E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Special Issue "Viroid-2018: International Conference on Viroids and Viroid-Like RNAs"

A special issue of Viruses (ISSN 1999-4915).

Deadline for manuscript submissions: 31 March 2019

Special Issue Editor

Guest Editor
Dr. José-Antonio Daròs

IBMCP (CSIC-Universitat Politècnica de València), 46022 Valencia, Spain
Website | E-Mail
Phone: +34 963877893
Interests: plant virus; viroids; RNA replication; RNA processing; viral vectors; antiviral strategies in plants; molecular farming

Special Issue Information

Dear Colleagues,

Viroids are a very intriguing type of infectious agent of higher plants, since they are exclusively constituted by a relatively small molecule (246–401 nt) of circular RNA. Particularly, all evidence indicates that viroid RNAs do not code for proteins. However, despite this simplicity, when viroid RNAs enter appropriate host cells they manage to replicate, move through the plant, and avoid the host defensive response, causing, in many instances, diseases that are most relevant to important agricultural crops. From their discovery in the late 1960s and early 1970s, a great deal is known about viroid biology and biochemistry, and the pathology of viroid diseases. However, more needs to be discovered about aspects, such as viroid replication, traffic and interaction with the host plant; structure of viroid molecules and functional domains; viroid transmission, pathogenesis and disease control; viroid diagnosis and identification of new viroid species. All these topics and more are to be discussed at Viroid-2018, an international conference on viroids and viroid-like RNAs that will be held in Valencia (Spain) 5–7 July, 2018. I invite all researchers in the viroid community, and particularly the participants of Viroid-2018, to present their recent discoveries about all aspects of viroid and viroid-like RNA biology in this Special Issue.

Dr. José-Antonio Daròs
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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 1800 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

  • Viroid
  • viroid-like RNA
  • viroid replication
  • viroid movement
  • viroid structure
  • viroid transmission
  • viroid pathogenesis
  • anti-viroid strategies
  • viroid diagnosis
  • new viroid species

Published Papers (12 papers)

View options order results:
result details:
Displaying articles 1-12
Export citation of selected articles as:

