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Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in...
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Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation

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 December 2026 | Viewed by 5193

Special Issue Editors

Dr. Judith K. Brown

E-Mail Website
Guest Editor
School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
Interests: Bemisia tabaci cryptic species; cacao viruses; cotton viruses; geminivirus–cotton–vegetable agroecosystem; psyllid-‘Ca. Liberibacter’ transmission pathway; soil rhizosphere–phyllosphere virome; water-transmissible plant viruses; whitefly-transmitted viruses; whitefly–virus transmission pathway
Dr. Jiban Kumar Kundu

E-Mail Website
Guest Editor
Plant Virus and Vector Interactions, Czech Agrifood Research Center, Drnovská 507, 16106 Prague, Czech Republic
Interests: plant virus and vector interactions; viruses of field and horticulture crops; resistance; diagnosis; plant defenses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Emerging and re-emerging plant viruses pose significant threats to global agriculture, impacting key food and fibre crops such as bananas, maize, potatoes, and wheat. These viruses can lead to substantial yield and economic losses. Emerging viruses are newly identified or have spread to new hosts or regions, while re-emerging viruses were once under control but have resurfaced due to factors like climate change, altered agricultural practices, and shifting crop varieties. Climate extremes and changing weather patterns affect the distribution of insect vectors, contributing to virus spread. Global trade further facilitates the movement of infected materials and vectors. Modern farming practices, such as monoculture and controlled environment systems, also create favourable conditions for virus and vector proliferation. The continuous evolution of viruses and their vectors complicates management efforts. Tackling these threats requires integrated approaches combining advanced research, early detection, better management strategies, and international cooperation.

The aim of this Special Issue is to bring together original research and review articles that highlight recent advancements and offer in-depth insights into emerging and re-emerging viruses and virus–vector complexes, within the context of evolving landscapes of crop and wild host species and changing environmental conditions.

We look forward to your contributions.

Dr. Judith K. Brown
Dr. Jiban Kumar Kundu
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 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

  • climate change and emerging/re-emerging virus threats
  • impact of virus evolution on the emerging/re-emerging virus diseases
  • innovative virus detection and surveillance methods
  • plant defense and virus resistance mechanisms responding to new outbreaks
  • plant defenses that respond to virus infection in lieu of extreme climate circumstances
  • plant virus diseases
  • plant–virus and/or plant–vector interactions, including tritrophic interactions
  • plant/crop resistance to viruses and/or arthropod vectors
  • strategies for management of viruses and vectors
  • virus–vector interactions
  • specific scenarios of emerging and reemerging viruses:
    • insect or mite-transmitted viruses of plants
    • seed-borne or seed-transmitted viruses of plants
    • soil-borne or soil-transmitted viruses
    • viruses infecting nursery crops and trees
    • water-borne or water-transmitted plant viruses

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Published Papers (5 papers)

