Viruses

10 pages, 631 KB

Open AccessEditor’s ChoiceArticle

VIP-DB: A Comprehensive Database of Virus–Insect–Plant Relationships

by Tao Deng, Dandan Liu, Xinghui Zhu, Hongyan Zhang and Zheng Zhang

Viruses 2026, 18(6), 679; https://doi.org/10.3390/v18060679 - 18 Jun 2026

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Insect-mediated transmission is central to the epidemiology of plant viruses and has major implications for global food security and agricultural production. Although several resources have compiled information on plant virus transmission, evidence-traceable integration of virus–insect vector–host plant relationships remains limited. Here, we developed [...] Read more.

Insect-mediated transmission is central to the epidemiology of plant viruses and has major implications for global food security and agricultural production. Although several resources have compiled information on plant virus transmission, evidence-traceable integration of virus–insect vector–host plant relationships remains limited. Here, we developed the Virus–Insect–Plant Database (VIP-DB), an evidence-guided database that links literature-derived virus–insect transmission records, host plant information, transmission mode annotations, taxonomic information, and traceable literature evidence. VIP-DB compiles 583 virus–insect transmission relationships, 855 virus–plant relationships with non-missing host plant information, and 1375 integrated virus–insect–plant records. Among these records, 120 lack host plant information and 51 lack transmission mode annotation. VIP-DB provides a curated and searchable resource for querying documented plant virus, insect vector, host plant, and transmission mode information. This database offers an evidence-traceable framework for comparative analyses of plant virus transmission relationships and supports future studies in plant virology, vector ecology, and disease management. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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23 pages, 10029 KB

Open AccessEditor’s ChoiceArticle

HMPV Impairs Macrophage Phagocytosis Through a Replication-Dependent Mechanism Associated with Reduced CD36 Expression and the Viral G Protein

by Iván Martínez-Espinoza, Pius I. Babawale, Basel Abuaita and Antonieta Guerrero-Plata

Viruses 2026, 18(6), 649; https://doi.org/10.3390/v18060649 - 4 Jun 2026

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Abstract

Human metapneumovirus (HMPV) is a major cause of respiratory infections, but its impact on macrophage antibacterial functions remains poorly understood. Macrophages play a crucial role in host defense through phagocytosis, and impairment of this function may increase susceptibility to secondary infections. Here, we [...] Read more.

Human metapneumovirus (HMPV) is a major cause of respiratory infections, but its impact on macrophage antibacterial functions remains poorly understood. Macrophages play a crucial role in host defense through phagocytosis, and impairment of this function may increase susceptibility to secondary infections. Here, we show that HMPV infection of THP-1-derived macrophages significantly reduces bacterial uptake in a replication-dependent manner. This effect was restricted to infected cells and was not recapitulated by cell-free supernatants, indicating a cell-intrinsic mechanism. HMPV infection was also associated with reduced expression of the scavenger receptor CD36. Viral gene knockdown studies further implicated the HMPV G protein in this phenotype, as silencing the G protein restored phagocytic function. Analysis of single-cell RNA-sequencing datasets from HMPV-infected mouse lungs revealed reduced CD36 expression and broader alterations in phagocytosis-associated gene programs across lung macrophage subsets. Supporting these observations, expression of Cd36 and Marco was reduced in lung tissue from HMPV-infected mice. Overall, these findings demonstrate that HMPV impairs macrophage-mediated bacterial uptake through a replication-dependent, cell-intrinsic mechanism and identify reduced scavenger receptor expression and the viral G protein as factors associated with this phenotype. These alterations may contribute to increase susceptibility to secondary bacterial infections during HMPV infection. Full article

(This article belongs to the Special Issue Viral Strategies to Regulate Host Immunity or Signal Pathways, 2nd Edition)

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16 pages, 8781 KB

Open AccessEditor’s ChoiceArticle

Specific Determinants of the Transmembrane Region of the Andes Virus Gc Glycoprotein Drive the Transition from Membrane Hemifusion to Pore Formation

by Chantal L. Márquez, Fernando Villalón-Letelier, Gianina Arata-Salas and Nicole D. Tischler

Viruses 2026, 18(6), 633; https://doi.org/10.3390/v18060633 - 31 May 2026

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Abstract

Andes virus (ANDV), a highly pathogenic orthohantavirus, enters host cells through low pH–triggered membrane fusion mediated by the Gc glycoprotein, a class II fusion protein containing a single C-terminal transmembrane domain (TMD). While the ectodomain has been extensively characterized, the role of the [...] Read more.

