Emerging and Reemerging Plant Viruses in a Changing World: 2nd 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: 28 February 2027 | Viewed by 3519

Editor


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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
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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

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Keywords

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

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Related Special Issue

Published Papers (4 papers)

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Research

13 pages, 7885 KB  
Communication
Plant Viral Metagenomic Analysis from a Preliminary Field Survey in Angola Reveals Complex Mixed Infections in Vegetable Crops
by Serafina Serena Amoia, Annalisa Giampetruzzi, Fernando Francisco de Sousa Neto, Luisa Flora António, Adérito Tomás Pais da Cunha and Angelantonio Minafra
Viruses 2026, 18(8), 822; https://doi.org/10.3390/v18080822 (registering DOI) - 26 Jul 2026
Abstract
Climatic changes are heavily affecting the sustainability of vegetable crops crucial for food supply worldwide, mainly in subtropical countries. One of the main threats to food security is the spread of diseases caused by plant viruses, favored by irregular rains and extreme temperatures, [...] Read more.
Climatic changes are heavily affecting the sustainability of vegetable crops crucial for food supply worldwide, mainly in subtropical countries. One of the main threats to food security is the spread of diseases caused by plant viruses, favored by irregular rains and extreme temperatures, which reduce crop yield and quality. During a preliminary field survey carried out in two provinces of Angola in 2024, a few symptomatic plants of tomato, habanero pepper, common bean and a wild weed were sampled. These plants generally showed dwarfing, yellowing and leaf curl and were submitted to high-throughput sequencing to detect any viral agent. The evidence of mixed infections of several polyphagous viruses with RNA or DNA genomes, variously affecting the selected plants, was assessed from the sequence analysis and further confirmed for most samples by molecular tests, like (RT)-PCR or qPCR. Emerging polero-, begomo and tobamoviruses were denoted as infecting these plants. A novel, previously unknown carlavirus was also described in a wild weed. Most of those viruses are efficiently mechanically transmitted or airborne vehiculated by insect vectors. Although based on a limited number of samples, this study provides a first insight into the diversity of viruses infecting vegetable crops in Angola. It also highlights the pressing need for a broader monitoring to better understand virus distribution and epidemiology, and suggests the use of virus-free seeds to reduce the potential risk to crop production. Full article
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16 pages, 5749 KB  
Article
High-Throughput Sequencing Reveals Previously Undetected Viruses and Mixed Infections in Pepper (Capsicum annuum) in Hungary
by Emese Demián, Réka Sáray, Asztéria Almási, Kata Pogácsás and Katalin Salánki
Viruses 2026, 18(4), 481; https://doi.org/10.3390/v18040481 - 21 Apr 2026
Viewed by 952
Abstract
The increasing global movement of plant material and the complexity of viral communities associated with cultivated crops complicate routine plant virus diagnostics. High-throughput sequencing (HTS) has therefore become an important tool for the comprehensive characterization of plant viromes. In this study, symptomatic pepper [...] Read more.
The increasing global movement of plant material and the complexity of viral communities associated with cultivated crops complicate routine plant virus diagnostics. High-throughput sequencing (HTS) has therefore become an important tool for the comprehensive characterization of plant viromes. In this study, symptomatic pepper (Capsicum annuum) samples submitted to our laboratory between 2020 and 2025 were investigated using HTS following unsuccessful routine diagnostic assays, despite the presence of virus-like symptoms. Virome analysis revealed the presence of multiple viruses with distinct biological characteristics. Eggplant mottled dwarf virus (EMDV) sequences were identified, representing, to our knowledge, the first sequence data from Hungary. In addition, sequences related to tobacco vein clearing virus (TVCV) showed highest similarity to endogenous viral element present in Capsicum annuum genome assemblies. Persistent viruses, including bell pepper alphaendornavirus (BPEV) and pepper cryptic virus 2 (PCV2), were also detected. These findings demonstrate the complex viral communities associated with cultivated pepper and highlight the limitations of strictly targeted diagnostic approaches. The results emphasize the value of HTS for comprehensive virome characterization in horticultural crops. Full article
