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Plant virus

Plant viruses are obligate intracellular parasites that infect plant cells, consisting of a nucleic acid genome—most commonly single-stranded RNA, though some are DNA-based—enclosed within a protective protein coat, and they replicate solely using the host's cellular machinery without independent metabolic activity.^[1] These viruses are non-cellular entities, ranging in size from approximately 30 nanometers for spherical forms to 300 by 18 nanometers for rod-shaped ones like the Tobacco mosaic virus (TMV), and they remain dormant outside living hosts until transmitted to a susceptible plant.^[1] More than 2,000 distinct plant viruses have been identified, classified into 49 families and 73 genera, with the majority featuring positive-sense single-stranded RNA genomes that encode between one and twelve proteins essential for replication and movement within the plant.^[2]^[3] Plant viruses exhibit diverse host ranges, from broad-spectrum infections affecting multiple crop species—such as Cucumber mosaic virus, which impacts over 1,200 plant types—to highly specific ones limited to particular hosts like the Sowbane mosaic virus.^[4] They induce a variety of symptoms depending on the virus-host interaction, including mosaic patterns of light and dark green on leaves, chlorosis (yellowing), necrosis (tissue death), stunting, leaf distortion, ringspots, and deformed flowers or fruits, which can severely compromise plant growth and yield.^[5] Transmission occurs through multiple vectors and mechanisms, such as insects (e.g., aphids, whiteflies, thrips), nematodes, fungi, mechanical wounding via tools or contact, seeds, pollen, grafting, or vegetative propagation, with some viruses like TMV persisting in the environment for decades.^[1] Economically, plant viruses represent a major threat to global agriculture, infecting nearly all cultivated plants and causing billions in annual losses; for instance, Tomato spotted wilt virus results in approximately $1 billion in damages yearly, while Rice tungro virus leads to $1.5 billion in crop reductions.^[1] Ecologically, they influence plant community dynamics, biodiversity, and interactions with other organisms, such as affecting pollinator behavior and natural vegetation resilience. Control strategies focus on prevention through certified virus-free planting material, vector management with insecticides or reflective mulches, sanitation practices like tool disinfection, and breeding or genetic engineering for host resistance, as exemplified by transgenic papaya varieties resistant to Papaya ringspot virus.^[5] Despite these measures, the absence of curative treatments underscores the importance of integrated approaches to mitigate their impact on food security and horticulture.^[4]

Overview

Definition and characteristics

Plant viruses are obligate intracellular parasites composed of a nucleic acid genome—either RNA or DNA—enclosed in a protective protein coat called a capsid, with some species featuring an additional outer lipoprotein envelope.^[1]^[6] Unlike cellular life forms, they possess no independent metabolic or reproductive capabilities, existing as inert particles outside host cells and relying entirely on the host plant's cellular machinery for uncoating, genome replication, protein synthesis, and virion assembly.^[1]^[7] This dependence defines their non-cellular nature, distinguishing them from bacteria, fungi, or other microbial pathogens that can grow autonomously.^[1] Their virions typically range in size from 20 to 300 nm, encompassing various morphologies such as isometric (spherical), rod-shaped, or filamentous forms.^[8] For example, many spherical plant viruses measure about 30 nm in diameter, while rod-shaped ones can extend up to 300 nm in length and 18 nm in width.^[1] A representative case is the Tobacco mosaic virus (TMV), a rigid rod-shaped virus with a single-stranded RNA genome of approximately 6,400 nucleotides encapsidated by over 2,000 copies of its coat protein, serving as a foundational model in plant virology.^[1] Plant viruses exhibit a host range restricted to plants, unable to directly infect animals or humans due to the lack of compatible receptors on non-plant cells.^[7]^[9] Genomes are predominantly single-stranded RNA (positive-sense), though variations include double-stranded RNA, single-stranded DNA, or double-stranded DNA in certain families.^[1] This plant-specific adaptation ensures their replication occurs solely within plant cells, hijacking host processes without the virus possessing its own ribosomes or energy-producing systems.^[1]^[6]

Economic and ecological significance

Plant viruses impose substantial economic burdens on global agriculture, contributing to significant annual crop yield losses worldwide and costing over $30 billion USD in damages. These losses threaten food security by reducing the productivity of staple and cash crops, with viruses accounting for nearly half of all infectious plant diseases in some assessments. For instance, Potato virus Y (PVY) alone causes significant reductions in potato yields, leading to economic impacts in major producing regions such as North America and Europe, where it diminishes tuber quality and market value. Similarly, Tomato mosaic virus affects tomato production, while Tobacco mosaic virus has historically devastated tobacco crops, and Citrus tristeza virus leads to widespread decline in citrus orchards, collectively underscoring the vulnerability of these key commodities.^[10]^[11]^[12] In sub-Saharan Africa, Cassava mosaic disease, caused by begomoviruses, exemplifies the severe socioeconomic consequences, resulting in annual economic losses of $1.9-2.7 billion USD in East and Central Africa and contributing to famine risks by slashing cassava yields—a critical staple for over 300 million people—by up to 50% in affected fields. This disease not only hampers food availability but also exacerbates poverty among smallholder farmers reliant on cassava for both subsistence and income. Beyond direct agricultural impacts, plant viruses influence global trade and rural economies, as infected crops face quarantines and reduced export values, amplifying food insecurity in developing regions.^[13]^[14] Ecologically, plant viruses play multifaceted roles in shaping ecosystems, influencing plant community structure, biodiversity, and interspecies interactions beyond their pathogenic effects. In natural settings, viruses can drive evolutionary adaptations in wild plants, potentially maintaining genetic diversity by selecting for resistant genotypes and altering competitive dynamics among species. For example, viral infections in wild flora may modify plant defenses and chemistry, indirectly affecting herbivore populations and pollinator behaviors, thereby influencing food webs and symbiosis in terrestrial ecosystems. Studies indicate that agriculture-induced changes, such as monocultures, can amplify virus spillover from crops to wild plants, reducing overall biodiversity and ecosystem resilience.^[15]^[16]^[17] Recent data from 2024-2025 highlight rising ecological and economic pressures from plant viruses, exacerbated by climate-driven shifts in vector distributions and host susceptibility. Warmer temperatures and altered precipitation patterns are projected to increase viral epidemics, with models forecasting a 20% rise in incidence in temperate zones by 2050 due to expanded ranges of aphid and other insect vectors. These changes could intensify biodiversity loss in vulnerable ecosystems while heightening crop vulnerabilities, particularly in regions like Europe and North America, underscoring the need for integrated surveillance to mitigate future outbreaks.^[18]^[19]^[20]

History

Early discoveries

In the late 19th century, observations of plant diseases began to reveal infectious agents smaller than bacteria. In 1882, Adolf Mayer, a German agricultural chemist, conducted experiments on the mosaic disease affecting tobacco plants in the Netherlands, noting that the disease spread through contact with infected plants or soil and could be transmitted via sap from diseased leaves to healthy ones. Mayer attempted to identify a bacterial cause using standard microbiological techniques but failed.^[21] Building on Mayer's work, Russian botanist Dmitri Ivanovsky investigated the same tobacco mosaic disease in 1892. He extracted sap from infected tobacco leaves and passed it through porcelain Chamberland filters with pores approximately 0.2 μm in diameter, designed to trap bacteria. Remarkably, the filtered sap remained infectious when applied to healthy tobacco plants, producing mosaic symptoms identical to the original disease. Ivanovsky suggested this indicated a sub-bacterial agent, possibly a toxin produced by bacteria, marking the first experimental evidence of a filterable pathogen in plants.^[22] In 1898, Dutch microbiologist Martinus Beijerinck independently replicated and extended Ivanovsky's filtration experiments on tobacco mosaic disease. Beijerinck demonstrated that the infectious agent multiplied within host plants, diffused through agar gels like a fluid, and could not be cultured on nutrient media, distinguishing it from bacteria. He coined the term "contagium vivum fluidum" (living infectious fluid) to describe this self-replicating, filterable entity that reproduced in partnership with the host cell's metabolism, laying the conceptual foundation for viruses as distinct biological agents.^[23] Early 20th-century research confirmed the particulate nature of plant viruses. In 1935, American biochemist Wendell Meredith Stanley isolated and crystallized the tobacco mosaic virus (TMV) from infected plant material, obtaining pure protein crystals that retained infectivity and induced disease symptoms upon inoculation. This achievement demonstrated that viruses could behave as crystallizable macromolecules, bridging chemistry and biology. For his pioneering work on virus purification and structure, Stanley shared the 1946 Nobel Prize in Chemistry with James B. Sumner and John H. Northrop.^[24]

