Plant Virus Spillovers

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: closed (31 January 2026) | Viewed by 11651

Special Issue Editors


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Guest Editor
State Agricultural Biotechnology Centre, Murdoch University, Perth, Australia
Interests: plant and fungal viruses; wild plant viruses; spillover; virus evolution
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Visiting Research Fellow, The University of Adelaide, and Senior Research Scientist with the Australian Wine Research Institute, P.O. Box 197, Glen Osmond, Adelaide 5064, SA, Australia
Interests: grapevine viruses; viroids and phytoplasmas; molecular diagnosis; emerging viruses of the grapevine; elimination of viruses from the grapevine by thermotherapy and chemotherapy; molecular diagnosis of Grapevine Trunk Diseases (GTD)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Most previous plant virus research focused on viruses that damage economically important plants. Wild plant viruses are largely unknown to science, yet those that appear in crops have wild plant origins.

Some plant viruses that infect domesticated plants cause great economic losses, while others, probably the majority, cause negligible economic costs. Some of the most damaging plant viruses, ones that cost growers millions of dollars, include tobacco mosaic virus (TMV), cucumber mosaic virus (CMV), African cassava mosaic virus, and citrus tristeza virus. Every year, several papers are published that announce a ‘new’ virus discovered in a valuable crop species. Some of these viruses go on to wreak havoc across a region or the world, while others are never mentioned again. A recent example of the former is tomato brown rugose fruit virus that appeared for the first time in Israel in tomatoes in 2014 and has since travelled across the globe depleting tomato and capsicum harvests. Such viruses are not ‘new’ in the strictest sense of the word, they are old viruses that have emerged from wild plants growing at the interface between wild and cultivated plant communities. Less well known, but perhaps occurring just as frequently, are spillovers of viruses in the opposite direction—from crops to wild plant communities. And, of course, viruses also spillover from a wild species to another wild species and from one domestic species to another domestic species. 

Spillover and emergence are terms used to describe the process by which a virus successfully undertakes the colonization of a new host species. A challenging number of barriers must be negotiated before this is achieved: breaching the physical distance between the original and new hosts, gaining access to the appropriate cell type, successful interactions with the new cellular machinery, successful replication while not inducing apoptosis, cell to cell and systemic movement within the plant, and transmission to other individuals of the same species. Viruses such as TMV and CMV have successfully negotiated this process hundreds of times and are thereby referred to as ‘broad host-range’ viruses. Many other viruses remain marooned within a single host species and appear to pose a negligible risk of spillover. Why this is so is not clearly understood, but it may relate to an inability to negotiate one or more of the potential barriers listed above.

Wide spillovers of viruses between kingdoms have occurred over evolutionary time, such as with the endornaviruses that infect fungi, oomycetes, and plants. It is probable that ongoing human encroachment into the remaining wild communities, and the ecological changes wrought by a heating climate and the extinction crisis, may trigger further spillovers.

This Special Issue welcomes papers that describe new spillover events by plant, fungal, and oomycete viruses in wild and/or domesticated systems, those that increase our understanding of spillover mechanisms, and reviews addressing the relevant aspects of this topic.

Dr. Steve Wylie
Dr. Nuredin Habili
Guest Editors

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Keywords

  • spillover
  • emergence
  • replication
  • wild-plant virus
  • transmission
  • virus-cell interaction
  • vector

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Published Papers (7 papers)