Andes virus (ANDV), a highly pathogenic orthohantavirus, enters host cells through low pH–triggered membrane fusion mediated by the Gc glycoprotein, a class II fusion protein containing a single C-terminal transmembrane domain (TMD). While the ectodomain has been extensively characterized, the role of the TMD in late-stage fusion remains unclear. Here, we investigated the minimal functional length and sequence requirements of the ANDV Gc TMD using site-directed mutagenesis. C-terminal deletion mutants and serine-to-alanine substitutions were evaluated for protein expression, virus-like particle production, cell–cell fusion, pseudotyped vector entry, and hemifusion activity. Deletion of the Gc cytoplasmic tail (CT) or a single C-terminal TMD residue was tolerated, whereas deletion of two or more residues impaired particle production and fusion, indicating that at least 21 of the 22 TMD residues are required for efficient membrane fusion and viral entry. Hemifusion assays showed that deletion of two or three residues, or substitution of the strictly conserved S1121, allowed lipid mixing but blocked progression to full fusion, while deletion of four residues also abolished hemifusion. In contrast, mutation of the less conserved S1126 had minimal effect. These results identify a precise TMD length and a conserved polar TMD residue as critical determinants of fusion pore formation in ANDV. Full article

(This article belongs to the Special Issue Viral Entry and Membrane Fusion)

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14 pages, 7937 KB

Open AccessEditor’s ChoiceArticle

Enterovirus D68 VP1 and VP3 Determine Neurotropism in Human Spinal Cord Organoids

by Jessica E. Packard, Jennifer E. Jones, Gal Yovel and Megan Culler Freeman

Viruses 2026, 18(6), 619; https://doi.org/10.3390/v18060619 - 28 May 2026

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Abstract

Enterovirus D68 (EV-D68) is a non-polio enterovirus that can cause a polio-like paralysis condition, acute flaccid myelitis (AFM). EV-D68-associated AFM cases waned in the US after 2018, and the reasons for this are unknown. It has recently been demonstrated that EV-D68 containing point [...] Read more.

Enterovirus D68 (EV-D68) is a non-polio enterovirus that can cause a polio-like paralysis condition, acute flaccid myelitis (AFM). EV-D68-associated AFM cases waned in the US after 2018, and the reasons for this are unknown. It has recently been demonstrated that EV-D68 containing point mutations in viral structural proteins VP1 and VP3 resulted in decreased paralysis in different neonatal mouse models. However, phenotypes of these mutations in a human multicellular central nervous system (CNS) model are unknown. We hypothesize that mutations in VP1 and VP3 will similarly direct neurotropism in human spinal cord organoids (hSCOs). To investigate this, we recreated viruses with mutations in VP3 (I88V) or VP1 (L1I/N2D/T98A/E283K or L1P/V148A/K282R) and infected hSCOs. We found that VP3 I88V and VP1 L1I/N2D/T98A/E283K resulted in decreased titer and viral protein staining, consistent with attenuated neurovirulence in previously published murine models. We also found through immunofluorescence that VP1 L1P/V148/K282R mutations altered cellular tropism, primarily infecting glial cells rather than neuronal cells. When these mutations were combined, their effects on neurotropism were not additive. Sequence analysis of recently circulating EV-D68 strains reveals that VP3 I88 and VP1 E283 have remained the dominant amino acid residues since 2014, whereas VP1 sites 1, 2, and 98 have higher population diversity, indicating that these residues may be contributing to newly reduced neurovirulence after 2018. Full article

(This article belongs to the Special Issue 3D Models in Viral Pathogenesis)

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22 pages, 6967 KB

Open AccessEditor’s ChoiceArticle

Type I Interferon Regulation of HLA-F Expression in Human Trophoblasts During Viral Infection

by Diana Manchorova, Jiahui Ding, Annie Thy Nguyen, Tanya Dimova, Sergey Slavov, Liubomir Djerov, Ruqun Zheng and Gil Mor

Viruses 2026, 18(6), 603; https://doi.org/10.3390/v18060603 - 26 May 2026

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Abstract

The role of human leukocyte antigen F (HLA-F) at the maternal–fetal interface (MFI) during viral infection and its regulation by interferon signaling remains poorly understood. Here, we investigated HLA-F expression and regulation in first-trimester trophoblast cells following activation of the type I interferon [...] Read more.