Key scientific milestones

In the 1940s and 1950s, the advent of electron microscopy revolutionized plant virology by enabling the first direct visualization of plant virus particles, including the rod-shaped virions of Tobacco mosaic virus (TMV), which confirmed their submicroscopic nature and facilitated initial structural classifications.^[25] This technology, developed during World War II, allowed researchers to observe viral morphology in detail, such as the helical symmetry in TMV, paving the way for understanding assembly and infection mechanisms.^[26] By the 1960s, electron microscopy had identified diverse virion shapes among plant viruses, including isometric particles in viruses like Tomato bushy stunt virus, advancing taxonomic efforts.^[27] The complete genome of TMV RNA, the first for any plant virus, was sequenced in 1982, revealing a 6395-nucleotide single-stranded RNA with four open reading frames encoding replicase, movement protein, coat protein, and a 183-kDa protein.^[28] In 1971, Theodor O. Diener discovered viroids, small (∼250–400 nucleotides), circular, non-protein-coding RNAs that cause diseases like potato spindle tuber, marking the identification of the smallest known pathogens and expanding concepts of infectivity beyond protein-coated viruses.^[29] Satellite viruses and satellite RNAs, dependent on helper viruses for replication and transmission, were first recognized in the 1960s with the satellite of Tobacco necrosis virus, and further characterized in the 1970s, such as Satellite tobacco mosaic virus.^[30] During the 1970s and 1980s, recombinant DNA techniques enabled the cloning of plant viral genes, exemplified by the insertion of TMV coat protein into plasmids for expression studies, which elucidated gene functions and supported the development of viral vectors for plant transformation.^[31] By the 1990s, these methods had been applied to engineer virus-resistant plants, such as those expressing TMV replicase transgenes to induce RNA silencing.^[27] In the 2000s, high-throughput sequencing (HTS) technologies, including 454 pyrosequencing and Illumina platforms, facilitated the discovery of thousands of novel plant viruses through metagenomic surveys of symptomatic crops, revealing diverse RNA and DNA genomes in mixed infections.^[32] This approach identified previously undetected viruses like Grapevine leafroll-associated virus variants and expanded virome catalogs.^[33] In 2011, a consensus "Top 10" list of plant viruses was published, ranking economically significant pathogens such as TMV, Tomato spotted wilt virus, and Cucumber mosaic virus based on scientific impact and research volume.^[34] Recent advances in the 2020s include CRISPR-based antiviral strategies, with a 2023 laboratory study demonstrating Cas13d (CasRx)-mediated resistance to Grapevine virus A in the model plant Nicotiana benthamiana by targeting viral RNA.^[35] Additionally, AI-driven models like the 2024 AutoPVPrimer pipeline integrate machine learning to predict and design primers for detecting diverse plant viruses, enhancing diagnostic efficiency and enabling rapid identification of emerging threats.^[36]

Classification

Taxonomic framework

The taxonomic classification of plant viruses is governed by the International Committee on Taxonomy of Viruses (ICTV), which establishes a hierarchical system to organize viruses based on shared characteristics. This framework aligns with a Linnaean-like structure, utilizing primary ranks including realm, kingdom, phylum, class, order, family, genus, and species, with optional intermediate subranks such as subrealm, subkingdom, subphylum, subclass, suborder, subfamily, and subgenus to accommodate finer distinctions.^[37]^[38] Classification criteria for plant viruses emphasize molecular and biological properties, including genome type (such as single-stranded RNA [ssRNA], double-stranded RNA [dsRNA], single-stranded DNA [ssDNA], or double-stranded DNA [dsDNA]), replication strategy (e.g., RNA-dependent RNA polymerase usage or reverse transcription), virion morphology (e.g., helical, icosahedral, or enveloped particles), and host range (primarily plants, with considerations for vector specificity and transmission modes). These attributes are assessed through sequence comparisons, phylogenetic analyses, and phenotypic data to delineate taxa, ensuring polythetic groupings where no single criterion is absolute but combinations define boundaries.^[39]^[40] As of 2025, the ICTV recognizes over 2,500 plant virus species, with the majority—approximately 90%—falling within the realm Riboviria, reflecting the dominance of RNA viruses among plant pathogens.^[41]^[2] Recent updates to the plant virus taxonomy, ratified in 2025 by the ICTV Plant Viruses Subcommittee, incorporated metagenomics data to classify numerous uncultured viruses, leading to the addition of 206 new species, one new order (Tombendovirales in Riboviria), three new families, six new genera, and two new subgenera. These revisions, building on high-throughput sequencing advancements, enhanced the framework by integrating genomic sequences from environmental samples without prior isolation, thereby expanding recognition of cryptic viral diversity in plant hosts.^[41]^[42]

Major virus families and genera

The Potyviridae family represents the largest group of plant-infecting viruses, comprising over 200 species with single-stranded, positive-sense RNA genomes and flexuous filamentous virions.^[43] This family is responsible for significant agricultural losses worldwide due to its diverse hosts and efficient aphid transmission. A prominent example is the genus Potyvirus, which includes Potato virus Y (Potyvirus potyvirus Y), a major pathogen of solanaceous crops like potatoes and tomatoes, causing symptoms such as leaf mosaics, necrotic streaks, and stunted growth.^[44] The Geminiviridae family consists of plant viruses with circular single-stranded DNA genomes packaged in distinctive twinned (geminate) particles, primarily affecting dicotyledonous crops in warmer climates. The genus Begomovirus is particularly impactful, with species like Tomato yellow leaf curl virus (Begomovirus tomato yellow leaf curl virus) causing severe yield reductions in tomato production through symptoms including leaf curling, yellowing, and plant stunting. This virus is efficiently transmitted by whitefly vectors (Bemisia tabaci) and poses a major threat in tropical and subtropical regions.^[45] Members of the Bromoviridae family possess tripartite or bipartite single-stranded, positive-sense RNA genomes and icosahedral virions, often exhibiting broad host ranges and mechanical or insect transmission. The genus Cucumovirus exemplifies this diversity, with Cucumber mosaic virus (Cucumovirus cucumovirus) infecting over 1,200 species across more than 100 plant families, leading to mosaic patterns, stunting, and fruit deformation in crops like cucumbers, tomatoes, and ornamentals.^[46] The Caulimoviridae family includes double-stranded DNA pararetroviruses that replicate via reverse transcription without integrating into the host genome, forming episomal minichromosomes in the nucleus. The genus Caulimovirus features Cauliflower mosaic virus (Caulimovirus cauliflower mosaic virus), which infects brassicas and other dicots, causing mosaic symptoms and vein chlorosis, and is transmitted by aphids in a non-persistent manner.^[47] Recent taxonomic updates as of 2025 highlight emerging threats from segmented RNA viruses, such as those in the genus Emaravirus (family Fimoviridae), which possess multipartite negative-sense RNA genomes and affect woody plants through ringspot and decline symptoms. A new species, Emaravirus clematis (associated with Clematis yellow mottle-associated virus), was ratified, underscoring the ongoing discovery of these vectors-transmitted pathogens in horticultural crops.^[42]

Structure and genome

Virion morphology

Plant virus virions exhibit diverse morphologies, primarily non-enveloped structures that protect the enclosed genome and facilitate transmission. The most common shapes include helical (rod-like), icosahedral (spherical), and bacilliform (bullet-shaped) forms. Helical virions, such as Tobacco Mosaic Virus (TMV), assemble into rigid rods approximately 300 nm in length and 18 nm in diameter, with the coat protein subunits arranged in a helical symmetry around the nucleic acid core.^[48] Icosahedral virions, exemplified by Cowpea Mosaic Virus (CPMV), form nearly spherical particles about 30 nm in diameter, characterized by icosahedral symmetry with 60 copies each of large and small coat proteins.^[49] Bacilliform shapes, like those of Alfalfa Mosaic Virus (AMV), are elongated with rounded ends, measuring 30–57 nm in length and 18 nm in diameter, based on a pseudo-icosahedral T=1 symmetry.^[50] The capsid, or protein shell, of plant virus virions is composed of self-assembling protein subunits known as capsomeres, which number from around 180 in smaller icosahedral particles (e.g., Cowpea Chlorotic Mottle Virus with 180 identical subunits) to over 2,000 in elongated helical forms (e.g., TMV with approximately 2,130 coat protein copies).^[51]^[52] These subunits, typically 150–200 amino acids long, polymerize into symmetric arrays that enclose and stabilize the viral genome, with the exact number and arrangement determined by the virion's symmetry and genome length.^[53] Envelopes, lipid membranes derived from host cells, are rare among plant viruses, unlike many animal viruses; most plant virions are non-enveloped to withstand mechanical transmission and environmental exposure. Exceptions include a few plant viruses that acquire host-derived lipids during replication in insect vectors. The virion's external structure thus primarily relies on the robust protein capsid to encase the genome. Many plant virus virions demonstrate high environmental stability, resisting drying, temperature fluctuations, and pH changes, which enhances their persistence outside hosts; for instance, TMV remains infectious in dried plant material or even processed tobacco products for years.^[52]^[53]

