Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics

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 April 2026 | Viewed by 3060

Special Issue Editor


E-Mail Website1 Website2
Guest Editor
Department of Biological Science, The University of Tulsa, Tulsa, OK, USA
Interests: emerging and re-emerging virus diseases; genetic diversity; mutations; recombination; reassortment; bottlenecks
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses are extraordinary biological entities capable of infecting all forms of life, including other viruses. Among them, plant-infecting viruses continue to pose a significant threat to global agriculture, causing devastating losses in crop productivity and quality. While direct control options for plant viruses are limited, effective management relies heavily on accurate diagnosis and an in-depth understanding of virus evolution.

This Special Issue will highlight recent advances in the diagnosis and evolutionary biology of plant viruses. Rapid, sensitive, and reliable diagnostic tools are essential in early detection and surveillance, forming the foundation of any effective disease management strategy. At the same time, the evolutionary dynamics of plant viruses, driven by various factors such as host resistance pressure, vector interactions, and environmental change continue to facilitate the emergence of new viral strains, complicating control efforts.

We invite contributions that explore innovative diagnostic techniques, molecular and evolutionary mechanisms of virus adaptation, and the factors contributing to viral emergence and spread in economically important crops. Manuscripts focusing on integrated strategies that link diagnostics and evolutionary insights to practical, long-term management solutions are particularly encouraged. This Special Issue will advance our understanding of plant virus evolution and guide future research into sustainable crop protection.

Prof. Dr. Akhtar Ali
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 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 250 words) can be sent to the Editorial Office for assessment.

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

  • high-throughput sequencing
  • RT-PCR and qRT-PCR
  • genetic diversity
  • virus evolution
  • mutations
  • reassortment
  • recombination

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

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

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

19 pages, 3052 KB  
Article
Genome-Wide Variation Profile of the Genus Tobamovirus
by Amany E. Gomaa and Hernan Garcia-Ruiz
Viruses 2025, 17(9), 1284; https://doi.org/10.3390/v17091284 - 22 Sep 2025
Viewed by 1673
Abstract
The genus Tobamovirus belongs to the family Virgaviridae, and the genome consists of monopartite, positive, single-strand RNA. Most species contain four open reading frames encoding four essential proteins. Transmission occurs primarily through mechanical contact between plants, and in some cases, via seed [...] Read more.
The genus Tobamovirus belongs to the family Virgaviridae, and the genome consists of monopartite, positive, single-strand RNA. Most species contain four open reading frames encoding four essential proteins. Transmission occurs primarily through mechanical contact between plants, and in some cases, via seed dispersal. Tobamovirus fructirugosum (tomato brown rugose fruit virus, ToBRFV), the most recently described species in the genus, was first reported in 2015. It overcame genetic resistance that had been effective in tomato for sixty years, causing devastating losses in tomato production worldwide, and highlights the importance of understanding Tobamovirus genomic variation and evolution. In this study, we measured and characterized nucleotide variation for the entire genome and for all species in the genus Tobamovirus. Additionally, we measured the selection pressure acting on each open reading frame. Results showed that low nucleotide diversity and negative selection pressure are general features of tobamoviruses, with values that are approximately the same across open reading frames and without hypervariable areas. A comparison of nucleotide diversity between T. fructirugosum and its close relatives, T. tomatotessellati (tomato mosaic virus, ToMV) and T. tabaci (tobacco mosaic virus, TMV), showed low nucleotide diversity in the movement protein region harboring the resistance-breaking mutation. Furthermore, phylogenetic and diversity analyses showed that T. fructirugosum continues to evolve, and geographical distribution and host influence genomic diversity. Full article
Show Figures

Graphical abstract

17 pages, 2037 KB  
Article
First Detection and Identification of Southern Tomato Virus Infecting Tomatoes in Oklahoma with Complete Genome Characterization and Insights into Global Genetic Diversity
by Salil Jindal and Akhtar Ali
Viruses 2025, 17(9), 1193; https://doi.org/10.3390/v17091193 - 30 Aug 2025
Viewed by 1140
Abstract
Southern tomato virus (STV) or Amalgavirus lycopersici is a persistent virus impacting tomato crops globally. This study identified new STV isolates from Oklahoma and analyzed their evolutionary relationship to global STV isolates. Phylogenetic analyses (complete genomes or individual genes) grouped STV isolates into [...] Read more.
Southern tomato virus (STV) or Amalgavirus lycopersici is a persistent virus impacting tomato crops globally. This study identified new STV isolates from Oklahoma and analyzed their evolutionary relationship to global STV isolates. Phylogenetic analyses (complete genomes or individual genes) grouped STV isolates into two distinct clades, independent of geographic origin or host. Notably, Oklahoma isolates formed a separate cluster from previously reported isolates in the United States of America (USA). Coalescent analysis suggested the most recent common ancestor of STV fusion protein emerged around 135 years ago. Genetic diversity among STV isolates was low, with slightly more variability in the RNA-dependent RNA polymerase (RdRp) gene than the p42 gene. Both genes showed strong purifying selection. No recombination events were detected across complete genomes. Structure analysis revealed that the p42 protein, particularly its C-terminal region, displayed higher disorder, indicating a possible role in host interactions and viral adaptability. These findings deepen our understanding of STV’s evolution and highlight the need for ongoing surveillance and broader genomic sampling. Full article
Show Figures

Figure 1

Back to TopTop