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15 pages, 928 KB  
Article
Mild to Virulent: Coat Protein Mutations Restore Mosaic Symptom Induction in a Korean PepMV Isolate
by Thuy T. B. Vo, Marjia Tabassum, Ika Agus Rini, Bupi Nattanong, Hyo-Jin Im, Minkwan Kim, Hee-Seong Byun, Hae-Ryun Kwak and Sukchan Lee
Viruses 2026, 18(2), 175; https://doi.org/10.3390/v18020175 - 28 Jan 2026
Viewed by 1113
Abstract
Pepino mosaic virus (PepMV) is a significant threat to global tomato production, with symptom severity varying widely among strains and often leading to significant economic losses. Despite extensive studies on aggressive variants, the molecular determinants of mild symptomatology in field isolates, particularly from [...] Read more.
Pepino mosaic virus (PepMV) is a significant threat to global tomato production, with symptom severity varying widely among strains and often leading to significant economic losses. Despite extensive studies on aggressive variants, the molecular determinants of mild symptomatology in field isolates, particularly from Korea, remain underexplored. In this study, we characterized a mildly infecting PepMV isolate from asymptomatic tomato plants during a field survey in Jeonju, South Korea. The full-length genome sequence and phylogenetic analysis classified it as a CH2 strain. A full-length cDNA infectious clone of this isolate was constructed and confirmed to induce no mosaic symptoms in tomato plants. To identify symptom determinants, targeted mutagenesis was performed in the coat protein (CP) open reading frame. Substitution mutations at CP position 236 or combined 6/155 substitutions converted the mild isolate into a severe variant, inducing strong mosaic symptoms and significantly higher viral accumulation (up to tenfold). These results demonstrated that specific CP residues act as key regulators of symptom severity in PepMV CH2 strains and provide defined severe mutants as useful tools for screening resistance in tomatoes. Although the mechanism underlying symptom modulation remains unclear, this work advanced our understanding of molecular differences between mild and severe strains and supported targeted strategies for managing this economically important virus. Full article
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11 pages, 2041 KB  
Communication
Virome Analysis of Lemon Plants with Vein Clearing Symptoms Reveals Mixed Infection of Citrus Vein Clearing Virus, Iris Domestica Betaflexivirus 1 and Hop Stunt Viroid
by Myeonghwan Kwak, Eui-Joon Kil, Angelo De Stradis and Giuseppe Parrella
Viruses 2026, 18(1), 141; https://doi.org/10.3390/v18010141 - 22 Jan 2026
Viewed by 914
Abstract
Citrus yellow vein clearing virus (CYVCV) is the causative agent of the yellow vein clearing disease (YVCD), a worldwide and highly destructive disease in lemon (Citrus lemon) and sour orange trees (C. aurantium). The typical symptoms of vein clearing [...] Read more.
Citrus yellow vein clearing virus (CYVCV) is the causative agent of the yellow vein clearing disease (YVCD), a worldwide and highly destructive disease in lemon (Citrus lemon) and sour orange trees (C. aurantium). The typical symptoms of vein clearing are believed to be associated with CYVCV infection in citrus, so virus-specific diagnostic systems are currently used to confirm infection. In the present study, virome analysis based on high-throughput sequencing (HTS) on a lemon plant showing YVCD revealed mixed infection of CYVCV, iris domestica betaflexyviridae 1 (IDBV), and hop stunt viroid (HSVd). This multiple infection was confirmed in other two lemon plants with similar symptoms using virus/viroid specific primers. This is the first report of IDBV in lemon. Through molecular characterization and the reconstruction of phylogenetic relationships, a possible origin of the viruses/viroid identified in lemon has been hypothesized. Such mixed infections raise new questions about their role in the expression of YVCD symptoms observed on lemon. Full article
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