Genome organization and types

Plant viruses exhibit a diverse array of genome types, primarily RNA-based, reflecting their evolutionary adaptations to host interactions and transmission strategies. The most prevalent are positive-sense single-stranded RNA (ssRNA+) genomes, comprising approximately 65% of known plant viruses, with sizes ranging from 1.2 to 20 kb.^[54] A representative example is Tobacco mosaic virus (TMV) from the genus Tobamovirus, which has a monopartite ssRNA+ genome of about 6.4 kb encoding essential proteins such as replicase and coat protein.^[55] Other types include negative-sense single-stranded RNA (ssRNA-) genomes, as seen in Tomato spotted wilt virus (TSWV) from the genus Tospovirus, featuring a tripartite ssRNA- genome totaling around 17 kb.^[56] Double-stranded RNA (dsRNA) genomes occur in families like Reoviridae, such as Rice dwarf virus, with multipartite structures consisting of 10-12 segments and a total size of approximately 25-30 kb.^[57] Single-stranded DNA (ssDNA) viruses, exemplified by Geminiviridae like Tomato yellow leaf curl virus (TYLCV), typically have small circular genomes of 2.5-5 kb, often bipartite.^[55] Finally, double-stranded DNA (dsDNA) genomes are found in Caulimoviridae, such as Cauliflower mosaic virus (CaMV), with a monopartite genome of about 8 kb that replicates via reverse transcription.^[56] Genome organization in plant viruses varies between monopartite and multipartite forms, influencing replication and packaging efficiency. Monopartite genomes consist of a single nucleic acid molecule containing all genetic information, as in TMV's linear ssRNA+ or CaMV's circular dsDNA.^[55] In contrast, multipartite genomes are divided into 2-8 separate segments packaged in individual virions or the same particle, requiring coordinated infection for complete replication; Brome mosaic virus (BMV) from the genus Bromovirus exemplifies this with three monopartite ssRNA+ segments totaling about 8 kb.^[57] These segments often encode specialized functions, such as RNA1 and RNA2 for replication in BMV.^[56] Key genomic features include open reading frames (ORFs) dedicated to core functions like RNA-dependent RNA polymerase (replicase) for RNA viruses and movement proteins for cell-to-cell spread, typically numbering 4-7 per genome.^[57] Many plant RNA viruses lack a 5' cap structure; approximately 55% of plant RNA virus genera use cap-independent translation strategies such as a viral protein genome-linked (VPg) at the 5' end, internal ribosome entry sites (IRES), or 3' cap-independent translation enhancers (3'CITE), with VPg employed by families including Potyviridae.^[58] Recent metagenomic studies, particularly using double-stranded RNA sequencing on wild plant populations, have revealed that 80-90% of detected viral operational taxonomic units (OTUs) represent undescribed species, highlighting the vast untapped diversity in natural ecosystems.^[59]

Replication cycle

Entry, uncoating, and replication

Plant viruses initiate infection through entry mechanisms that exploit physical breaches in the host cell wall, rather than receptor-mediated endocytosis, which is uncommon due to the rigid plant cell wall structure. Entry typically occurs via wound-mediated penetration, where mechanical damage from abrasion, pruning, or grafting allows virions to access the plasma membrane and cytoplasm. Alternatively, vector-assisted entry involves insects, nematodes, or fungi that breach the cell wall during feeding or movement, depositing virions directly into damaged tissues; for example, aphids transmit luteoviruses by stylet penetration, bypassing intact barriers. Unlike animal viruses, plant virus entry does not rely on specific surface receptors for uptake, as the cell wall precludes standard endocytic pathways.^[60]^[61]^[62] Following entry, uncoating disassembles the viral capsid to release the genome into the host cytoplasm or appropriate organelle. This process often involves host cellular factors, such as changes in pH or ion concentrations that destabilize capsid interactions; for instance, in carnation mottle virus (CarMV), a positive-sense single-stranded RNA (ssRNA+) virus, chelation of calcium ions at neutral pH weakens subunit interfaces, promoting an expanded intermediate state that facilitates RNA release through electrostatic interactions at the icosahedral asymmetric unit. Host proteases may also contribute by cleaving capsid proteins, though this is less documented in plants compared to animal systems; uncoating sites vary, with geminiviruses releasing DNA in the nucleus via fibrillar ring formation and rhabdoviruses disassembling on endoplasmic reticulum (ER) membranes to free nucleocapsids. The released genome then becomes accessible for replication, marking the transition to intracellular propagation.^[63]^[62] Replication of the viral genome employs diverse strategies tailored to genome type, utilizing host machinery while encoding essential viral enzymes. For the majority of plant viruses with RNA genomes, particularly positive-sense ssRNA+ viruses like tobacco mosaic virus (TMV), replication occurs in the cytoplasm within membrane-bound viral replication complexes (VRCs) associated with ER-derived vesicles, peroxisomes, or chloroplasts; the viral RNA-dependent RNA polymerase (RdRp), featuring a conserved GDD motif, synthesizes a complementary negative-sense (-) strand from the genomic (+) strand, followed by production of new (+) strands. Replication follows a semiconservative model, where the template strand is displaced during synthesis, though conservative elements—such as transient unwinding without full displacement—may occur in some cases. DNA plant viruses, such as geminiviruses, replicate in the nucleus by reactivating host S-phase DNA polymerases, employing a rolling-circle mechanism where the viral Rep protein nicks the circular ssDNA at a conserved origin (TAATATT/AC), priming continuous synthesis of complementary strands, interspersed with recombination-dependent replication for double-stranded intermediates. Chloroplasts serve as sites for certain RNA viruses, like tombusviruses, where VRCs exploit thylakoid membranes for anchored replication. These error-prone processes, driven by low-fidelity polymerases, yield mutation rates of 10^{-4} to 10^{-6} substitutions per nucleotide per replication cycle, enabling rapid adaptation but limiting genome complexity.^[62]^[64]

Protein translation and assembly

In plant viruses, particularly those with positive-sense single-stranded RNA (+ssRNA) genomes, viral RNAs often lack the 5' cap structure typical of eukaryotic mRNAs, necessitating alternative mechanisms for translation initiation. Instead, these viruses employ cap-independent strategies such as internal ribosome entry sites (IRES) or genome-linked viral proteins (VPg) to recruit host ribosomes. For instance, in members of the Potyviridae family, the VPg covalently attached to the 5' end of the viral RNA interacts with host eukaryotic initiation factor 4E (eIF4E) to facilitate ribosome binding and scanning to the start codon.^[65] Similarly, IRES elements in viruses like those in the Luteoviridae enable direct ribosome recruitment without eIF4E dependency, allowing efficient translation in the cytoplasm where viral replication occurs.^[66] To express multiple proteins from a compact genome, plant viruses utilize specialized recoding events during translation. One common strategy is stop codon readthrough suppression, where a leaky termination codon allows continued translation to produce an extended protein. In Potato leafroll luteovirus (genus Luteovirus), the amber (UAG) stop codon terminating the coat protein open reading frame (ORF) is suppressed at low efficiency (~1-10%), yielding a readthrough product that extends the coat protein; this fusion is essential for long-distance movement and aphid transmission but arises during translation of the genomic RNA.^[65]^[67] Another approach involves the production of subgenomic RNAs (sgRNAs) by +ssRNA viruses to translate downstream ORFs that are not accessible from the full-length genomic RNA. These 5'-capped sgRNAs, synthesized during replication, act as independent mRNAs; for example, in Red clover necrotic mosaic virus (RCNMV, genus Dianthovirus), a subgenomic RNA derived from RNA1 directs translation of the coat protein from an internal start site, while the movement protein is translated from the genomic RNA2.^[65]^[68] Defective interfering (DI) RNAs, which are truncated variants, can also generate additional sgRNAs to modulate protein expression and interference with helper virus replication.^[69] In viruses with large polyprotein precursors, such as those in the Potyviridae, translation yields a single polyprotein from the genomic RNA, which is subsequently cleaved into functional units. This processing is mediated by virus-encoded proteases, notably the nuclear inclusion a (NIa) protease, a chymotrypsin-like cysteine protease homologous to the picornaviral 3C protease. The NIa protease cleaves the polyprotein at seven specific sites with conserved Q/S or Q/G motifs, releasing mature proteins including the replicase, helper component-proteinase, and coat protein; mutations in the protease active site abolish infectivity by preventing maturation.^[70] Virion assembly in plant viruses typically initiates with nucleation, where coat proteins bind to specific packaging signals—structured RNA motifs—within the viral genome to form a stable core. In TMV, for example, the 126/183-kDa replicase proteins first associate with the genomic RNA, followed by coat protein trimerization and helical nucleation around RNA packaging signals, resulting in rod-shaped virions up to 300 nm long.^[71] These assembled virions often accumulate in cytoplasmic inclusion bodies and are transported to plasmodesmata, the plant cell's intercellular channels, where they facilitate cell-to-cell spread without exiting the cell. In viruses with segmented genomes, such as Brome mosaic virus (genus Bromovirus), productive assembly requires co-infection of the same cell by all RNA segments (typically three), as each encodes distinct proteins or components; incomplete sets lead to abortive infections due to lack of complementation.^[72]