The role of human leukocyte antigen F (HLA-F) at the maternal–fetal interface (MFI) during viral infection and its regulation by interferon signaling remains poorly understood. Here, we investigated HLA-F expression and regulation in first-trimester trophoblast cells following activation of the type I interferon pathway and viral infection. We demonstrate that HLA-F is significantly upregulated at both mRNA and protein levels in response to Poly(I:C) and IFN-β in a dose- and time-dependent manner, suggesting its regulation as an interferon-stimulated gene (ISG). Zika virus (ZIKV) infection similarly induced HLA-F upregulation over time. In contrast, HSV-2 infection downregulated HLA-F mRNA while maintaining steady protein levels, indicative of virus-specific regulatory mechanisms. Moreover, we identified a soluble form of HLA-F secreted following Poly(I:C) stimulation. These findings reveal that HLA-F is dynamically regulated in trophoblasts during viral challenge and type I IFN signaling activation, supporting its broader immunomodulatory role in antiviral defense and immune tolerance at the MFI. Full article

(This article belongs to the Special Issue Viruses in the Reproductive Tract)

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18 pages, 3149 KB

Open AccessEditor’s ChoiceArticle

Dynamics of Paraspeckle Components in Herpes Simplex Virus 1 (HSV-1)-Infected Human Neuronal Cells

by Carolina Filipponi, David C. Bloom, Carlo Gambotto, Callen T. Wallace, Jadranka Milosevic, Simon C. Watkins, Shane Buckley, Maribeth A. Wesesky, Vishwajit L. Nimgaonkar and Leonardo D’Aiuto

Viruses 2026, 18(5), 552; https://doi.org/10.3390/v18050552 - 12 May 2026

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Abstract

Paraspeckles are subnuclear ribonucleoprotein condensates that regulate host stress responses, including those triggered by viral infection. In vitro studies using non-neuronal cells have shown the involvement of specific paraspeckle components in facilitating the replication of certain viruses, including Herpes Simplex Virus 1 (HSV-1), [...] Read more.

Paraspeckles are subnuclear ribonucleoprotein condensates that regulate host stress responses, including those triggered by viral infection. In vitro studies using non-neuronal cells have shown the involvement of specific paraspeckle components in facilitating the replication of certain viruses, including Herpes Simplex Virus 1 (HSV-1), but these processes have not been investigated in human neuronal cells, which represent a relevant target of the virus. We employed human neural precursor cells (NPCs), neurons, and brain organoids derived from hiPSCs to investigate the previously unexplored dynamics of paraspeckle components in HSV-1-infected human neuronal cells. Our results reveal cell-type-specific differences in the expression of paraspeckle genes in response to HSV-1 infection. Unlike other viruses, HSV-1 orchestrates a previously unreported redistribution of paraspeckle proteins, leading to their accumulation in viral replication compartments (VRCs). Importantly, the expression of the paraspeckle proteins NONO and SFPQ correlates with HSV-1 permissiveness in human neuronal cells and may be required to establish a nuclear environment favoring viral transcription/replication. This enhances our understanding of how stress-response pathways in cells can be exploited by viruses in a cell-type-specific manner. Full article

(This article belongs to the Special Issue 3D Models in Viral Pathogenesis)

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20 pages, 2135 KB

Open AccessEditor’s ChoiceArticle

Identification of Cyclin L1 as a Host Factor Regulating Hepatitis B Virus Replication

by Collins Oduor Owino, Balakrishnan Chakrapani Narmada, Gian Yi Lin, Pauline Poh Kim Aw, Nivrithi Ganesh, Jovi Tan Siying, Marie-Laure Plissonnier, Thangavelu Thangavelu Matan, Niranjan Shirgaonkar, Pablo Bifani, Massimo Levrero, Giridharan Periyasamy, Seng Gee Lim and Ramanuj DasGupta

Viruses 2026, 18(5), 545; https://doi.org/10.3390/v18050545 - 8 May 2026

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Abstract

Background and Aims: Understanding regulatory interactions between hepatitis B virus (HBV) and host factors is essential for the development of next generation host-directed antiviral therapies and the achievement of a functional HBV cure. Here, we investigated HBV-induced alterations in host gene expression in [...] Read more.