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Research

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16 pages, 2881 KB  
Article
Serological and Molecular Characterization of Prevalent Olive-Associated Viruses in Saudi Arabia
by Mahmoud A. Amer, Muhammad Amir, Khadim Hussain, Ibrahim M. Al-Shahwan and Mohammed A. Al-Saleh
Viruses 2026, 18(3), 328; https://doi.org/10.3390/v18030328 - 6 Mar 2026
Viewed by 440
Abstract
A survey was carried out during 2023–2024, and 363 asymptomatic and symptomatic olive samples with deformed leaves, mosaic, and yellow spots were collected from different regions in Saudi Arabia. These samples were tested by ELISA against eight important olive viruses. To investigate the [...] Read more.
A survey was carried out during 2023–2024, and 363 asymptomatic and symptomatic olive samples with deformed leaves, mosaic, and yellow spots were collected from different regions in Saudi Arabia. These samples were tested by ELISA against eight important olive viruses. To investigate the presence of these viruses in olive trees, PCR and RT-PCR techniques were employed using the virus-specific primers. The obtained results from serological tests indicated that 44.4% of the collected samples were found to be positive with at least one of the tested viruses. The most prevalent virus was OEGV (14.3%), followed by ArMV (11.9%), SLRSV (11.3%), CLRV (9.4%), TuYV (5%), TNV-D (4.4%), OMMV (3.6%), whereas OLV-1, OLV-2, CMV, TMV, OLV-3, OLYaV, and OLRSV were not positive in the tested samples. Single, as well as mixed infections, were observed in a number of samples with 9.4% and 34.7%, respectively. The nucleotide sequence analysis of PCR amplified fragments revealed 99.7–100% identity to OEGV, 95–99% to TuYV, 85–98% to OMMV, 83–93% to ArMV, 92–97% to CLRV, 84–98% to TNV-D, and 85–97% to SLRSV isolates, according to the pairwise nucleotide identity percentage calculated by SDT software. This is the first comprehensive survey to investigate the genetic diversity and phylogenetic relationship of seven olive viruses detected in olive trees in Saudi Arabia, which can provide the missing local epidemiological understanding. Full article
(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)
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15 pages, 2242 KB  
Article
Historical and Contemporary Evidence Confirms a Higrevirus as the Causal Agent of Citrus Zonate Chlorosis in Brazil
by Laura R. Pereira, Mariane C. Rodrigues, Camila Chabi-Jesus, Pedro L. Ramos-González, Cristiane J. Barbosa, Magno G. Santos, Helcio Costa, Luana C. Maro, Aline D. Tassi, Elliot W. Kitajima, Ricardo Harakava and Juliana Freitas-Astúa
Viruses 2025, 17(11), 1428; https://doi.org/10.3390/v17111428 - 28 Oct 2025
Viewed by 1069
Abstract
Citrus leprosis (CL) and citrus zonate chlorosis (ZC) were first described in Brazil in the 1930s. Both diseases, which caused non-systemic lesions primarily characterized by chlorotic and/or necrotic spots, were associated with the presence of Brevipalpus mites. While CL has since been well [...] Read more.
Citrus leprosis (CL) and citrus zonate chlorosis (ZC) were first described in Brazil in the 1930s. Both diseases, which caused non-systemic lesions primarily characterized by chlorotic and/or necrotic spots, were associated with the presence of Brevipalpus mites. While CL has since been well characterized as being caused by viruses of the genera Cilevirus (family Kitaviridae) and Dichorhavirus (family Rhabdoviridae) and transmitted by several species of Brevipalpus mites, the causal agent of ZC remained unknown. In this study, we analyzed Citrus spp. samples exhibiting typical ZC symptoms using high-throughput sequencing (HTS) to determine the etiology of ZC. We examined historical herbarium specimens collected between 1933 and 1965 alongside fresh samples collected from 2016 to 2022. Our results identified the higrevirus hibiscus green spot virus 2 (HGSV2, Higrevirus waimanalo) as the causal agent of ZC. In addition, we report for the first time the presence of a higrevirus in continental America, expand the diversity of known kitaviruses infecting citrus in Brazil, and demonstrate the transmission of an higrevirus by Brevipalpus yothersi and B. papayensis. Full article
(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)
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12 pages, 1870 KB  
Article
A Novel Cogu-like Virus Identified in Wine Grapes
by Jennifer Dahan, Gardenia E. Orellana, Edison Reyes-Proaño, Jungmin Lee and Alexander V. Karasev
Viruses 2025, 17(9), 1175; https://doi.org/10.3390/v17091175 - 28 Aug 2025
Cited by 1 | Viewed by 1321
Abstract
A new negative-strand RNA virus was identified in grapevines from a 38-year-old ‘Chardonnay’ block in Idaho through high-throughput sequencing (HTS) of total RNA. This virus was tentatively named grapevine-associated cogu-like Idaho virus (GaCLIdV). GaCLIdV has three negative-sense, single-stranded RNA genome segments of ca. [...] Read more.
A new negative-strand RNA virus was identified in grapevines from a 38-year-old ‘Chardonnay’ block in Idaho through high-throughput sequencing (HTS) of total RNA. This virus was tentatively named grapevine-associated cogu-like Idaho virus (GaCLIdV). GaCLIdV has three negative-sense, single-stranded RNA genome segments of ca. 7 kb, 1.9 kb, and 1.3 kb, encoding L protein (RNA-dependent RNA polymerase, RdRP), a movement protein (MP), and a nucleocapsid protein (NC), respectively, identified based on pair-wise comparisons with other cogu- and cogu-like viruses. In phylogenetic analysis based on the RdRP, GaCLIdV grouped within the family Phenuiviridae and was placed in a lineage of plant-infecting phenuiviruses as a sister clade of the genus Laulavirus, clustering most closely with switchgrass phenui-like virus 1 (SgPLV-1) and more distantly related to grapevine-associated cogu-like viruses from the Laulavirus and Coguvirus clades. Both GaCLIdV and SgPhLV-1 are proposed to form a new genus, Switvirus, within the family Phenuiviridae. The presence of GaCLIdV in the original ‘Chardonnay’ samples was confirmed by RT-PCR amplification and Sanger sequencing. This new virus was found in five wine grape cultivars and in six vineyards sampled in Idaho and in Oregon during the 2020–2024 seasons. GaCLIdV may have contributed to the decline observed in the old ‘Chardonnay’ block, although the role of the virus in symptom development awaits further investigation. Full article
(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)
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28 pages, 3103 KB  
Article
First Complete Genome Sequence of Palo Verde Broom Emaravirus, Virus-Derived siRNA Signatures, and Phytohormone-Metabolite Profiling of Witches’ Broom-Affected Palo Verde Trees
by Raphael O. Adegbola, Muhammad Ilyas, Dinusha C. Maheepala, Ursula K. Schuch and Judith K. Brown
Viruses 2025, 17(8), 1122; https://doi.org/10.3390/v17081122 - 15 Aug 2025
Cited by 1 | Viewed by 1295
Abstract
Witches’ broom disease of blue palo verde (Parkinsonia florida) was reported more than sixty years ago. Characteristic symptoms consist of dense clusters of shortened, brittle branches and stunted leaves. The suspect causal agent has been identified as palo verde broom virus [...] Read more.
Witches’ broom disease of blue palo verde (Parkinsonia florida) was reported more than sixty years ago. Characteristic symptoms consist of dense clusters of shortened, brittle branches and stunted leaves. The suspect causal agent has been identified as palo verde broom virus (PVBV), genus, Emaravirus, family, Fimoviridae. Here, the first complete PVBV genome sequence was determined, and virus small interfering RNAs (vsiRNAs), primary metabolites, and phytohormone profiles were characterized from infected palo verde leaves, adventitious shoots, flowers, and seeds. Based on pairwise distances, PVBV RNAs 1–4 shared 54–65% nucleotide identity and 19–51% amino acid similarity, respectively, with other emaraviruses, while PVBV RNA 5 shared no sequence homology with any emaravirus. The 21–24-nt virus-derived vsiRNAs, indicative of post-transcriptional gene silencing (PTGS), represented nearly the entire PVBV genome in flowers, leaves, seeds, and adventitious shoots; however, PVBV RNA 3 and RNA 4 were most heavily targeted in all plant parts. Evidence that six major phytohormones were altered in PVBV-infected compared to virus-free trees indicated that emaravirus-infected trees mount classical defense responses to virus infection and/or eriophyid mite infestations. Detection of PVBV RNA genome segments 1–5, accumulation of predominantly 21-nt vsiRNAs, homologous to the PVBV genome and transcripts, and altered levels of phytohormones and metabolites in PVBV-infected trees strongly implicate PVBV as the causal agent of witches’ broom disease. Full article
(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)
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Review