Transmission

Mechanical and seed-based

Mechanical transmission of plant viruses occurs primarily through physical contact that transfers virus-laden sap between infected and healthy plants, often facilitated by human activities such as pruning, grafting, or handling. This mode of spread is common for viruses with robust virions that survive outside the host, allowing contamination of tools, hands, or clothing to inoculate wounds on susceptible plants. For instance, Tobacco mosaic virus (TMV) is readily transmitted mechanically when contaminated cutting tools or fingers contact healthy tobacco or tomato plants during cultivation practices, leading to widespread infection in greenhouses and fields.^[73]^[74] Grafting, a deliberate human intervention, further exacerbates this by directly linking vascular tissues of infected scions or rootstocks to healthy ones, as seen with viruses like Tomato brown rugose fruit virus (ToBRFV), which spreads via sap transfer during propagation.^[75] Seed transmission represents a form of vertical transmission where viruses move from infected parent plants to offspring through reproductive structures, establishing systemic infection in seedlings and enabling long-distance dispersal via seed trade. Transmission rates vary widely by virus-host combination, typically ranging from 0.1% to 30%, influenced by factors such as infection timing and maternal tissue invasion. A notable example is Barley stripe mosaic virus (BSMV) in barley, where seed transmission rates can reach up to 32% in certain cultivars when mother plants are infected early in development, resulting in mosaic symptoms and yield losses in subsequent generations.^[76] Similarly, Soybean mosaic virus (SMV) exhibits rates of 25.7% to 91.7% in soybean seeds, underscoring the potential for high vertical spread in legumes.^[77] Pollen transmission of plant viruses is relatively rare but can occur when virions adhere to or invade pollen grains, allowing infection during pollination of healthy stigmas or ovules. This pathway facilitates both horizontal spread within orchards and vertical transmission to seeds, though efficiency is often low due to pollen's brief viability. Prunus necrotic ringspot virus (PNRSV), an ilarvirus affecting stone fruits, exemplifies this mode, with the virus localizing on the external surface of almond pollen grains and transmitting to receptive flowers, contributing to rapid dissemination in Prunus orchards despite its infrequent occurrence compared to seed or mechanical routes.^[78]^[79]^[80] Human activities significantly amplify the global spread of plant viruses through inadvertent transport of infected propagative materials, bypassing natural barriers and introducing pathogens to new regions. International trade in nursery stock and seeds serves as a primary vector for long-distance dissemination, with viruses persisting in dormant tissues during shipping. Plum pox virus (PPV), a potyvirus causing sharka disease in stone fruits, has been propagated worldwide via infected budwood and nursery plants, where insufficient phytosanitary controls in global markets enable its establishment in previously virus-free areas, leading to quarantines and eradication efforts.^[81]^[82] Quarantine lapses in seed imports have been linked to emerging outbreaks, as undetected seedborne viruses evade post-entry inspections and infect crops upon planting.^[83]

Vector-mediated

Vector-mediated transmission of plant viruses occurs through living organisms that act as intermediaries, facilitating the spread from infected to healthy plants. These vectors, primarily insects, nematodes, and fungi, acquire the virus during feeding on infected hosts and subsequently inoculate it into new plants, often with high efficiency due to specific molecular interactions between the virus and vector. This mode contrasts with direct mechanical or seed transmission by relying on biotic carriers that can actively disseminate viruses over distances.^[84] Insects represent the most common vectors, with aphids, whiteflies, beetles, and thrips playing key roles in diverse transmission strategies. Aphids transmit viruses in both non-persistent and persistent manners; for instance, non-persistent, stylet-borne transmission involves viruses like Potato virus Y (PVY, genus Potyvirus), where the virus adheres to the aphid's stylets and is acquired and inoculated in seconds to minutes during brief probes into epidermal cells. In contrast, persistent circulative transmission, exemplified by Potato leafroll virus (PLRV, genus Polerovirus), requires aphids to acquire the virus over hours via phloem feeding, with the virus circulating through the vector's hemolymph to salivary glands before inoculation, often taking days for effective spread. Whiteflies, particularly Bemisia tabaci, transmit viruses such as Tomato yellow leaf curl virus (TYLCV, genus Begomovirus) in a persistent circulative manner, where the virus is ingested from phloem, passes through the gut epithelium into the hemolymph, and reaches salivary glands for inoculation after a latent period of several hours to days. Beetles, including species in the family Chrysomelidae, vector viruses like those in the genus Sobemovirus through semi-persistent transmission during feeding on plant tissues, while thrips (order Thysanoptera) propagate viruses such as Tomato spotted wilt virus (TSWV, genus Orthotospovirus) persistently, with the virus replicating within vector cells after acquisition during larval stages.^[85]^[86]^[87]^[88]^[89]^[90] Nematodes, as soil-dwelling vectors, enable subsurface transmission of certain viruses, particularly in perennial or root crops. For example, Tobacco rattle virus (TRV, genus Tobravirus) is transmitted by stubby-root nematodes such as Trichodorus primitivus and Paratrichodorus spp., where the virus particles are retained on the nematodes' stylets or in the esophageal region after ingestion from infected roots, allowing inoculation during subsequent feeding with acquisition and transmission occurring over minutes to hours. This retention mechanism permits long-distance soil movement of the virus, persisting in nematode populations for extended periods.^[91]^[92]^[93] Fungi and fungus-like organisms, such as plasmodiophorids, vector viruses through soil moisture and root infections. Polymyxa graminis, an obligate root parasite, transmits Soil-borne wheat mosaic virus (SBWMV, genus Furovirus) by encasing viral particles within its resting spores or zoospores, which infect cereal roots and release the virus during fungal penetration, with transmission efficiency heightened in wet soils where zoospores swim to new hosts. This vector survives in soil for years, facilitating persistent reservoirs of the virus in agricultural fields.^[94]^[95]^[96] Transmission mechanisms broadly classify as non-persistent or persistent based on virus-vector interactions. In non-persistent transmission, viruses are acquired and inoculated rapidly (seconds to minutes) without entering vector cells, relying on superficial attachment to mouthparts, as seen in aphid stylet-borne viruses. Persistent transmission involves longer acquisition (hours to days) and inoculation periods (minutes to hours), with the virus circulating internally and sometimes replicating in the vector, as in whitefly-mediated geminiviruses or thrips-tospoviruses, enhancing vector specificity and efficiency. These distinctions influence epidemic dynamics, with persistent modes allowing broader dissemination.^[97]^[98]^[99] Climate change exacerbates vector-mediated transmission, as warmer temperatures expand vector ranges and populations, increasing virus spread. For aphid-vectored viruses, elevated temperatures enhance reproduction and flight activity, leading to higher transmission rates; for example, higher temperatures (25–30 °C) can increase transmission efficiency of viruses like Potato virus Y and Potato leafroll virus by 30–35% due to enhanced vector activity.^[100]^[101]

Host interactions

Infection symptoms and effects

Plant viruses induce a range of visible symptoms in infected hosts, often manifesting first as local effects on specific tissues before spreading systemically. Local symptoms typically include necrosis, characterized by dead tissue forming spots, streaks, or lesions, and mosaics, which appear as irregular chlorotic or mottled patches on leaves due to uneven chlorophyll distribution. For instance, Tobacco mosaic virus (TMV) infection on tobacco leaves produces characteristic mosaic patterns with light and dark green areas, sometimes accompanied by necrotic lesions.^[102] These localized changes disrupt cellular function in the affected area, often triggered by viral interference with host metabolism.^[103] Systemic symptoms emerge as the virus spreads through the vascular system, leading to widespread physiological disruption and altered plant morphology. Common effects include stunting, where overall growth is reduced, leaf curling or distortion, and fruit deformation such as misshapen or underdeveloped produce. Cucumber mosaic virus (CMV), for example, causes severe dwarfing in cucurbits, with shortened internodes, smaller leaves, and malformed fruits, severely impacting plant architecture.^[102] These symptoms can vary by host, virus strain, environmental conditions, and infection timing, but they collectively impair plant vigor and reproductive capacity.^[104] Beyond visible signs, plant viruses exert profound physiological effects, notably reducing photosynthesis through chloroplast degradation and altered pigment synthesis, with drops of 20-50% commonly observed in infected tissues. This photosynthetic inhibition, as seen in grapevines infected with grapevine leafroll-associated virus, stems from decreased Rubisco activity and mesophyll conductance without significant stomatal closure, leading to energy deficits that exacerbate growth suppression.^[105] Viruses also disrupt hormone balance, such as auxin transport, contributing to curling and stunting. Yield losses from these effects can reach 100% in severe cases, with yield losses from wheat streak mosaic virus (WSMV) averaging 5% in the US Great Plains and exceeding 30% in regions like Australia and Canada, with up to 95% in localized epidemics as of 2025.^[106] Barley yellow dwarf viruses similarly account for 15-25% worldwide cereal yield losses annually.^[107] Some plant viruses establish latent infections, remaining asymptomatic in certain hosts while subtly reducing vigor over time without overt symptoms. For example, latent tobamoviruses can systemically infect plants like Arabidopsis thaliana without visible damage, yet they may alter resource allocation and increase susceptibility to other stresses. These cryptic infections, often detected only through molecular methods, highlight the hidden impact of viruses in wild or tolerant hosts.^[102]

