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Viruses
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Emerging and Reemerging Plant Viruses in a Changing World
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Emerging and Reemerging Plant Viruses in a Changing World

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: 31 August 2025 | Viewed by 4801

Special Issue Editors

Dr. Giuseppe Parrella

E-Mail Website
Guest Editor
Institute for Sustainable Plant Protection of Italian National Research Council (IPSP-CNR), Portici, NA, Italy
Interests: plant virome analysis; plant resistance to viruses; plant-virus-vector relationships
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Raed Alkowni

E-Mail Website
Guest Editor Assistant
Biology and Biotechnology Department, An-Najah National University, Nablus, Palestine
Interests: plant viruses; molecular detection; virus epidemiology; plant-virus-vector relationships

Special Issue Information

Dear Colleagues,

In recent years, numerous factors have contributed to the spread of serious viral diseases in plants. Some current examples include the epidemics caused by ToLCNDV in cucurbits in several countries of the Mediterranean basin, transmitted by its efficient vector Bemisia tabaci, and those caused by the ToBRFV, a seed-borne virus which is considered a global threat to tomato production. The establishment of a viral infection is genetically determined by the availability of host factors necessary for virus replication and movement, and by the balance between plant defense and the viral suppression of defense responses. Continuous planetary changes influence these factors and are relevant to such infections in their alteration of the pathogen’s pressure, the exposure to pathogens, the plant response to infection, or their ability to facilitate the introduction of viruses and vectors into new areas. Furthermore, the expansion of agricultural frontiers leads to greater contact between natural and altered ecosystems, increasing the exposure of plants to new viruses. In particular, ongoing climate change alters the distribution and phenology of plant virus vectors, resulting in the spread of viruses that have colonized or recolonized new areas and new hosts, most often in mixed infections, while global trade leads to the unwilling movement of plants, viruses, and vectors, contributing to their worldwide diffusion.

This Special Issue welcomes original research submissions and perspective and review articles focused on epidemiology, transmission pathways and natural cycles, and virulence and plant resistance concerning new emerging and re-emerging viruses. Methods papers covering the development and evaluation of diagnostic assays for the diagnosis of new emerging viruses are also welcome. Studies aiming at the discovery of new viruses (together with physiological insights into virus and/or host life histories), or at establishing the pathogenesis of viruses correlating to global changes, are also within the scope of this Special Issue.

Dr. Giuseppe Parrella
Guest Editor
Prof. Dr. Raed Alkowni
Guest Editor Assistant

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

  • emerging and re-emerging viruses
  • virus spillover
  • climate change and global trade
  • mixed infections
  • plant–virus–vector relationships

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Published Papers (5 papers)