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Research

17 pages, 2744 KB  
Article
The Alarming Eastward Front of Cassava Mosaic Disease Reported in Guinea and Sierra Leone Reaches Western Côte d’Ivoire
by Justin S. Pita, Fidèle Tiendrébéogo, Angela O. Eni, William J.-L. Amoakon, Bekanvié S. M. Kouakou, Mariam Combala, Aya Ange Nate Yoboue, Guy R. Eboulem, Daniel H. Otron, Maïmouna M. Koné, John Steven S. Seka, Richard A. K. Aka, Merveille Koissi Savi, Cyrielle Ndougonna and Nazaire K. Kouassi
Viruses 2026, 18(3), 319; https://doi.org/10.3390/v18030319 - 4 Mar 2026
Viewed by 1119
Abstract
Cassava mosaic begomoviruses are a major threat to cassava cultivation in Africa. The virulent Ugandan variant of the East African cassava mosaic virus (EACMV-Ug), which caused substantial damage to cassava production in Uganda in the 1990s and which was previously confined to East [...] Read more.
Cassava mosaic begomoviruses are a major threat to cassava cultivation in Africa. The virulent Ugandan variant of the East African cassava mosaic virus (EACMV-Ug), which caused substantial damage to cassava production in Uganda in the 1990s and which was previously confined to East and Central Africa, was recently found to be well established in Guinea and Sierra Leone in West Africa. Molecular analysis of cassava leaf samples from a nationwide cassava fields survey conducted in Côte d’Ivoire in 2022 suggested the absence of EACMV-Ug in the country in 2022. Given the proximity of some confirmed EACMV-Ug infected locations in Guinea to Côte d’Ivoire, we conducted another survey in 2025 along the entire western border of Côte d’Ivoire, bordering Guinea and Liberia, to update the status of EACMV-Ug in the country. Molecular analysis of the leaf samples collected confirmed the presence of EACMV-Ug in Côte d’Ivoire for the first time, along with other begomoviruses. The infection rate of EACMV-Ug along the Liberian border was higher (28.85%) than the 17.07% observed along the Guinean border. African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCMV) were detected both as a single infection and in double co-infections (ACMV+EACMCMV) in some plants, whereas EACMV-Ug was found as a double co-infection (EACMCMV+EACMV-Ug) and as a triple co-infection (ACMV+EACMCMV+EACMV-Ug). Our results also show that all the cassava varieties grown in the surveyed locations were susceptible to EACMV-Ug. Epidemiological assessment of cassava fields revealed that the incidence and severity of cassava mosaic disease (CMD) were significantly higher along the Liberian border compared to the Guinean border. However, whitefly populations were relatively low across the entire area surveyed. Furthermore, we found that the spread of CMD in the survey area was mainly through the use of infected cassava cuttings for the establishment of new farms. Based on these results, it is imperative to conduct an urgent nationwide cassava fields survey to assess the extent of EACMV-Ug spread in Côte d’Ivoire and implement containment measures to stop further spread. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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10 pages, 3681 KB  
Article
Metavirome Detection and Analysis of Viruses Present in Diseased Pumpkin in Shandong, China
by Kaijie Shang, Shenglin Luan, Qian Zhao, Xuli Gao, Weiqin Zhao, Xi Duan, Lehao Li, Wenbao Liu and Weihua Zhang
Viruses 2026, 18(2), 232; https://doi.org/10.3390/v18020232 - 12 Feb 2026
Viewed by 498
Abstract
Viral diseases pose a serious threat to pumpkin cultivation, which is an important cucurbitaceous vegetable crop. Recently, multi-virus mixed infections in plants have been continuously detected and reported. However, studies on mixed virus infections in pumpkins are limited. Through metavirome and polymerase chain [...] Read more.
Viral diseases pose a serious threat to pumpkin cultivation, which is an important cucurbitaceous vegetable crop. Recently, multi-virus mixed infections in plants have been continuously detected and reported. However, studies on mixed virus infections in pumpkins are limited. Through metavirome and polymerase chain reaction (PCR) analysis, we found that pumpkins exhibiting severe viral symptoms were co-infected with squash leaf curl China virus and tomato leaf curl New Delhi virus. Transcriptome analysis revealed that 2927 genes were upregulated, and 2273 were downregulated in virus-infected pumpkin plants, compared to the gene expression in healthy pumpkin plants. Cluster analysis showed that the expression of genes related to RNA silencing and the salicylic acid resistance pathway was higher in virus-infected pumpkin plants than in healthy pumpkin plants. Furthermore, quantitative real-time PCR confirmed that the expression pattern of genes related to RNA silencing and the salicylic acid resistance pathway aligned with the transcriptome sequencing results. Our findings provide a reference for investigating the mechanism of mixed infections by these two viruses to aid in the prevention and control of viral diseases in pumpkins. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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21 pages, 3352 KB  
Article
High-Throughput Sequencing Reveals Regional Diversification of Cucurbit-Infecting Begomoviruses in Eastern Saudi Arabia
by Muhammad Naeem Sattar, Sallah A. Al Hashedi, Mostafa I. Almaghasla, Sherif M. El-Ganainy, Adil A. Al-Shoaibi and Muhammad Munir
Viruses 2026, 18(1), 75; https://doi.org/10.3390/v18010075 - 5 Jan 2026
Viewed by 742
Abstract
In Saudi Arabia, cucurbit crops such as zucchini (Cucurbita pepo) and snake gourd (Trichosanthes cucumerina) are major vegetables and key dietary components, yet their associated viral threats remain poorly understood. We surveyed symptomatic cucurbit samples from greenhouses and open [...] Read more.
In Saudi Arabia, cucurbit crops such as zucchini (Cucurbita pepo) and snake gourd (Trichosanthes cucumerina) are major vegetables and key dietary components, yet their associated viral threats remain poorly understood. We surveyed symptomatic cucurbit samples from greenhouses and open fields in the Al-Ahsa and Qatif regions. The detection methods employed included PCR, RCA, and Illumina NGS. Based on nucleotide sequence comparisons and maximum-likelihood phylogenetic analysis, we identified three viruses, i.e., TYLCV, WmCSV, and ToLCPalV, present as both single and mixed infections. Sequence analyses revealed a novel strain, TYLCV-Hasa, representing a distinct lineage of TYLCV. Analysis revealed that recombination occurred solely in the DNA-A components of the identified viruses, while DNA-B segments showed no evidence of recombination. Notably, no DNA satellites were detected, suggesting cucurbits may act as independent reservoirs of begomovirus diversity. These results provide a comprehensive genomic insight into cucurbit-infecting begomoviruses in Eastern Saudi Arabia. The discovery of TYLCV-Hasa and evidence of recombination raise concerns about the emergence of novel viral variants that could pose risks to cucurbit cultivation. The results establish a foundation for advanced molecular surveillance and breeding strategies, contributing to improved food security and supporting Saudi Arabia’s Vision 2030 goals for sustainable agriculture. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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22 pages, 5682 KB  
Article
Contrasting Evolutionary Dynamics and Global Dissemination of the DNA-A and DNA-B Components of Watermelon Chlorotic Stunt Virus
by Zafar Iqbal
Viruses 2025, 17(12), 1571; https://doi.org/10.3390/v17121571 - 30 Nov 2025
Cited by 1 | Viewed by 762
Abstract
Watermelon chlorotic stunt virus (WmCSV), a bipartite begomovirus, poses a severe and expanding threat to global cucurbit and watermelon production, driving an urgent need to unravel its genetic diversity indices and evolutionary complexities. To elucidate its evolutionary history, this study investigated the genetic [...] Read more.
Watermelon chlorotic stunt virus (WmCSV), a bipartite begomovirus, poses a severe and expanding threat to global cucurbit and watermelon production, driving an urgent need to unravel its genetic diversity indices and evolutionary complexities. To elucidate its evolutionary history, this study investigated the genetic diversity, evolutionary dynamics, and global dispersal of its genomic components, DNA-A (WmA) and DNA-B (WmB). The analyses uncovered striking contrasts between the components. WmB exhibited markedly greater genetic diversity (π = 0.0508 vs. 0.0119 for WmA), a slightly faster evolutionary rate (1.26 × 10−4 vs. 1.44 × 10−3 substitutions/site/year), and a far more complex recombination profile, with 34 events detected compared to only one in WmA. The abundance of recombination breakpoints in WmB underscores its central role in shaping genomic variability and adaptive potential. Phylogenetic analyses of both components unveil eight robustly supported clades per