Pathogenesis mechanisms

Plant viruses employ various molecular strategies to suppress host defenses, particularly RNA silencing, a key antiviral mechanism in plants. Viral suppressors of RNA silencing (VSRs) interfere with this pathway by targeting components such as Argonaute proteins, which are essential for siRNA-mediated degradation of viral RNA. For instance, the 126-kDa replicase protein of Tobacco mosaic virus (TMV) acts as a VSR by binding to small interfering RNAs and inhibiting the slicer activity of Argonaute, thereby preventing the formation of the RNA-induced silencing complex and allowing viral accumulation.^[108] This suppression enables the virus to evade degradation and establish infection, as demonstrated in Nicotiana benthamiana where TMV p126 enhances viral replication by disrupting silencing initiation.^[109] To facilitate cell-to-cell movement, plant viruses utilize movement proteins that modify plasmodesmata, the cytoplasmic channels connecting adjacent cells. These proteins increase the size exclusion limit of plasmodesmata, a process known as gating, which allows passage of viral ribonucleoprotein complexes or virions. In potyviruses, the coat protein (CP) plays a critical role in this gating, forming complexes with other viral proteins like the cylindrical inclusion and helper component-proteinase at plasmodesmata to promote trafficking.^[110] For example, in Turnip mosaic virus (a potyvirus), the CP interacts with host actin and microtubules to target plasmodesmata, enabling efficient local spread without disrupting host cell integrity entirely.^[111] Systemic spread of plant viruses occurs primarily through the phloem, where viruses exploit companion cells for loading into sieve elements. Viral movement proteins facilitate entry into the phloem by altering symplastic connections between companion cells and sieve elements, allowing long-distance transport via mass flow.^[112] However, hosts counter this by inducing callose deposition at plasmodesmata and sieve plates, which plugs channels to restrict viral movement; viruses counteract this through encoded enzymes like β-1,3-glucanases that degrade callose, maintaining open pathways.^[113] In Soybean mosaic virus infections, for instance, reduced callose accumulation correlates with enhanced phloem loading and systemic invasion.^[114] Plant viruses further evade immunity by mimicking host proteins and suppressing programmed cell death (PCD), which limits pathogen spread. Molecular mimicry involves viral effectors structurally resembling host regulatory proteins, thereby interfering with immune signaling; for example, some viral proteins mimic plant transcription factors to dysregulate defense gene expression.^[115] Additionally, viruses block PCD pathways to prevent hypersensitive response lesions that confine infection, with certain RNA viruses inhibiting apoptosis-like processes in host cells to sustain replication sites.^[116] This evasion is evident in TMV, where replicase components suppress reactive oxygen species-mediated PCD, promoting unchecked proliferation.^[117] Interactions with other pathogens often amplify damage through synergism, where co-infection enhances virulence beyond additive effects. In mixed infections, viruses can suppress host RNA silencing, indirectly benefiting fungal partners by weakening overall defenses; for example, co-infection of Grapevine leafroll-associated virus 3 with the fungus Phaeomoniella chlamydospora increases symptom severity compared to single infections, due to compounded phloem disruption and toxin production.^[118] Such synergism underscores how viruses exploit multi-pathogen environments to exacerbate host damage and facilitate transmission.

Diagnosis and detection

Traditional methods

Traditional methods for diagnosing plant viruses rely on biological, serological, and microscopic techniques that have been foundational since the early 20th century, predating molecular approaches. These methods emphasize direct observation of symptoms, infectivity testing through host plants, and antigen detection, offering accessible means for field and laboratory identification despite their manual nature. They are particularly valuable in resource-limited settings where advanced equipment is unavailable, though they often require confirmation due to inherent variability in viral expression and host responses.^[119] Symptom-based indexing begins with visual inspection of infected plants for characteristic signs such as mosaics, chlorosis, necrosis, or stunting, which can indicate viral presence but are influenced by environmental factors, plant age, and strain variability. To enhance reliability, bioassays use indicator plants that produce distinct, reproducible symptoms upon infection; for instance, Chenopodium amaranticolor or Chenopodium quinoa develop local necrotic lesions when inoculated with Tobacco mosaic virus (TMV), allowing qualitative assessment of viral infectivity. These herbaceous hosts from genera like Nicotiana, Solanum, and Phaseolus are selected for their sensitivity to specific viruses, enabling broad screening without prior knowledge of the pathogen. Mechanical inoculation supports these bioassays by extracting sap from symptomatic tissue, buffering it (often with phosphate at pH 7-8), and rubbing it onto abraded leaves of test plants to transmit the virus and observe symptom development over days to weeks. This technique confirms transmissibility and host range but depends on factors like leaf age and inoculation pressure for consistent results.^[120]^[119] Serological methods, particularly enzyme-linked immunosorbent assay (ELISA), detect viral coat proteins using virus-specific antibodies in formats like direct antigen coating (DAC)-ELISA or double antibody sandwich (DAS)-ELISA. In DAC-ELISA, crude plant sap is adsorbed to microtiter plates, followed by antiserum and enzyme conjugate for colorimetric detection, enabling high-throughput screening of multiple samples. ELISA achieves sensitivities of approximately 10^3 to 10^5 viral particles per mL, depending on the virus and antibody quality, making it suitable for routine surveys in crops like potatoes for Potato virus Y. Microscopy complements these by visualizing virions: transmission electron microscopy (TEM) reveals particle morphology (e.g., rod-shaped TMV at 300 nm length) after negative staining of leaf dips, while immunofluorescence localizes viral antigens in tissue sections using fluorescently labeled antibodies for in situ confirmation. TEM typically requires at least 10^5-10^6 particles/mL for reliable detection and is valued for its direct evidence of virus presence.^[121]^[119]^[122] Despite their utility, traditional methods suffer from limitations including low specificity, as similar symptoms or particle morphologies can occur across virus groups, leading to false positives or negatives—particularly for latent infections or mixed populations. They are also time-intensive, with bioassays and mechanical inoculations requiring 7-21 days for symptom expression, and demand skilled personnel for accurate interpretation, restricting scalability in large-scale diagnostics. These constraints often necessitate integration with emerging techniques for comprehensive verification.^[120]^[119]