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Research

15 pages, 2012 KiB  
Communication
Development of a Multiplex TaqMan Assay for Rapid Detection of Groundnut Bud Necrosis Virus: A Quarantine Pathogen in the USA
by Anushi Suwaneththiya Deraniyagala, Avijit Roy, Shyam Tallury, Hari Kishan Sudini, Albert K. Culbreath and Sudeep Bag
Viruses 2025, 17(4), 532; https://doi.org/10.3390/v17040532 - 5 Apr 2025
Viewed by 226
Abstract
Groundnut bud necrosis orthotospovirus (GBNV), a tripartite single-stranded RNA virus, poses a significant threat to United States agriculture. GBNV is a quarantine pathogen, and its introduction could lead to severe damage to economically important crops, such as groundnuts, tomatoes, potatoes, peas, and soybeans. [...] Read more.
Groundnut bud necrosis orthotospovirus (GBNV), a tripartite single-stranded RNA virus, poses a significant threat to United States agriculture. GBNV is a quarantine pathogen, and its introduction could lead to severe damage to economically important crops, such as groundnuts, tomatoes, potatoes, peas, and soybeans. For the rapid and accurate detection of GBNV at points of entry, TaqMan reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) assays were developed and the results validated using conventional reverse transcriptase–polymerase chain reaction (RT-PCR) followed by Sanger sequencing. These assays target highly conserved regions of the nucleocapsid (NP) and movement (MP) proteins within the viral genome. Multiplex GBNV detection assays targeting the NP and MP genes, as well as an internal control plant gene, ACT11, showed efficiency rates between 90% and 100% and R2 values of 0.98 to 0.99, indicating high accuracy and precision. Moreover, there was no significant difference in sensitivity between multiplex and singleplex assays, ensuring reliable detection across various plant tissues. This rapid, sensitive, and specific diagnostic assay will provide a valuable tool at ports of entry to prevent the entry of GBNV into the United States. Full article
(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)
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16 pages, 2806 KiB  
Article
Molecular Dissection of Symptom Determinants in Tomato Leaf Curl New Delhi Virus in Zucchini Through Mechanical Transmission
by Thuy T. B. Vo, Eui-Joon Kil, Marjia Tabassum, Bupi Nattanong, Muhammad Amir Qureshi, Hyo-Jin Im, Giuseppe Parrella, Taek-Kyun Lee and Sukchan Lee
Viruses 2025, 17(3), 294; https://doi.org/10.3390/v17030294 - 20 Feb 2025
Viewed by 474
Abstract
Among begomovirus species, tomato leaf curl New Delhi virus (ToLCNDV) is significant and stands out as a mechanically transmissible bipartite begomovirus originating from the Old World. However, the mechanisms underlying the mechanical transmission of different ToLCNDV strains remain understudied, as their natural transmission [...] Read more.
Among begomovirus species, tomato leaf curl New Delhi virus (ToLCNDV) is significant and stands out as a mechanically transmissible bipartite begomovirus originating from the Old World. However, the mechanisms underlying the mechanical transmission of different ToLCNDV strains remain understudied, as their natural transmission occurs via insect vectors. In this study, we investigated the mechanical transmissibility of two ToLCNDVs, one from Italy and another from Pakistan, in host plants. Several cucurbit species were screened, and symptom differences between the two ToLCNDV clones were observed only in zucchini when subjected to rubbing inoculation. The Italian isolate (ToLCNDV-ES) induced typical disease symptoms such as leaf curling, yellow mosaic, and internode stunting, whereas a normal phenotype was observed in zucchini mechanically infected with ToLCNDV-In (Pakistani isolate). Subsequently, a gene-swapping experiment between the two ToLCNDVs was conducted, and ToLCNDV-ES DNA-B was identified as a crucial factor in mechanical transmission. We then constructed chimeric mutant clones based on the DNA-B sequence and assessed their ability to induce symptoms in zucchini. These results indicated that the nuclear shuttle protein is a determinant of symptom development during ToLCNDV mechanical transmission. Moreover, several defense-related host genes showed significant changes in relative expression in different ToLCNDV clones, indicating their potential role in disease symptom development through the mechanical transmission of ToLCNDV. This is the first report comparing the mechanical transmissibility of two isolates of different ToLCNDV strains from the Mediterranean region and the Indian subcontinent in the same host plant, providing new insights into the virus’s pathogenicity across different geographic regions. Full article
(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)
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13 pages, 2108 KiB  
Article
Genomic, Evolutionary, and Pathogenic Characterization of a New Polerovirus in Traditional Chinese Medicine Viola philippica
by Yuanling Chen, Gaoxiang Chen, Jiaping Yu, Yali Zhou, Shifang Fei, Haorong Chen, Jianxiang Wu and Shuai Fu
Viruses 2025, 17(1), 114; https://doi.org/10.3390/v17010114 - 15 Jan 2025
Viewed by 779
Abstract
Viola philippica, a medicinal herbaceous plant documented in the Chinese Pharmacopoeia, is a promising candidate for research into plant-derived pharmaceuticals. However, the study of newly emerging viruses that threaten the cultivation of V. philippica remains limited. In this study, V. philippica plants [...] Read more.