Research

Jump to: Review, Other

Open AccessArticle Viroid-infected Tomato and Capsicum Seed Shipments to Australia
Viruses 2019, 11(2), 98; https://doi.org/10.3390/v11020098
Received: 12 December 2018 / Revised: 15 January 2019 / Accepted: 19 January 2019 / Published: 24 January 2019
PDF Full-text (1398 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have [...] Read more.
Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have been tested for pospiviroids before they are released from border quarantine, and capsicum seed lots have been similarly tested in quarantine since 2013. Altogether, more than 2000 seed lots have been tested. Pospiviroids were detected in more than 10% of the seed lots in the first years of mandatory testing, but the proportion of lots that were infected declined in subsequent years to less than 5%. Six pospiviroid species were detected: Citrus exocortis viroid, Columnea latent viroid, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato chlorotic dwarf viroid and Tomato apical stunt viroid. They were detected in seed lots exported from 18 countries from every production region. In many seed lots, the detectable fraction (prevalence) of infected seeds was estimated to be very small, as low as 6 × 10−5 (~1 in 16,000; CI 5 × 10−6 to 2.5 × 10−4) for some lots. These findings raise questions about seed production practices, and the study indicates the geographic distributions of these pathogens are uncertain, and there is a continuing threat of invasion. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessArticle Innate Immunity Activation and RNAi Interplay in Citrus Exocortis Viroid—Tomato Pathosystem
Viruses 2018, 10(11), 587; https://doi.org/10.3390/v10110587
Received: 25 August 2018 / Revised: 18 October 2018 / Accepted: 24 October 2018 / Published: 26 October 2018
PDF Full-text (1526 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Although viroids are the smallest and simplest plant pathogens known, the molecular mechanisms underlying their pathogenesis remain unclear. To unravel these mechanisms, a dual approach was implemented consisting of in silico identification of potential tomato silencing targets of pospiviroids, and the experimental validation [...] Read more.
Although viroids are the smallest and simplest plant pathogens known, the molecular mechanisms underlying their pathogenesis remain unclear. To unravel these mechanisms, a dual approach was implemented consisting of in silico identification of potential tomato silencing targets of pospiviroids, and the experimental validation of these targets through the sequencing of small RNAs and RNA ends extracted from tomatoes infected with a severe isolate of Citrus exocortis viroid (CEVd). The generated RNA ends were also used to monitor the differentially-expressed genes. These analyses showed that when CEVd symptoms are well established: (i) CEVd are degraded by at least three Dicer-like (DCL) proteins and possibly by RNA-induced silencing complex (RISC), (ii) five different mRNAs are partially degraded through post-transcriptional gene silencing (PTGS), including argonaute 2a, which is further degraded in phasiRNAs, (iii) Dicer-like 2b and 2d are both upregulated and degraded in phasiRNAs, and (iv) CEVd infection induced a significant shift in gene expression allowing to explain the usual symptoms of pospiviroids on tomato and to demonstrate the constant activation of host innate immunity and systemic acquired resistance (SAR) by these pathogenic RNAs. Finally, based on in silico analysis, potential immunity receptor candidates of viroid-derived RNAs are suggested. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessArticle Genome-Wide Transcriptomic Analysis Reveals Insights into the Response to Citrus bark cracking viroid (CBCVd) in Hop (Humulus lupulus L.)
Viruses 2018, 10(10), 570; https://doi.org/10.3390/v10100570
Received: 27 September 2018 / Revised: 12 October 2018 / Accepted: 16 October 2018 / Published: 18 October 2018
Cited by 1 | PDF Full-text (1025 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Viroids are smallest known pathogen that consist of non-capsidated, single-stranded non-coding RNA replicons and they exploits host factors for their replication and propagation. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) is a serious threat, which spreads rapidly within hop [...] Read more.