Modern and emerging techniques

Modern nucleic acid-based techniques have revolutionized plant virus detection by offering high sensitivity and specificity, particularly for RNA viruses prevalent in agricultural systems. Reverse transcription polymerase chain reaction (RT-PCR), including quantitative variants (qRT-PCR), enables the amplification and detection of viral RNA with sensitivities as low as fewer than 10 copies per reaction, allowing early identification in symptomatic or asymptomatic plants.^[123] Next-generation sequencing (NGS) and metagenomic approaches further extend this capability by unbiasedly surveying viral communities, facilitating the discovery of unknown viruses without prior sequence knowledge; for instance, a 2024 metagenomic study revealed several novel plant viruses in wild species, enhancing understanding of viral diversity beyond targeted assays.^[124] Biosensor technologies provide portable, field-deployable alternatives to lab-based methods, addressing the need for rapid on-site diagnostics. Loop-mediated isothermal amplification (LAMP) amplifies viral nucleic acids at a constant temperature (typically 60-65°C), requiring minimal equipment and enabling detection in crude plant extracts within 20-60 minutes, ideal for resource-limited settings like remote farms.^[125] Complementing this, CRISPR-Cas12a systems integrate with isothermal amplification for collateral cleavage-based readout, yielding results in approximately 30 minutes via lateral flow assays or fluorescence; methods developed in 2023, such as RT-RAA/CRISPR-Cas12a assays, have demonstrated high specificity for viruses such as maize chlorotic mottle virus, with limits of detection comparable to PCR.^[126] Artificial intelligence (AI) integrations are enhancing the efficiency of detection pipelines by automating design and prediction tasks. The AutoPVPrimer pipeline, released in 2025, leverages machine learning algorithms to retrieve viral genomes from databases like NCBI, design optimized primers, and predict variants, streamlining RT-PCR and LAMP assays for diverse plant viruses while reducing manual optimization time.^[36] This AI-driven approach not only accelerates primer validation but also improves coverage across viral strains, supporting scalable surveillance in breeding programs and outbreak responses. Remote sensing techniques enable non-invasive, large-scale monitoring of viral infections through symptom detection. Hyperspectral imaging captures reflectance spectra across hundreds of wavelengths to identify physiological changes indicative of virus presence, achieving classification accuracies of 85-95% for viral diseases like grapevine leafroll-associated virus in field conditions.^[127] By integrating with machine learning models such as partial least squares-discriminant analysis, these methods distinguish viral symptoms from abiotic stresses early in infection, facilitating targeted interventions over vast areas. Recent advances, particularly in 2024, have addressed longstanding gaps in ecological sampling by applying metagenomic and high-throughput methods to wild plants, where traditional assays often fail due to diverse hosts and low viral loads. Studies using environmental nucleic acid sampling and NGS have uncovered virus spillovers from crops to native flora, filling voids in biodiversity monitoring and informing conservation strategies against emerging threats.^[124]^[128]

Control and management

Cultural and chemical strategies

Cultural strategies for managing plant viruses emphasize altering agricultural practices to disrupt transmission cycles and reduce inoculum sources. Crop rotation involves alternating susceptible host crops with non-hosts, which breaks the continuity of viral reservoirs and vectors, thereby lowering disease incidence in subsequent plantings. For instance, rotating tomatoes with non-solanaceous crops has been shown to decrease Tomato yellow leaf curl virus (TYLCV) inoculum in weeds. Rogueing, the manual removal and destruction of infected plants early in the season, prevents local spread and limits the source of viruliferous vectors; this practice is particularly effective in perennial crops like citrus, where prompt rogueing can reduce overall infection rates by isolating symptomatic individuals. Using certified virus-free seeds is a cornerstone of prevention, as it minimizes seed-borne transmission; studies indicate that such seeds can significantly reduce virus incidence in crops like beans and lettuce by eliminating primary infection foci from the outset.^[129]^[130] Sanitation practices further support cultural controls by eliminating potential reservoirs and transmission pathways. Tool sterilization, using disinfectants like 10% bleach or 70% ethanol between operations, prevents mechanical transmission of viruses such as Tobacco mosaic virus (TMV) during pruning or grafting; dipping tools for 30 seconds has been demonstrated to inactivate viral particles on surfaces. Weed control targets alternative hosts that serve as viral reservoirs, such as broadleaf weeds harboring Cucumber mosaic virus (CMV); integrated weeding reduces vector populations and inoculum in affected fields, as weeds like Chenopodium album bridge crop cycles. These measures collectively enhance field hygiene and are most impactful when combined in an ongoing management plan.^[131] Chemical strategies focus on targeting vectors and, to a lesser extent, direct antiviral applications. Insecticides like neonicotinoids (e.g., imidacloprid) are applied systemically to control aphid vectors of viruses such as Potato virus Y (PVY), reducing transmission by limiting vector populations; seed treatments can suppress aphid colonization by 80-90% in early growth stages. However, widespread resistance in aphid species like Myzus persicae has emerged, with metabolic detoxification via cytochrome P450 enzymes diminishing efficacy in over 50% of field populations, necessitating rotation with alternative chemistries. Antiviral compounds like ribavirin, a guanosine analog, inhibit viral replication through RNA mutagenesis and are applied foliarly or via irrigation for systemic uptake; it has been used to inhibit viral replication, though efficacy varies and phytotoxicity limits dosages. These chemicals are used judiciously to avoid non-target effects on beneficial insects.^[132]^[133] Barrier methods provide physical deterrence against vectors without relying on genetics or broad-spectrum chemicals. Reflective mulches, such as silver- or aluminum-coated plastics laid around crop bases, disorient whiteflies by reflecting UV light, repelling them from landing and feeding; this reduces whitefly-mediated transmission of viruses like TYLCV by 30-50% in cucurbits and tomatoes during the first 4-6 weeks post-planting. Mulches also enhance plant growth through improved light and heat reflection, indirectly bolstering crop vigor against infection. Effectiveness wanes as foliage covers the mulch, but integration with other tactics sustains benefits.^[134]^[135] As of 2025, integrated pest management (IPM) programs increasingly incorporate drone-based monitoring for early detection and targeted intervention in plant virus control. Drones equipped with multispectral cameras scan fields to identify symptomatic patches or vector hotspots, enabling precise rogueing or insecticide applications that reduce chemical use by 40-60% while maintaining efficacy against viruses like Barley yellow dwarf virus. This technology supports real-time data integration with AI for predictive modeling, aligning cultural and chemical strategies in a sustainable framework.^[136]^[137]

Host resistance and breeding

Host resistance to plant viruses often relies on natural genetic mechanisms encoded by resistance (R) genes, which recognize specific viral effectors and trigger defense responses. A prominent example is the N gene in tobacco (Nicotiana tabacum), a Toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) protein that confers resistance to tobacco mosaic virus (TMV) by detecting the viral helicase domain. Upon recognition, the N gene activates the hypersensitive response (HR), a form of programmed cell death that confines the infection to localized lesions, preventing systemic spread.^[138] This HR-mediated resistance limits viral replication and movement, thereby protecting the plant while inducing systemic acquired resistance (SAR) against subsequent infections.^[139] Conventional breeding strategies have successfully incorporated polygenic resistance into crops through crosses between susceptible varieties and wild or resistant accessions, stacking multiple quantitative trait loci (QTLs) for durable protection. In potatoes (Solanum tuberosum), breeders have developed varieties resistant to potato virus Y (PVY), such as those incorporating the Ry genes (e.g., Rysto from Solanum stoloniferum and Ryadg from Solanum tuberosum subsp. andigena), which provide extreme resistance (ER) to all PVY strains by inhibiting viral replication.^[140] These efforts often use marker-assisted selection to introgress resistance loci, resulting in commercial cultivars like Harimaru, which combine PVY resistance with other traits for improved yield and quality.^[141] Biotechnological approaches enhance host resistance by targeting viral genes or host susceptibility factors. RNA interference (RNAi) silences viral RNA through the expression of double-stranded RNA (dsRNA) constructs complementary to viral sequences, such as the coat protein (CP) gene of papaya ringspot virus (PRSV). In 2024, topical application of dsRNA targeting PRSV genes achieved up to 100% resistance in papaya plants against certain strains, demonstrating the efficacy of exogenous RNAi for broad-spectrum protection without genetic modification.^[142] Similarly, CRISPR/Cas9 editing of host susceptibility genes like eukaryotic initiation factor 4E (eIF4E), which potyviruses hijack for translation, has produced resistant lines; for instance, quadruple eIF4E knockouts in tobacco conferred 90% resistance to PVY in progeny plants by disrupting viral protein-genome linkage.^[143] Virus-induced gene silencing (VIGS) serves as a high-throughput tool for screening candidate resistance genes by transiently suppressing their expression using viral vectors like tobacco rattle virus (TRV). This method rapidly identifies genes involved in defense pathways, such as those mediating HR, allowing functional validation before stable transformation; for example, VIGS in Nicotiana benthamiana has implicated heat shock protein genes in TMV resistance.^[144] Despite these advances, viral evolution poses significant challenges, as pathogens can mutate to evade R-gene recognition, leading to resistance breakdowns. In 2023, reports documented the emergence of tomato yellow leaf curl virus (TYLCV) variants overcoming Ty-1-based resistance in tomato, a geminivirus R-gene that encodes RNA-dependent RNA polymerase, highlighting the need for pyramiding multiple genes or editing susceptibility factors for durability.^[145]

