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Viruses
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Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition
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Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition

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: 30 June 2025 | Viewed by 3983

Special Issue Editors

Dr. Islam Hamim

E-Mail Website
Guest Editor
1. Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
2. Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 89081 Ulm, Germany
Interests: virology; plant pathology; insect/pollinator pathology; plant-microbe interactions; pesticide resistance; biodiversity and ecology of agriculture landscape
Special Issues, Collections and Topics in MDPI journals
Dr. Ken Komatsu

E-Mail Website
Guest Editor
Laboratory of Plant Pathology, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
Interests: plant pathology; plant virology; molecular biology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Hiromitsu Moriyama

E-Mail Website
Guest Editor
Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
Interests: plant protection science; applied microbiology; applied molecular cell biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genetic background of a virus in an infected plant or fungus is not uniform. The highly heterogeneous nature of virus populations affects symptom expressions in a host. Indeed, a virus isolated from a single plant often exhibits genomic sequence differences within sub-isolates and can impact phenotypic changes in a host. Coinfection with another virus alters symptom expression in a host plant, resulting in more severe symptoms and, eventually, worse disease consequences. Coinfections among fungal viruses may be also generated by two or more viruses that are phylogenetically diverse, and are very frequent in the field, sometimes even in laboratory conditions.

Therefore, the goal of this Special Issue is to invite respective scientists to submit original research articles, short communications, case studies and reviews regarding plant or fungal viruses. Manuscripts concerning a single virus or a mixture of viruses covering either individual or multiple host species are welcomed. The scope of this Special Issue includes, but is not limited to:

  • The detection, diversity and biology of viruses;
  • Virus emergence, ecology and evolution;
  • Diversity or co-infection or function of a virus or viruses;
  • Mechanisms of altered symptoms or phenotypic changes caused by interactions between different virus species or virus variants;
  • Pathogenesis and management of viruses or virus-like agents or virus variants.

Dr. Islam Hamim
Dr. Ken Komatsu
Prof. Dr. Hiromitsu Moriyama
Guest Editors

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 submissions that pass pre-check are 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 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

  • diagnosis
  • surveillance
  • molecular mechanism
  • viroid
  • subviral agents
  • mycoviruses
  • biological control
  • pesticide resistance
  • antiviral defense mechanism
  • population genetics
  • recombination
  • gene expressions
  • host range

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

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17 pages, 819 KiB  
Article
High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic
by Karima Ben Mansour, Igor Koloniuk, Jana Brožová, Marcela Komínková, Jaroslava Přibylová, Tatiana Sarkisova, Jiří Sedlák, Josef Špak and Petr Komínek
Viruses 2025, 17(5), 650; https://doi.org/10.3390/v17050650 (registering DOI) - 29 Apr 2025
Abstract
Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. [...] Read more.
Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. Additionally, two novel viruses, ARWV1 and ARWV2 were identified for the first time in the Czech Republic. Phylogenetic analyses showed low genetic variability among ARWV2 isolates, suggesting a possible recent introduction or limited diversification. In contrast, ARWV1 isolates displayed distinct clustering in the coat protein coding region, separating symptomatic and asymptomatic samples, indicating a potential involvement of genetic determinants in symptom expression. Mixed infections were prevalent, with multiple molecular variants of ACLSV, ASPV, and AGCaV detected within individual samples, along with co-infections involving viruses from different families. Recombination analysis identified frequent recombination events in ACLSV and ASPV, often involving non-apple parental sequences, suggesting their potential for cross-host infections. Additionally, an interspecific recombination event was detected in an almond ApMV isolate, with PNRSV as a minor parent. These findings highlight the impact of agricultural practices on viral evolution and host adaptation. This study demonstrates the utility of HTS as a powerful tool for uncovering viral diversity, recombination events, and evolutionary dynamics. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition)
10 pages, 1290 KiB  
Article
Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay
by Juliana Osse de Souza, Vicki Klaassen, Kristian Stevens, Teresa M. Erickson, Claire Heinitz and Maher Al Rwahnih
Viruses 2024, 16(9), 1457; https://doi.org/10.3390/v16091457 - 13 Sep 2024
Viewed by 1007
Abstract
The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long [...] Read more.
The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition)
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Review

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22 pages, 422 KiB  
Review
Mycologists and Virologists Align: Proposing Botrytis cinerea for Global Mycovirus Studies
by Mahmoud E. Khalifa, María A. Ayllón, Lorena Rodriguez Coy, Kim M. Plummer, Anthony R. Gendall, Kar Mun Chooi, Jan A.L. van Kan and Robin M. MacDiarmid
Viruses 2024, 16(9), 1483; https://doi.org/10.3390/v16091483 - 18 Sep 2024
Viewed by 2673
Abstract
Mycoviruses are highly genetically diverse and can significantly change their fungal host’s phenotype, yet they are generally under-described in genotypic and biological studies. We propose Botrytis cinerea as a model mycovirus system in which to develop a deeper understanding of mycovirus epidemiology including [...] Read more.
Mycoviruses are highly genetically diverse and can significantly change their fungal host’s phenotype, yet they are generally under-described in genotypic and biological studies. We propose Botrytis cinerea as a model mycovirus system in which to develop a deeper understanding of mycovirus epidemiology including diversity, impact, and the associated cellular biology of the host and virus interaction. Over 100 mycoviruses have been described in this fungal host. B. cinerea is an ideal model fungus for mycovirology as it has highly tractable characteristics—it is easy to culture, has a worldwide distribution, infects a wide range of host plants, can be transformed and gene-edited, and has an existing depth of biological resources including annotated genomes, transcriptomes, and isolates with gene knockouts. Focusing on a model system for mycoviruses will enable the research community to address deep research questions that cannot be answered in a non-systematic manner. Since B. cinerea is a major plant pathogen, new insights may have immediate utility as well as creating new knowledge that complements and extends the knowledge of mycovirus interactions in other fungi, alone or with their respective plant hosts. In this review, we set out some of the critical steps required to develop B. cinerea as a model mycovirus system and how this may be used in the future. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition)
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