Viroids are smallest known pathogen that consist of non-capsidated, single-stranded non-coding RNA replicons and they exploits host factors for their replication and propagation. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) is a serious threat, which spreads rapidly within hop gardens. In this study, we employed comprehensive transcriptome analyses to dissect host-viroid interactions and identify gene expression changes that are associated with disease development in hop. Our analysis revealed that CBCVd-infection resulted in the massive modulation of activity of over 2000 genes. Expression of genes associated with plant immune responses (protein kinase and mitogen-activated protein kinase), hypersensitive responses, phytohormone signaling pathways, photosynthesis, pigment metabolism, protein metabolism, sugar metabolism, and modification, and others were altered, which could be attributed to systemic symptom development upon CBCVd-infection in hop. In addition, genes encoding RNA-dependent RNA polymerase, pathogenesis-related protein, chitinase, as well as those related to basal defense responses were up-regulated. The expression levels of several genes identified from RNA sequencing analysis were confirmed by qRT-PCR. Our systematic comprehensive CBCVd-responsive transcriptome analysis provides a better understanding and insights into complex viroid-hop plant interaction. This information will assist further in the development of future measures for the prevention of CBCVd spread in hop fields. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessArticle Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development
Viruses 2018, 10(10), 516; https://doi.org/10.3390/v10100516
Received: 22 May 2018 / Revised: 11 September 2018 / Accepted: 14 September 2018 / Published: 21 September 2018
PDF Full-text (1963 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and [...] Read more.
Viroids are unencapsidated, single-stranded, covalently-closed circular, highly structured, noncoding RNAs of 239–401 nucleotides that cause disease in several economically important crop plants. In tomato (Solanum lycopersicum cv. Rutgers), symptoms of pospiviroid infection include stunting, reduced vigor, flower abortion, and reduced size and number of fruits, resulting in significant crop losses. Dramatic alterations in plant development triggered by viroid infection are the result of differential gene expression; in our study, we focused on the effect of tomato planta macho viroid (TPMVd) and Mexican papita viroid (MPVd) infection on gene networks associated with the regulation of flower and fruit development. The expression of several of the genes were previously reported to be affected by viroid infection, but two genes not previously studied were included. Changes in gene expression of SlBIGPETAL1 (bHLH transcription factor) and SlOVA6 (proline-like tRNA synthetase) are involved in petal morphology and fertility, respectively. Expression of SlOVA6 was down-regulated in flowers of TPMVd- and MPVd-infected plants, while expression of SlBIGPETAL1 was up-regulated in flowers. Up-regulation of SlBIGPETAL1 and down-regulation of SlOVA6 were positively correlated with symptoms such as reduced petal size and flower abortion. Expression analysis of additional tomato genes and a prediction of a global network association of genes involved in flower and fruit development and impacted by viroid infection may further elucidate the pathways underlying viroid pathogenicity. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessArticle Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid
Viruses 2018, 10(5), 257; https://doi.org/10.3390/v10050257
Received: 25 April 2018 / Revised: 9 May 2018 / Accepted: 12 May 2018 / Published: 15 May 2018
Cited by 3 | PDF Full-text (3438 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of [...] Read more.
Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in “Rutgers” tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage; (ii) early symptoms; (iii) full spectrum of symptoms and (iv) the so-called ‘recovery’ stage, when stem regrowth was observed in severely affected plants. Gene expression profiles differed depending on stage of infection and variant. In S23-infected plants, the expression of over 3000 genes was affected, while M-infected plants showed 3-fold fewer differentially expressed genes, only 20% of which were specific to the M variant. The differentially expressed genes included many genes related to stress; defense; hormone metabolism and signaling; photosynthesis and chloroplasts; cell wall; RNA regulation, processing and binding; protein metabolism and modification and others. The expression levels of several genes were confirmed by nCounter analysis. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Review