Applications

Biotechnology and nanotechnology

Plant viruses have emerged as versatile platforms in biotechnology due to their nanoscale structures, self-assembly properties, and ability to be genetically engineered for targeted applications in agriculture and materials science. Tobacco mosaic virus (TMV), one of the most studied plant viruses, serves as an effective vector for gene delivery in plants, enabling systemic expression of foreign genes through agroinfiltration-based systems. For instance, TMV-based vectors like the tobacco rattle virus overexpression (TRBO) system facilitate high-level recombinant protein accumulation, up to 100-fold higher than non-viral methods, by deleting the coat protein gene to insert target sequences while retaining cell-to-cell movement. These vectors have been pivotal in functional genomics and crop trait enhancement, with seminal work demonstrating stable expression in Nicotiana benthamiana leaves.^[146] In nanotechnology, plant virus-derived virus-like particles (VLPs) offer robust scaffolds for nanomaterial fabrication and sensing applications. Cowpea mosaic virus (CPMV) nanoparticles, with their icosahedral symmetry, have been engineered for bioimaging, providing high-contrast labeling in cellular environments due to their biocompatibility and surface functionalization potential. Similarly, TMV's rod-shaped capsids enable the creation of conductive nanowires and enzyme-immobilized sensors, enhancing detection capabilities in agricultural settings. A notable example includes TMV-templated thin-film sensors for volatile organic compounds, which achieve sensitivity in the parts-per-billion range, adaptable for monitoring environmental pollutants like pesticide residues. Plant VLPs, produced cost-effectively in hosts such as Nicotiana benthamiana, support these applications by allowing precise chemical modifications without infectivity risks.^[147]^[148]^[149] Pharming leverages plant viruses to express recombinant proteins in infected plant tissues, bypassing traditional fermentation systems for scalable production. TMV and potato virus X (PVX) vectors have been deconstructed to amplify target genes, yielding up to 4 g/kg fresh weight of proteins like vaccines or antibodies within days via transient expression. This approach has produced virus-like particles for antigen display, such as CPMV-based VLPs expressing malaria epitopes, highlighting its utility in agricultural biotechnology for crop protection antigens. The systemic spread in plants ensures uniform protein distribution, making it ideal for industrial-scale biomanufacturing.^[150]^[151] Synthetic biology advances include engineering plant viruses as chimeras for precise gene editing in crops. TMV vectors co-delivering CRISPR/Cas9 components and guide RNAs achieve up to 60% indel frequencies in target genes like GFP, enhanced by RNA silencing suppressors such as P19 for improved expression in mature plants. Recent innovations, like biocontainable tomato spotted wilt virus (TSWV) vectors, enable non-transgenic editing across genotypes, inducing heritable mutations in genes for disease resistance with efficiencies up to 85% after antiviral treatment. These CRISPR-virus hybrids accelerate crop improvement by targeting polygenic traits without stable transgenes, as demonstrated in tobacco and tomato for enhanced yield and resilience.^[146]^[151] Environmental applications exploit viral capsids for bioremediation, where their binding affinity aids pollutant sequestration. Engineered TMV and cowpea chlorotic mottle virus (CCMV) capsids have been modified to encapsulate or bind heavy metals and organic contaminants, leveraging electrostatic interactions for selective adsorption in soil and water systems. For example, CCMV disassembly-reassembly cycles allow loading of remediation enzymes, facilitating degradation of hydrocarbons in phytoremediation setups with plants like Arabidopsis. These virus-based nanomaterials provide a sustainable, non-toxic alternative for site-specific cleanup, with ongoing research emphasizing their integration into microbial-plant consortia for enhanced efficiency.^[152]^[153]

Therapeutic and vaccine uses

Plant viruses and their derivatives have emerged as versatile platforms for therapeutic and vaccine applications in human and animal health, owing to their ability to form stable, non-infectious nanoparticles that can be engineered for targeted delivery without eliciting pathogenic responses in mammals. These structures, such as virus-like particles (VLPs) and coat protein scaffolds, enable the presentation of antigens or therapeutic payloads, facilitating immune stimulation or precise molecular interventions. Unlike animal viruses, plant viruses pose minimal risk of horizontal transmission to humans, making them attractive for scalable production in plant hosts like Nicotiana benthamiana.^[154] In vaccine development, tobacco mosaic virus (TMV) has been prominently utilized as a scaffold to display viral epitopes, enhancing immunogenicity through multivalent presentation. For instance, a 2024 candidate vaccine employed TMV to present peptides from the SARS-CoV-2 spike protein, produced via transient expression in N. benthamiana, demonstrating robust humoral and cellular immune responses in preclinical models without reported adverse effects. These approaches leverage agroinfiltration for high-yield antigen assembly, bypassing the need for cell culture systems.^[155] Antiviral therapies have benefited from plant virus-derived components, particularly in cancer targeting. Cowpea mosaic virus (CPMV) nanoparticles, functionalized with photosensitizers, have been applied in photodynamic therapy (PDT) to selectively eliminate tumor-associated macrophages and cancer cells by generating reactive oxygen species upon light activation. In preclinical studies, CPMV conjugates targeted inflammatory tumor microenvironments, reducing tumor burden in melanoma models through enhanced uptake and localized cytotoxicity, with no systemic toxicity observed. This strategy exploits the virus's natural tropism and biocompatibility to deliver therapeutic peptides or drugs directly to malignant sites.^[156] Modified plant viruses also serve as vectors in gene therapy for mammalian cells, offering alternatives to traditional viral carriers with lower immunogenicity. Additionally, TMV-based nanoparticles have facilitated nucleic acid delivery to human cells, supporting gene silencing or editing in therapeutic contexts.^[157] Virus-like particles from plant viruses contribute to diagnostics for human pathogens, integrated into lateral flow assays for point-of-care detection. CPMV and TMV-derived VLPs, labeled with detection moieties, enable sensitive identification of viral antigens in samples, such as those from respiratory infections, by mimicking viral morphology to capture antibodies or epitopes with high specificity. These assays provide rapid results comparable to ELISA, suitable for resource-limited settings.^[158] Recent advances in omics-guided design have accelerated the identification of plant virus-inspired antivirals. Metabolomics analyses in 2024 revealed bioactive extracts from antiviral plants, such as flavonoids and terpenoids, that inhibit viral replication pathways, informing the engineering of virus-derived therapeutics with enhanced potency against human viruses like influenza. These data-driven approaches integrate transcriptomics and proteomics to optimize peptide modifications for broader-spectrum efficacy.^[159]

Ecology and evolution

Ecological roles and interactions

Plant viruses exhibit non-pathogenic roles in natural ecosystems, including mutualistic interactions that can enhance host fitness under environmental stress. For instance, infection by certain viruses, such as Turnip mosaic virus, can confer drought tolerance to infected plants by modulating physiological responses, thereby increasing survival rates compared to uninfected counterparts under water-limited conditions.^[160] These mutualistic effects emerge rapidly under stress, shifting the virus from a parasitic to a beneficial partner that improves plant resilience without apparent long-term harm.^[160] While horizontal gene transfer from viruses to plant genomes has contributed to evolutionary adaptations like stress-related traits in ancestral lineages, contemporary mutualisms primarily involve transient infections that alter host gene expression rather than permanent genetic integration.^[161] Plant viruses engage in complex tripartite interactions with hosts and vectors, influencing ecological dynamics beyond direct transmission. In these systems, viruses can manipulate host plant chemistry to favor vector attraction; for example, aphid-vectored viruses like Cucumber mosaic virus induce changes in plant volatile organic compounds, enhancing emission of aphid-attracting scents while potentially repelling non-vector insects, including pollinators.^[162] This alteration not only facilitates viral spread but also indirectly affects pollinator behavior by modifying floral cues, potentially disrupting pollination networks in affected ecosystems.^[163] Such interactions highlight viruses as mediators in multi-trophic webs, where vector preferences and host defenses co-evolve to sustain viral persistence.^[164] Wild plants serve as primary reservoirs for plant viruses, harboring a diverse array of viral communities that frequently spill over into agricultural crops. Studies indicate that persistent infections in wild hosts can reach incidence rates up to 70% in some populations, acting as sources for emergent diseases in cultivated species through shared vectors or proximity.^[165] This spillover underscores the role of natural vegetation in maintaining viral reservoirs, with implications for biodiversity conservation and crop protection strategies.^[166] By exerting selective pressure on hosts, plant viruses contribute to maintaining genetic diversity within plant populations, driving evolutionary processes that enhance overall ecosystem resilience. Viral infections prompt genetic variation through mechanisms like recombination and host adaptation, as evidenced by metagenomic analyses of forest ecosystems revealing diverse viral communities that correlate with host genetic heterogeneity.^[167] These interactions foster co-evolutionary arms races, preserving adaptive traits across wild plant lineages.^[168] Despite these insights, ecological roles of plant viruses remain understudied in non-crop ecosystems, with significant knowledge deficits where biodiversity hotspots amplify potential impacts.^[169] Recent reviews emphasize the need for expanded metagenomic surveys in these areas to fully elucidate viral contributions to ecosystem function.^[170]

