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

A Special Issue of Viruses (ISSN 1999-4915) belonging to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: 28 February 2027 | Viewed by 9130

Editor

Prof. Dr. Akhtar Ali

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-anonymized 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

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Published Papers (6 papers)

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Research

28 pages, 4808 KB  
Article
Circular DNA Enrichment Sequencing (CIDER-Seq) Facilitated the Discovery of a New World (NW) Begomovirus–Alphasatellite Complex Associated with Leaf Curl Disease of Tomato in Morelos, Mexico
by Enrique Alejandro Guevara-Rivera, Edgar Antonio Rodríguez-Negrete, Karina Atriztán-Hernández, Beatríz Eugenia Jiménez-Moraila, Guillermo Corona-Armenta, Norma Elena Leyva-López, Marianne Lizbeth Mireles-Varela, Eduardo Rodríguez-Bejarano, Rosa Lozano-Durán and Jesús Méndez-Lozano
Viruses 2026, 18(9), 950; https://doi.org/10.3390/v18090950 - 30 Aug 2026
Viewed by 548
Abstract
A circular DNA enrichment sequencing (CIDER-Seq) approach identified a New World (NW) begomovirus–alphasatellite complex associated with a leaf curl disease of tomato from plants collected in Morelos, México. Using one of 21 samples showing virosis-associated symptoms, CIDER-Seq data revealed the presence of various [...] Read more.
A circular DNA enrichment sequencing (CIDER-Seq) approach identified a New World (NW) begomovirus–alphasatellite complex associated with a leaf curl disease of tomato from plants collected in Morelos, México. Using one of 21 samples showing virosis-associated symptoms, CIDER-Seq data revealed the presence of various NW begomovirus species, namely Begomovirus solanumaureivariati (tomato golden mottle virus: ToGMoV), Begomovirus solanumseveri (tomato severe leaf curl virus: ToSLCV), and Begomovirus solanumlapazense (tomato chino La Paz virus: ToChLPV). Additionally, the alphasatellites Whiflysatellite guatemalaense (whitefly-associated Guatemala alphasatellite 1: WfaGA1) and Clecrusatellite guatemalaense (whitefly-associated Guatemala alphasatellite 2: WfaGA2) were identified, demonstrating that begomoviruses can co-infect with alphasatellites; however, the pathogenic implications of the alphasatellite–helper begomovirus association remain incompletely understood. PCR-based detection and Sanger sequencing of circular viral genomes revealed a high frequency of detection of mixed infections comprising all components of the begomovirus–alphasatellite complex, confirming the reliability of the CIDER-Seq approach in producing high-fidelity sequences. Molecular and biological analysis revealed the complex adaptation to tomato, the monopartite nature of ToSLCV/ToChLPV species, and the ability of these begomovirus species to act as helper viruses. To the best of our knowledge, this is the first report of leaf curl disease of tomato associated with a begomovirus–alphasatellite complex in Mexico. Full article
(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)
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15 pages, 3252 KB  
Article
Phylogeographic Structure and Molecular Evolution of Squash Leaf Curl China Virus
by Jingwen Yu, Xue Han, Yaqin Liu, Deliang Peng, Huan Peng, Houxiang Kang, Mingjun Li, Gentu Wu, Ling Qing and Wenkun Huang
Viruses 2026, 18(7), 794; https://doi.org/10.3390/v18070794 - 19 Jul 2026
Viewed by 548
Abstract
Squash leaf curl China virus (SLCCNV) is an important geminivirus that infects cucurbit crops and is widely distributed across Asia. To elucidate its population structure and molecular evolution, 101 DNA-A and 67 DNA-B strain sequences of SLCCNV that were publicly available from 2001 [...] Read more.
Squash leaf curl China virus (SLCCNV) is an important geminivirus that infects cucurbit crops and is widely distributed across Asia. To elucidate its population structure and molecular evolution, 101 DNA-A and 67 DNA-B strain sequences of SLCCNV that were publicly available from 2001 to 2024 were analyzed. The strains clustered into three major geographic clades, including South Asia, the Malay Archipelago, and Mainland Southeast Asia. Recombination analysis revealed breakpoints mainly concentrated in the AC2 and BC1 regions. Signals of positive selection were indicated for AC4 and AC5 by selection pressure analysis. Significant genetic differentiation among SLCCNV populations from different geographic origins, but frequent gene flow was observed between among populations from South Asia, the Malay Archipelago, and Mainland Southeast Asia. In addition, AC5 and AV2 exhibited high variability at both the nucleotide and amino acid levels, while AC1, AC2, and AC3 were relatively conserved. Collectively, the evolutionary dynamics of SLCCNV are shaped by geographic isolation, recombination events, and differential selection pressures. This study provides important insights into the molecular evolution of SLCCNV and offers valuable guidance for region-specific surveillance, quarantine strategies, and the deployment of durable resistance against emerging viral variants. Full article