Jump to: Research, Other

Open AccessReview Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics
Viruses 2019, 11(2), 120; https://doi.org/10.3390/v11020120
Received: 3 January 2019 / Revised: 24 January 2019 / Accepted: 25 January 2019 / Published: 29 January 2019
PDF Full-text (661 KB) | HTML Full-text | XML Full-text
Abstract
Viroid discovery as well as the economic significance of viroids and biological properties are presented. Next-generation sequencing (NGS) technologies combined with informatics have been applied to viroid research and diagnostics for almost a decade. NGS provides highly efficient, rapid, low-cost high-throughput sequencing of [...] Read more.
Viroid discovery as well as the economic significance of viroids and biological properties are presented. Next-generation sequencing (NGS) technologies combined with informatics have been applied to viroid research and diagnostics for almost a decade. NGS provides highly efficient, rapid, low-cost high-throughput sequencing of viroid genomes and of the 21–24 nt vd-sRNAs generated by the RNA silencing defense of the host. NGS has been utilized in various viroid studies which are presented. The discovery during the last few years that prokaryotes have heritable adaptive immunity mediated through clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably genome engineering and most recently molecular diagnostics. The potential application of the CRISPR-Cas13a system for engineering viroid interference in plants is suggested by targeting specific motifs of three economically important viroids. The CRISPR-Cas13 system has been utilized recently for the accurate detection of human RNA viruses by visual read out in 90 min or less and by paper-based assay. Multitarget RNA tests by this technology have a good potential for application as a rapid and accurate diagnostic assay for known viroids. The CRISPR/Cas system will work only for known viroids in contrast to NGS, but it should be much faster. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessReview Insight into the Contribution and Disruption of Host Processes during HDV Replication
Viruses 2019, 11(1), 21; https://doi.org/10.3390/v11010021
Received: 29 November 2018 / Revised: 18 December 2018 / Accepted: 30 December 2018 / Published: 31 December 2018
PDF Full-text (704 KB) | HTML Full-text | XML Full-text
Abstract
Hepatitis delta virus (HDV) is unique among animal viruses. HDV is a satellite virus of the hepatitis B virus (HBV), however it shares no sequence similarity with its helper virus and replicates independently in infected cells. HDV is the smallest human pathogenic RNA [...] Read more.
Hepatitis delta virus (HDV) is unique among animal viruses. HDV is a satellite virus of the hepatitis B virus (HBV), however it shares no sequence similarity with its helper virus and replicates independently in infected cells. HDV is the smallest human pathogenic RNA virus and shares numerous characteristics with viroids. Like viroids, HDV has a circular RNA genome which adopts a rod-like secondary structure, possesses ribozyme domains, replicates in the nucleus of infected cells by redirecting host DNA-dependent RNA polymerases (RNAP), and relies heavily on host proteins for its replication due to its small size and limited protein coding capacity. These similarities suggest an evolutionary relationship between HDV and viroids, and information on HDV could allow a better understanding of viroids and might globally help understanding the pathogenesis and molecular biology of these subviral RNAs. In this review, we discuss the host involvement in HDV replication and its implication for HDV pathogenesis. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessReview Chrysanthemum Stunt Viroid Resistance in Chrysanthemum
Viruses 2018, 10(12), 719; https://doi.org/10.3390/v10120719
Received: 26 November 2018 / Revised: 12 December 2018 / Accepted: 13 December 2018 / Published: 17 December 2018
PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
Chrysanthemum stunt viroid (CSVd) is one of the most severe threats in Chrysanthemum morifolium production. Over the last decade, several studies have reported the natural occurrence of CSVd resistance in chrysanthemum germplasms. Such CSVd-resistant germplasms are desirable for the stable production of chrysanthemum [...] Read more.
Chrysanthemum stunt viroid (CSVd) is one of the most severe threats in Chrysanthemum morifolium production. Over the last decade, several studies have reported the natural occurrence of CSVd resistance in chrysanthemum germplasms. Such CSVd-resistant germplasms are desirable for the stable production of chrysanthemum plants. Current surveys include finding new resistant chrysanthemum cultivars, breeding, and revealing resistant mechanisms. We review the progress, from discovery to current status, of CSVd-resistance studies, while introducing information on the improvement of associated inoculation and diagnostic techniques. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Open AccessReview Vertical and Horizontal Transmission of Pospiviroids
Viruses 2018, 10(12), 706; https://doi.org/10.3390/v10120706
Received: 15 November 2018 / Revised: 3 December 2018 / Accepted: 5 December 2018 / Published: 12 December 2018
PDF Full-text (3410 KB) | HTML Full-text | XML Full-text
Abstract
Viroids are highly structured, single-stranded, non-protein-coding circular RNA pathogens. Some viroids are vertically transmitted through both viroid-infected ovule and pollen. For example, potato spindle tuber viroid, a species that belongs to Pospiviroidae family, is delivered to the embryo through the ovule or pollen [...] Read more.
Viroids are highly structured, single-stranded, non-protein-coding circular RNA pathogens. Some viroids are vertically transmitted through both viroid-infected ovule and pollen. For example, potato spindle tuber viroid, a species that belongs to Pospiviroidae family, is delivered to the embryo through the ovule or pollen during the development of reproductive tissues before embryogenesis. In addition, some of Pospiviroidae are also horizontally transmitted by pollen. Tomato planta macho viroid in pollen infects to the ovary from pollen tube during pollen tube elongation and eventually causes systemic infection, resulting in the establishment of horizontal transmission. Furthermore, fertilization is not required to accomplish the horizontal transmission. In this review, we will overview the recent research progress in vertical and horizontal transmission of viroids, mainly by focusing on histopathological studies, and also discuss the impact of seed transmission on viroid dissemination and seed health. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessReview Potato Spindle Tuber Viroid RNA-Templated Transcription: Factors and Regulation
Viruses 2018, 10(9), 503; https://doi.org/10.3390/v10090503
Received: 27 August 2018 / Revised: 10 September 2018 / Accepted: 15 September 2018 / Published: 17 September 2018
PDF Full-text (1888 KB) | HTML Full-text | XML Full-text
Abstract
Viroids are circular noncoding RNAs that infect plants. Without encoding any protein, these noncoding RNAs contain the necessary genetic information for propagation in hosts. Nuclear-replicating viroids employ DNA-dependent RNA polymerase II (Pol II) for replication, a process that makes a DNA-dependent enzyme recognize [...] Read more.
Viroids are circular noncoding RNAs that infect plants. Without encoding any protein, these noncoding RNAs contain the necessary genetic information for propagation in hosts. Nuclear-replicating viroids employ DNA-dependent RNA polymerase II (Pol II) for replication, a process that makes a DNA-dependent enzyme recognize RNA templates. Recently, a splicing variant of transcription factor IIIA (TFIIIA-7ZF) was identified as essential for Pol II to replicate potato spindle tuber viroid (PSTVd). The expression of TFIIIA-7ZF, particularly the splicing event, is regulated by a ribosomal protein (RPL5). PSTVd modulates its expression through a direct interaction with RPL5 resulting in optimized expression of TFIIIA-7ZF. This review summarizes the recent discoveries of host factors and regulatory mechanisms underlying PSTVd-templated transcription processes and raises new questions that may help future exploration in this direction. In addition, it briefly compares the machinery and the regulatory mechanism for PSTVd with the replication/transcription system of human hepatitis delta virus. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Graphical abstract