Evolutionary patterns and climate impacts

Plant viruses exhibit ancient origins, having co-evolved with their host plants over vast timescales, as evidenced by metagenomic analyses that uncover diverse RNA virus lineages deeply intertwined with plant evolutionary history.^[171] These studies suggest that RNA viruses, including those infecting plants, trace back to early cellular life forms, with proteomic data indicating origins from ancient cells harboring segmented RNA genomes that facilitated viral diversification.^[172] For instance, the basal plant virome reconstructed from transcriptomic data reveals core gene modules and genome segments that have persisted through millions of years of host-virus interactions.^[173] Evolutionary patterns in plant viruses are driven by high mutation and recombination rates, particularly in RNA viruses, which exhibit error-prone replication leading to rapid genetic variation at rates of 10^{-3} to 10^{-5} substitutions per site per replication cycle.^[174] Recombination is prevalent, especially in families like Potyviridae, where it generates hybrid strains by shuffling genetic material between co-infecting viruses, enhancing adaptability and virulence; for example, recombinant potyviruses such as those in Turnip mosaic virus populations have emerged through multiple recombination events, contributing to new epidemiological threats.^[175] Host jumps are common, often from wild or weed hosts to cultivated crops, facilitated by agricultural practices that bring reservoirs into proximity with susceptible varieties.^[176] Segmented genomes in viruses like those in Reoviridae further promote evolution via reassortment, where entire genome segments are exchanged during co-infection, accelerating diversification and potentially creating novel pathogenic combinations.^[177] Climate change profoundly influences these evolutionary dynamics by altering transmission pathways and selective pressures. Rising temperatures are expanding the geographic ranges of insect vectors, such as mealybugs and soft scale insects, enabling viruses like those causing grapevine leafroll disease to shift northward and increase incidence in temperate regions; modeling projections indicate up to a 20-50% expansion in suitable habitats for key vectors by mid-century under moderate warming scenarios.^[178] Altered rainfall patterns, including more intense storms and droughts, impact mechanical transmission by modifying soil moisture levels and promoting splash dispersal of viruses in crops like tomatoes and cereals.^[179] In epidemiology, improving proactive management.^[180] Looking ahead, while zoonotic spillover from plant viruses to humans or animals remains minimal due to host specificity barriers, climate-induced disruptions in agroecosystems—such as intensified vector activity and habitat shifts—are poised to elevate the frequency of viral emergence and recombination events, threatening global food security.^[181] These trajectories underscore the need for integrated surveillance to track evolutionary responses to environmental pressures.

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[PDF] Location of Prunus Necrotic Ringspot Virus on Pollen Grains
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Plum pox virus and sharka: a model potyvirus and a major disease
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DISRUPTION OF INSECT TRANSMISSION OF PLANT VIRUSES
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The majority of plant-infecting viruses are transmitted to their host plants by vectors. The interactions between viruses and vector vary in duration and ...
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With the exception of PLRV, aphids transmit almost all other viruses non-persistently; PLRV is transmitted by aphids in a persistent and circulative manner. In ...
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Implication of whitefly vesicle associated membrane protein ...
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TRV is transmitted by several species of stubby-root nematodes in the genera Paratrichodorus and Trichodorus. Nematodes are microscopic-worm like organisms that ...
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Soilborne Wheat Mosaic Virus - WSU small grains
Polymyxa graminis is an obligate parasite in the roots of many higher plants. It produces a spore, called a zoospore, that swims in the soil solution and ...
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Insect Vectors of Plant Viruses: Host Interactions, Their Effects, and ...
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Variability, Functions and Interactions of Plant Virus Movement ...
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Callose deposited at soybean sieve element inhibits long-distance ...
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Chapter 8: Methods of Combating Seed-Transmitted Virus Diseases
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The Updated Seed Testing Rule for Lettuce mosaic virus in Florida
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Weeds as Reservoirs of Plant Pathogens Affecting Economically ...
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Novel N Gene-Associated, Temperature-Independent Resistance to ...
Infection of tobacco containing the N gene by TMV results in a hypersensitive response (HR) accompanied by generic systemic acquired resistance (SAR) that ...
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Although the agronomically best clone lacked the R1 gene, we successfully bred it as a locally adapted, tasty potato resistant to PVX, PVY, and golden cyst ...Seedling Selection Using... · Growth Habit And... · Tuber Yield And Quality
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High throughput virus-induced gene silencing implicates heat shock ...
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Breakdown of Ty-1-Based Resistance to Tomato Yellow Leaf Curl ...
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RNA silencing suppressor-influenced performance of a virus vector ...
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Plant Viruses in Plant Molecular Pharming: Toward the Use of ... - NIH
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Application of Plant Viruses as a Biotemplate for Nanomaterial ...
The CCMV capsid protects the packaged RNA against degradation during storage and delivery [80]. Targeting can be achieved by chemically or genetically adding ...
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Organochlorine contamination enriches virus-encoded metabolism ...
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Application of Plant Viruses in Biotechnology, Medicine, and Human ...
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Development of a Candidate TMV Epitope Display Vaccine against ...
We developed a potential vaccine using a tobacco mosaic virus (TMV) epitope display model presenting peptides derived from the SARS-CoV-2 spike protein.
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Efficacy and Safety of a Recombinant Plant-Based Adjuvanted ...
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Horizontal Gene Transfer in Plants and Implications for Biotechnology
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Plant Virus Impacts on Yield and Plant–Pollinator Interactions Are ...
Jun 3, 2024 · ZYMV can alter volatile organic compounds profiles of cucurbits, attracting its aphid vectors and repelling cucumber beetles, which frequently ...
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Effector-mediated plant–virus–vector interactions - Oxford Academic
A review of advances in effector-mediated plant–virus–vector interactions suggesting that molecular synergisms sometimes occur that benefit both the virus.Effector-Mediated... · Introduction · Mutualisms Are Common In...
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Lifestyles of plant viruses - PMC - NIH
The vast majority of well-characterized eukaryotic viruses are those that cause acute or chronic infections in humans and domestic plants and animals.
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Metagenomic Studies of Viruses in Weeds and Wild Plants
Viruses can emerge in cultivated plants from wild hosts or, conversely, virus infections in crops may spill over and affect wild plant populations. Spread from ...
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Plant Virus Diversity and Evolution - PMC - PubMed Central - NIH
In this chapter we discuss the state of our knowledge of virus diversity, both in agricultural systems as well as in native wild systems.
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Viral metagenomics reveals diverse virus-host interactions ...
Nov 30, 2023 · The genetic diversity of infecting viruses can direct the evolution of host defense strategies, such that low viral diversity may favor ...
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Addressing Research Needs in the Field of Plant Virus Ecology by ...
Thanks to these efforts, we now know that wild plants frequently harbor infections by a wide diversity of plant viruses, which almost certainly influence host ...Missing: percentage | Show results with:percentage
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Addressing Research Needs in the Field of Plant Virus Ecology by ...
Jan 9, 2019 · Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems.
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Metagenomics reshapes the concepts of RNA virus evolution by ...
Virus metagenomics has expanded known RNA virus diversity and emphasized connections between evolution of viruses and hosts.
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A phylogenomic data-driven exploration of viral origins and evolution
The most parsimonious hypothesis inferred from proteomic data suggests that viruses originated from multiple ancient cells that harbored segmented RNA genomes ...
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Transcriptome Mining Expands Knowledge of RNA Viruses across ...
May 31, 2022 · The detection rate of plant viruses was highest in the most basal angiosperms (57%) and monocots (50%). No significant difference in virus ...
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The population genetics and evolutionary epidemiology of RNA ...
mutation, recombination, natural selection, genetic drift and migration ...
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The Potyviruses: An Evolutionary Synthesis Is Emerging - PMC
Recombinants are common in many potyvirus populations (20%–64% in five examined), but recombination seems to be an uncommon speciation mechanism as, of 149 ...
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The Evolutionary Genetics of Emerging Plant RNA Viruses
Therefore, the preexistence of host-range mutants within the standing genetic variation in the reservoir host increases the probabilities of a successful jump.
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Determinants of Virus Variation, Evolution, and Host Adaptation - PMC
Plant viruses are obligate parasites that use host processes and resources to replicate and spread. They consist of single- or double-stranded DNA or RNA ...
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Climate Change Drives the Distribution of Insect Vectors for GLRaV ...
Oct 14, 2025 · As a well-documented consequence of global warming, a rise in insect-borne plant diseases is expected due to expanding vector ranges and rapid ...
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(PDF) Influence of climate change on plant disease infections and ...
Aug 9, 2025 · The analysis suggested that climate change is likely to modify many critical viral and bacterial epidemic components in different ways.<|control11|><|separator|>
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Artificial intelligence‐based prediction of pathogen emergence and ...
Oct 4, 2024 · New technology is changing how we monitor and control the evolution of pathogens. AI cannot predict the future but it can help us by looking at how laboratory ...
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Editorial: Emerging and reemerging plant viruses in a context of ...
In this context, environmental factors play an important role in driving virus evolution. In addition, the rapid expansion of human activity in the world of ...