(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)
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30 pages, 5470 KB  
Article
Investigation of the Viromes of Solanaceous Weeds in Hungary Using High-Throughput Sequencing Adds New Insights to Their Hidden Complexity
by Burim Ismajli, Zsuzsanna N. Galbács, Lilla Dorottya Péri, György Pasztor, András Péter Takács and Éva Várallyay
Viruses 2026, 18(4), 474; https://doi.org/10.3390/v18040474 - 17 Apr 2026
Viewed by 1173
Abstract
Weed control of solanaceous weeds growing with solanaceous crops is a constant challenge. Infected by viruses, they can also act as virus reservoirs, complicating this problem further. Viromes of annual Solanum nigrum, Datura stramonium, and Solanum dulcamara, a perennial climbing [...] Read more.
Weed control of solanaceous weeds growing with solanaceous crops is a constant challenge. Infected by viruses, they can also act as virus reservoirs, complicating this problem further. Viromes of annual Solanum nigrum, Datura stramonium, and Solanum dulcamara, a perennial climbing shrub, were investigated using RNA sequencing and validated using RT-PCR, revealing infection with nine viruses. Broad bean wilt virus 1 (BBWV1), cucumber mosaic virus (CMV), and potato virus M (PVM) were found to infect S. nigrum. Investigating only 46 plants revealed infection with Solanum dulcamara yellow fleck virus (SDYFV) not only in S. dulcamara but in a new host, D. stramonium, which also represents a new host of turnip yellows virus (TuYV). We described the first presence of a potato virus H (PVH)-like, and Oxybasis rubra mitovirus 1 (OxruMV1)-like virus in Europe, in S. dulcamara as a new host. Our results highlight the unexpected complexity of the viromes of solanaceous weeds, which should be considered during reliable and efficient plant protection strategies, in order to alleviate the virus reservoir role of the weeds. Full article
(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)
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9 pages, 1116 KB  
Article
A Rapid, Cost-Effective RNA Recovery of Cowpea Mild Mottle Virus (CPMMV) Directly from PCR Tubes Adsorption for Routine-Scale Detection in Soybean
by Pedro Henrique Ribeiro, Marcos R. Ribeiro-Junior, Bárbara R. R. Silveira, Francisco M. Ochoa-Corona and Renate Krause-Sakate
Viruses 2026, 18(1), 41; https://doi.org/10.3390/v18010041 - 25 Dec 2025
Cited by 1 | Viewed by 1089
Abstract
This study describes an optimized plastic surface-based capsid protein adsorption/capturing method for detection of cowpea mild mottle virus (CPMMV) adapted from the direct antigen-capture method reported for the extraction of rose rosette virus (RRV) and other direct virus capturing attempts. Briefly, the method [...] Read more.
This study describes an optimized plastic surface-based capsid protein adsorption/capturing method for detection of cowpea mild mottle virus (CPMMV) adapted from the direct antigen-capture method reported for the extraction of rose rosette virus (RRV) and other direct virus capturing attempts. Briefly, the method starts with sap incubation, removal of unbound residual tissue and inhibitors by washing, and the viral RNA release using nuclease-free water and heat, in the presence of an RNase inhibitor. The protocol’s efficiency was assessed across different pH conditions, RNaseOUT concentrations, and reverse-transcriptase choices, and its performance was compared with commercial RNA-extraction methods. Three hundred thirty-two positive samples for CPMMV were processed using the optimized protocol (PBS-T, pH 7.4; RNaseOUT at 0.5 U/µL; and M-MLV reverse transcriptase). RT-PCR detection results were consistent with those obtained using the standard method. Cost estimates for tissue trapping indicate reductions of approximately 70% and 90% compared with the Qiagen RNeasy kit (Qiagen, Hilden, Germany) and the Bertheau method, respectively. The tissue-absorption protocol combines simplicity and low cost, making it particularly well suited for field diagnostics; by enabling rapid recovery of viral RNA without commercial kits and substantially reducing processing steps, it represents a practical, cost-effective alternative for routine CPMMV testing. Full article
(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)
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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
Cited by 5 | Viewed by 2975
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
(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)
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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 1788
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
(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)
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