Other

Jump to: Research, Review

Open AccessCommentary Viroids as Companions of a Professional Career
Viruses 2019, 11(3), 245; https://doi.org/10.3390/v11030245
Received: 18 February 2019 / Revised: 7 March 2019 / Accepted: 8 March 2019 / Published: 12 March 2019
PDF Full-text (5379 KB) | HTML Full-text | XML Full-text
Abstract
Since the early 1970s when “virus-like” agents were considered as the cause of two diseases (potato spindle tuber and citrus exocortis), their study and further characterization have been linked to the development and use of molecular biology tools. Sucrose density gradient centrifugation and [...] Read more.
Since the early 1970s when “virus-like” agents were considered as the cause of two diseases (potato spindle tuber and citrus exocortis), their study and further characterization have been linked to the development and use of molecular biology tools. Sucrose density gradient centrifugation and polyacrylamide gel electrophoresis (PAGE) played a critical role in the pioneering studies of PSTVd and citrus exocortis viroid (CEVd). This was later modified by using other PAGEs (sequential PAGE, return PAGE, two-dimensional PAGE), and/or different staining methods (ethidium bromide, silver nitrate, etc.). Since then, disease-causing agents suspected to be viroids were usually subjected to a number of tests to define their: (i) Molecular nature (RNA or DNA; single stranded or double stranded; circular or linear RNA); (ii) molecular weight; (iii) secondary and tertiary structure. Further biological assays are also essential to establish the relationship of a viroid with plant disease and to fulfill Koch’s postulates. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
Figures

Figure 1

Open AccessCommentary Of Viroids and Prions
Viruses 2018, 10(12), 663; https://doi.org/10.3390/v10120663
Received: 29 September 2018 / Revised: 15 November 2018 / Accepted: 15 November 2018 / Published: 23 November 2018
PDF Full-text (156 KB) | HTML Full-text | XML Full-text
Abstract
In 2017, Hadidi et al. edited a voluminous monograph entitled “Viroids and Satellites”, in which each known viroid and viroid-like satellite species was described in detail from many perspectives by more than 100 experts from 24 countries. In its 700+ pages, the book [...] Read more.
In 2017, Hadidi et al. edited a voluminous monograph entitled “Viroids and Satellites”, in which each known viroid and viroid-like satellite species was described in detail from many perspectives by more than 100 experts from 24 countries. In its 700+ pages, the book is a much needed detailed and reliable compendium of a subject, which, undoubtedly, is still little known by many potential readers. Because most users of the book may be expected to be practical plant pathologists, it appears essential that the book contain, in addition to the detailed viroid and satellite descriptions, one chapter, in which the basic molecular biology of viroids and satellites is described. Full article
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Authors: Theodor O. Diener