segment, predominantly shaped by geographical boundaries, hinting at localized evolutionary trajectories with constrained long-distance gene flow, with the exception of Oman. Bayesian time-scaled phylogenies and phylogeographic reconstructions further illuminate distinct dissemination pathways, suggesting an intriguing origin, with WmA likely emerging from the United States and WmB tracing back to Saudi Arabia, while the Middle East emerges as a dynamic epicenter for regional spread and subsequent incursions into the Americas. Together, these findings reveal contrasting evolutionary forces driving WmCSV diversification and provide critical insights into its origins and ongoing global emergence. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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23 pages, 4964 KB  
Article
Genetic Diversity, Population Structure, and Cross-Border Dispersal Patterns of Tomato Leaf Curl Palampur Virus in South and West Asia
by Muhammad Naeem Sattar, Biju V. Chellappan, Sherif M. ElGanainy, Mustafa I. Almaghaslah, Sallah A. Al Hashedi and Adil A. Al-Shoaibi
Viruses 2025, 17(5), 678; https://doi.org/10.3390/v17050678 - 6 May 2025
Cited by 2 | Viewed by 2056
Abstract
Tomato leaf curl Palampur virus (ToLCPalV) is an economically important bipartite begomovirus in the agro-ecological regions in south and western Asia. This study was designed to investigate the sequence variation dynamics, regional delineation, genetic diversity, population structure, and cross-border dispersal patterns of ToLCPalV. [...] Read more.
Tomato leaf curl Palampur virus (ToLCPalV) is an economically important bipartite begomovirus in the agro-ecological regions in south and western Asia. This study was designed to investigate the sequence variation dynamics, regional delineation, genetic diversity, population structure, and cross-border dispersal patterns of ToLCPalV. The research revealed clear geographical structuring, with distinct Indo–Pak subcontinent and Middle Eastern clades, but no host-specific differentiation. Genetic diversity analysis indicated higher diversity in the Indo–Pak subcontinent, particularly in the DNA-B component, suggesting an older, more diverse population of ToLCPalV prevailing in this region. Neutrality tests and selection pressure analyses revealed predominantly purifying selection, with limited positive selection observed in BV1 of DNA-B. The primary source of dispersal of ToLCPalV progenitor was estimated in Varnasi, India in 1955, from where the virus was spread. No recombination events were detected, suggesting that mutation and selection are the primary drivers of ToLCPalV evolution. Furthermore, a detailed SDT-based nucleotide sequence comparison analysis also identified two potential strains of ToLCPalV. This study elucidates the spatiotemporal dynamics and evolutionary history of ToLCPalV, revealing its cross-border spread and adaptive evolution. These findings contribute to a more comprehensive understanding of begomovirus epidemiology and provide valuable insights into ToLCPalV’s phylogeography and evolutionary dynamics. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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19 pages, 2897 KB  
Article
Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection
by Raj Vansia, Malek Smadi, James Phelan, Aiming Wang, Guillaume J. Bilodeau, Stephen F. Pernal, M. Marta Guarna, Michael Rott and Jonathan S. Griffiths
Viruses 2024, 16(10), 1614; https://doi.org/10.3390/v16101614 - 15 Oct 2024
Viewed by 3129
Abstract
Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing [...] Read more.
Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato ringspot virus (genus Nepovirus), tobacco ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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18 pages, 2375 KB  
Article
A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses
by Mohammad Hajizadeh, Karima Ben Mansour and Adrian J. Gibbs
Viruses 2024, 16(9), 1351; https://doi.org/10.3390/v16091351 - 23 Aug 2024
Cited by 3 | Viewed by 1863
Abstract
Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their “centre of [...] Read more.
Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their “centre of emergence”. We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima’s D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility. Full article
(This article belongs to the Special Issue Plant Virus Spillovers)
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