSV, ToRSV, and BlScV, were detected most frequently. In the southeast, BRRV and BNRBV were the most widespread viruses. BlLV, a cryptic virus with no known symptoms or effect on plant growth or yield was present in all regions. There are other viruses present at low levels in each of the areas, but with the lower incidence they pose minimal threat to nursery systems or fruit production. These results indicate that there are hotspots for individual virus groups that normally coincide with the presence of the vectors. The information presented highlights the high risk viruses for nursery and fruit production each pose a different challenge for control. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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12 pages, 704 KiB  
Communication
Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary
by Dániel Baráth, Nikoletta Jaksa-Czotter, János Molnár, Tünde Varga, Júlia Balássy, Luca Krisztina Szabó, Zoltán Kirilla, Gábor E. Tusnády, Éva Preininger and Éva Várallyay
Viruses 2018, 10(6), 318; https://0-doi-org.brum.beds.ac.uk/10.3390/v10060318 - 11 Jun 2018
Cited by 11 | Viewed by 4565
Abstract
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic [...] Read more.
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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14 pages, 6996 KiB  
Article
Blackcurrant Leaf Chlorosis Associated Virus: Evidence of the Presence of Circular RNA during Infections
by Delano James, James Phelan and Daniel Sanderson
Viruses 2018, 10(5), 260; https://0-doi-org.brum.beds.ac.uk/10.3390/v10050260 - 15 May 2018
Cited by 5 | Viewed by 3377
Abstract
Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and a new and distinct species in the genus Idaeovirus was proposed. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3′-terminus and 5′-terminus of RNA-2 [...] Read more.
Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and a new and distinct species in the genus Idaeovirus was proposed. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3′-terminus and 5′-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also, RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments, with denaturation at 95 °C preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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13 pages, 2450 KiB  
Article
Variability Studies of Two Prunus-Infecting Fabaviruses with the Aid of High-Throughput Sequencing
by Igor Koloniuk, Tatiana Sarkisova, Karel Petrzik, Ondřej Lenz, Jaroslava Přibylová, Jana Fránová, Josef Špak, Leonidas Lotos, Christina Beta, Asimina Katsiani, Thierry Candresse and Varvara I. Maliogka
Viruses 2018, 10(4), 204; https://0-doi-org.brum.beds.ac.uk/10.3390/v10040204 - 18 Apr 2018
Cited by 13 | Viewed by 5198
Abstract
During their lifetime, perennial woody plants are expected to face multiple infection events. Furthermore, multiple genotypes of individual virus species may co-infect the same host. This may eventually lead to a situation where plants harbor complex communities of viral species/strains. Using high-throughput sequencing, [...] Read more.
During their lifetime, perennial woody plants are expected to face multiple infection events. Furthermore, multiple genotypes of individual virus species may co-infect the same host. This may eventually lead to a situation where plants harbor complex communities of viral species/strains. Using high-throughput sequencing, we describe co-infection of sweet and sour cherry trees with diverse genomic variants of two closely related viruses, namely prunus virus F (PrVF) and cherry virus F (CVF). Both viruses are most homologous to members of the Fabavirus genus (Secoviridae family). The comparison of CVF and PrVF RNA2 genomic sequences suggests that the two viruses may significantly differ in their expression strategy. Indeed, similar to comoviruses, the smaller genomic segment of PrVF, RNA2, may be translated in two collinear proteins while CVF likely expresses only the shorter of these two proteins. Linked with the observation that identity levels between the coat proteins of these two viruses are significantly below the family species demarcation cut-off, these findings support the idea that CVF and PrVF represent two separate Fabavirus species. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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8 pages, 970 KiB  
Communication
Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume)
by Armelle Marais, Chantal Faure, Sébastien Theil and Thierry Candresse
Viruses 2018, 10(4), 144; https://0-doi-org.brum.beds.ac.uk/10.3390/v10040144 - 23 Mar 2018
Cited by 11 | Viewed by 4681
Abstract
With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunus mume) tree from Japan were purified and analyzed [...] Read more.
With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunus mume) tree from Japan were purified and analyzed by Illumina sequencing. Blast comparisons of reconstructed contigs showed that the P. mume sample was infected by a putative novel virus with homologies to Cherry virus A (CVA) and to the newly described Currant virus A (CuVA), both members of genus Capillovirus. Completion of the genome showed the new agent to have a genomic organization typical of capilloviruses, with two overlapping open reading frames encoding a large replication-associated protein fused to the coat protein (CP), and a putative movement protein (MP). This virus shares only, respectively, 63.2% and 62.7% CP amino acid identity with the most closely related viruses, CVA and CuVA. Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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15 pages, 1090 KiB  
Article
The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia
by Wycliff M. Kinoti, Fiona E. Constable, Narelle Nancarrow, Kim M. Plummer and Brendan Rodoni
Viruses 2018, 10(3), 136; https://0-doi-org.brum.beds.ac.uk/10.3390/v10030136 - 19 Mar 2018
Cited by 10 | Viewed by 4840
Abstract
Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in [...] Read more.
Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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Review

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15 pages, 2456 KiB  
Review
Viroid Diseases in Pome and Stone Fruit Trees and Koch’s Postulates: A Critical Assessment
by Francesco Di Serio, Silvia Ambrós, Teruo Sano, Ricardo Flores and Beatriz Navarro
Viruses 2018, 10(11), 612; https://0-doi-org.brum.beds.ac.uk/10.3390/v10110612 - 07 Nov 2018
Cited by 20 | Viewed by 7642
Abstract
Composed of a naked circular non-protein-coding genomic RNA, counting only a few hundred nucleotides, viroids—the smallest infectious agents known so far—are able to replicate and move systemically in herbaceous and woody host plants, which concomitantly may develop specific diseases or remain symptomless. Several [...] Read more.
Composed of a naked circular non-protein-coding genomic RNA, counting only a few hundred nucleotides, viroids—the smallest infectious agents known so far—are able to replicate and move systemically in herbaceous and woody host plants, which concomitantly may develop specific diseases or remain symptomless. Several viroids have been reported to naturally infect pome and stone fruit trees, showing symptoms on leaves, fruits and/or bark. However, Koch’s postulates required for establishing on firm grounds the viroid etiology of these diseases, have not been met in all instances. Here, pome and stone fruit tree diseases, conclusively proven to be caused by viroids, are reviewed, and the need to pay closer attention to fulfilling Koch’s postulates is emphasized. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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23 pages, 318 KiB  
Review
Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies
by Varvara I. Maliogka, Angelantonio Minafra, Pasquale Saldarelli, Ana B. Ruiz-García, Miroslav Glasa, Nikolaos Katis and Antonio Olmos
Viruses 2018, 10(8), 436; https://0-doi-org.brum.beds.ac.uk/10.3390/v10080436 - 17 Aug 2018
Cited by 87 | Viewed by 7111
Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization [...] Read more.
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed. Full article
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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