Abstract: Viroids, the smallest known infectious pathogens, have been isolated only from infected higher plants. Why not from animals? Do they not exist in animals, or do we need methodolo- gies different from those used with plant viroids? Judging from literature, few efforts have been made to find animal viroids, which is surprising, because the first virus discovered was also a plant virus, tobacco mosaic virus, which was only later followed by the discovery of the first animal viruses and eventually to the thousands of viruses now comprising the virus kingdom. Thus, in analogy with the history of virus discovery, one would expect animal viroids not only to exist, but possibly to far outstrip the number and importance of plant viroids.
    A search for cited publications touching on the above question yielded few hits and no convincing evidence of the existence of animal viroids, but also not sufficient negative data to conclude that animal viroids do not exist [1].
    What might possibly explain the apparent disinterest of animal- (human-) virologists in the viroid discovery and its possibly important consequences beyond plant pathology? Offhand, we may point out three reasons:
    1. an imagined complexity of the plant virologists’ methodologies used for the isolation and characterization of plant viroids, best expressed by Ding [2], who thought “the classical approaches technically demanding and time consuming,” and thus discouraging in comparison to modern technologies with their plug-in platforms and ready-made intermediates;
    2. an excessive anthropocentric bias of many animal and medical investigators, who a priori discount results obtained in plant systems in the mistaken belief that they were of little concern to them, despite the fact that many important biological concepts were first developed in plant, not animal systems, such as, for example, those of mutation, the fundamental laws of genetics, the existence of submicroscopic (viruses) and subviral (viroids) organisms;
    3. an understandable hesitation, particularly by young, budding scientists, to enter a field of inquiry that may---or may not---yield pathbreaking new scientific insights, in preference to choosing less dramatic research, which likely leads to publishable results and good positions. They thereby reduce the number of scientists available to attack the more fundamental scientific questions and run the risk of becoming well trained technologists, but not scientists.
    Here, I discuss the meager crop of publications I located with some possible significance regarding the existence of animal viroids.

References
1, Diener, T. O. J. Virol. Antivir. Res, 2016; 5: 4
2. Zhang, Z. et al.PLoS Pathog. 10: e1004553

 

Title: Next-Generation Sequencing and CRISPR-Cas Proteins in Viroid Research and Diagnostics

Authors: Ahmed Hadidi

Abstract: Advances in next-generation sequencing (NGS) capabilities and the discovery during the last few years that bacteria and archaea have heritable adaptive immunity mediated through clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably DNA and RNA sequencing, gene editing and molecular diagnostics. NGS combined with informatics has been applied to viroids for almost a decade. NGS provides highly efficient, rapid, low cost high-throughput sequencing of viroid genomes and of the 21-24 nt viroid-derived small RNAs (vd-sRNAs) generated during the infection process. These vd-sRNAs, cover frequently the whole viroid genome. NGS has been used in a number of viroid studies including, but not limited to, discovery of novel viroids or viroid variants, detection and identification of known viroids, extending the known viroid host range, viroid-host interactions, viroid evolution and pathogenesis, mutation and quasispecies composition, mRNA targeting, symptom expression, and others. The potential applications of the CRISPR-Cas proteins for targeting viroid-specific nucleotide sites for genome editing were recently reported. Functionally relevant motifs of potato spindle tuber viroid, peach latent mosaic viroid and avocado sunblotch viroid that could be specifically targeted by CRISPR-based technologies were highlighted. The CRISPR-Cas systems have been utilized very recently for detection of two ssRNA human viruses, one synthetic ssRNA and one synthetic dsDNA in a single reaction by visual read out in less than 1.5 h. Multitarget RNA tests by the CRISPR-Cas systems have a good potential for its application as a rapid and accurate diagnostic assay for viroids.

Keywords: clustered regularly interspaced short palindromic repeats (CRISPR); CRISPR-Cas proteins; gene editing; molecular diagnostics; next-generation sequencing (NGS); viroids

Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top