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37 pages, 4424 KB  
Review
Australian Cool-Season Pulse Seed-Borne Virus Research: 3 Pea Seed-Borne Mosaic Virus
by Roger A. C. Jones and Benjamin S. Congdon
Viruses 2026, 18(3), 322; https://doi.org/10.3390/v18030322 - 4 Mar 2026
Viewed by 387
Abstract
Here, we adopt an historical approach towards reviewing research since the 1970s on the seed-borne virus diseases of cool-season pulses caused by pea seed-borne mosaic virus (PSbMV) in Australia’s grain cropping regions. All relevant investigations concerning the principal cool-season pulse crops infected; field [...] Read more.
Here, we adopt an historical approach towards reviewing research since the 1970s on the seed-borne virus diseases of cool-season pulses caused by pea seed-borne mosaic virus (PSbMV) in Australia’s grain cropping regions. All relevant investigations concerning the principal cool-season pulse crops infected; field pea, lentil, faba bean, chickpea, and the minor ones, Lathyrus species, vetches and narbon bean, are covered. However, as the PSbMV field pea pathosystem is the most studied, this receives greatest emphasis. The review starts with brief background information, and by describing the disease symptoms caused and the advances in sample testing procedures. Next, findings from past PSbMV studies are covered in greater detail including transmission by aphids, contact and seeds; occurrence in crops and seed stocks; pathotypes and genetic diversity; host resistance; and phytosanitary, cultural and chemical control measures. What these studies found about PSbMV biology, epidemiology and control is emphasized by describing past glasshouse and field experimentation. Then, practical research outcomes identifying PSbMV’s epidemic drivers, forecasting its epidemics and devising an integrated disease management strategy are emphasized. Examples of images that illustrate past investigations and research outputs are provided. Finally, principal research achievements and priorities for future Australian PSbMV cool-season pulse research are highlighted. Full article
(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)
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