Viola philippica, a medicinal herbaceous plant documented in the Chinese Pharmacopoeia, is a promising candidate for research into plant-derived pharmaceuticals. However, the study of newly emerging viruses that threaten the cultivation of V. philippica remains limited. In this study, V. philippica plants exhibiting symptoms such as leaf yellowing, mottled leaves, and vein chlorosis were collected and subjected to RNA sequencing to identify potential viral pathogens. A novel polerovirus, named Viola Philippica Polerovirus (VPPV), was identified in V. philippica. VPPV possesses a linear, positive-sense, single-stranded RNA genome consisting of 5535 nucleotides (nt) and encodes seven highly overlapping open reading frames (ORFs). Two potential recombination events were identified within ORF2, ORF3a, and ORF3, providing insights into the genetic diversity and evolution history of this novel polerovirus. An infectious cDNA clone of VPPV was successfully constructed and shown to infect Nicotiana benthamiana. Using a PVX-based heterologous expression system, the VPPV P0 protein was shown to trigger a systemic hypersensitive response (HR)-like reaction in N. benthamiana, indicating that P0 functions as the main pathogenicity determinant. These findings contributed to the detection and understanding of pathogenic mechanisms and control strategies for VPPV in V. philippica. Full article
(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)
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9 pages, 1331 KiB  
Article
A Survey of Wild Indigenous Cryptostylis ovata Orchid Populations in Western Australia Reveals Spillover of Exotic Viruses
by Stephen Wylie, Hua Li and Shu Hui Koh
Viruses 2025, 17(1), 108; https://doi.org/10.3390/v17010108 - 14 Jan 2025
Viewed by 733
Abstract
Cryptostylis ovata is a terrestrial orchid endemic to southwestern Australia. The virus status of C. ovata has not been studied. Eighty-three C. ovata samples from 16 populations were collected, and sequencing was used to identify RNA viruses from them. In one population, all [...] Read more.
Cryptostylis ovata is a terrestrial orchid endemic to southwestern Australia. The virus status of C. ovata has not been studied. Eighty-three C. ovata samples from 16 populations were collected, and sequencing was used to identify RNA viruses from them. In one population, all tested plants were co-infected with isolates of the exotic-to-Australia viruses Ornithogalum mosaic virus (OrMV) and bean yellow mosaic virus (BYMV). In another population, one plant was infected with BYMV. No viruses were detected in the remaining populations. The OrMV isolate shared 98–99% nucleotide identity with isolates identified from wild indigenous Lachenalia (Iridaceae) plants in South Africa. This suggests that the source of OrMV in C. ovata may be one or more bulbous iridaceous flowering plants of southern African origin that were introduced to Western Australia as ornamentals and that have since become invasive weeds. One BYMV isolate from C. ovata also exhibited 99% nucleotide identity with strains isolated from the exotic leguminous crop Lupinus angustifolius in Western Australia, suggesting possible spillover to indigenous species from this source. This study with C. ovata highlights the probable role of invasive weeds and exotic crops as sources of exotic virus spillovers to indigenous plants. Full article
(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)
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16 pages, 5639 KiB  
Article
An Alarming Eastward Front of Cassava Mosaic Disease in Development in West Africa
by Mariam Combala, Justin S. Pita, Michel Gbonamou, Alusaine Edward Samura, William J.-L. Amoakon, Bekanvié S. M. Kouakou, Olabode Onile-ere, Seydou Sawadogo, Guy R. Eboulem, Daniel H. Otron, John Steven S. Seka, Angela Eni, Cyrielle Ndougonna and Fidèle Tiendrébéogo
Viruses 2024, 16(11), 1691; https://doi.org/10.3390/v16111691 - 29 Oct 2024
Cited by 1 | Viewed by 1903
Abstract
Begomoviruses are a major threat to cassava production in Africa. Indeed, during the 1990s, the emergence of a recombinant begomovirus (East African cassava mosaic virus-Uganda, EACMV-Ug) resulted in crop devastation and severe famine in Uganda. In 2023, during a pre-survey of cassava farms [...] Read more.
Begomoviruses are a major threat to cassava production in Africa. Indeed, during the 1990s, the emergence of a recombinant begomovirus (East African cassava mosaic virus-Uganda, EACMV-Ug) resulted in crop devastation and severe famine in Uganda. In 2023, during a pre-survey of cassava farms at Forécariah, South-West Guinea, 22 samples showing peculiar cassava mosaic disease (CMD) symptoms were collected, and subsequent laboratory analysis confirmed the presence of EACMV-Ug in the samples. Deep analysis of DNA-A and DNA-B of the EACMV-Ug isolates from Guinea indicated that they are similar to those associated with the severe CMD epidemic in Uganda in the 1990s. Therefore, a country-wide survey was conducted throughout Guinea in April 2024 to evaluate the extent of the spread of EACMV-Ug in the country and to collect critical CMD epidemiological data. Findings showed a high whitefly population in Lower Guinea averaging 17 per plant; however, the data suggest a spread of EACMV-Ug via infected cuttings. High CMD incidence was found in Lower Guinea and Forest Guinea, whereas the highest CMD severity was observed in Forest Guinea (2.70 ± 0.06) and the lowest CMD severity was found in Middle Guinea (2.20 ± 0.05). Several cases of double and triple infections involving African cassava mosaic virus, East African cassava mosaic virus, East African cassava mosaic Cameroon virus, and EACMV-Ug were observed. EACMV-Ug was detected throughout Guinea, as well as from samples collected in 2022 in Kambia (Sierra Leone). The 63 accessions cultivated in Guinea that were assessed in this study were found susceptible to at least one of the viruses cited above. This study alerts us to an alarming situation in development in West Africa and provides scientific evidence to guide the rapid response needed to contain and stop the progression of EACMV-Ug in West Africa. Full article
(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)
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