Background and Aims: Understanding regulatory interactions between hepatitis B virus (HBV) and host factors is essential for the development of next generation host-directed antiviral therapies and the achievement of a functional HBV cure. Here, we investigated HBV-induced alterations in host gene expression in primary human hepatocytes (PHH) to identify host factors exploited by the virus for replication and persistence. Whole-transcriptome sequencing (WTS) of HBV-infected PHH identified host pathways with potential roles in the HBV life cycle. RNA interference-based functional screening of dysregulated candidate genes identified cyclin L1 (CCNL1) as a key host factor. RNAi-mediated knockdown of CCNL1 reduced HBV gene expression, including hepatitis B surface antigen (HBsAg). Mechanistically, CCNL1 regulates phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII) at serine 2 (S2), consistent with a role in transcriptional regulation. CCNL1 knockdown further reduced the binding of total and phospho- (Ser2/Ser5) RNAPII, pan-acetylated histone H3 (H3ac), and H3K27ac to HBV covalently closed circular DNA (cccDNA), indicating impaired cccDNA-dependent transcription. In addition, CCNL1 expression was elevated in chronic hepatitis B patients compared with those with resolved infection. Collectively, these data demonstrate that CCNL1 promotes HBV transcription and replication through modulation of RNAPII phosphorylation and chromatin-associated transcriptional activity, identifying CCNL1 as a potential host susceptibility factor for HBV. Importance: Hepatitis B virus infection remains a major threat to human health in areas with high prevalence. There is need to fully understand the complex interactions between the virus and human host factors/processes to support ongoing efforts to develop anti-HBV therapies that can be used with existing therapies to achieve a better cure. HBV relies on host cellular factors and biological processes to establish and maintain efficient infection, making host–virus interactions attractive targets for therapeutic intervention. Thus, identifying host factors that support and/or restrict HBV infection is essential for understanding the molecular basis of chronic HBV infection and for developing host-targeting anti-HBV drugs. This study identifies cyclin L1 (CCNL1) as a host susceptibility factor that promotes HBV transcription and replication through regulation of RNA polymerase II activity and or post-transcriptional mechanisms. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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14 pages, 1244 KB

Open AccessEditor’s ChoiceArticle

Efficient Plasmid-Based Rescue of T7 RNA Polymerase-Driven Calicivirus Reverse Genetics Systems in Mammalian Cells Using Vaccinia Virus RNA-Capping Enzymes

by Frazer J. T. Buchanan, Markella Loi, Charlotte Chim, ShuXian Zhou, Rebekah Penrice-Randal, Leandro X. Neves, Maximilian Erdmann and Edward Emmott

Viruses 2026, 18(5), 536; https://doi.org/10.3390/v18050536 - 4 May 2026

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Abstract

The caliciviruses include important human and animal pathogens such as norovirus, sapovirus and feline calicivirus. Viral reverse genetics is performed to understand the fundamental biology of these viruses, as well as a potential route to generate live-attenuated vaccines. Calicivirus reverse genetics systems have [...] Read more.

The caliciviruses include important human and animal pathogens such as norovirus, sapovirus and feline calicivirus. Viral reverse genetics is performed to understand the fundamental biology of these viruses, as well as a potential route to generate live-attenuated vaccines. Calicivirus reverse genetics systems have typically relied on either the production of in vitro-transcribed RNA or plasmid-based rescue, either from a mammalian promoter or through supplementing with helper enzymes through means of a helper virus. Here, we present a novel system integrating vaccinia capping enzymes D1R and D12L encoded on plasmids as part of a system for murine norovirus (MNV) reverse genetics. The addition of D1R, D12L and T7 RNA polymerase-expressing plasmids increases the viral titres of rescued MNV in both BSR-T7 cells and transgenic BSR-T7 cells expressing murine CD300LF (BSR-T7^CD300LF), and viral protein abundance. When the murine norovirus receptor is expressed in BSR-T7^CD300LF, viral titres increased 100–1000-fold compared to standard BSR-T7 cells. This system offers a robust, increased throughput means of assessing viral mutants over parallel in vitro transcription and capping reactions for multiple mutants, without requiring a helper virus. Full article

(This article belongs to the Section General Virology)

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12 pages, 919 KB

Open AccessEditor’s ChoiceArticle

Chronic HDV Infection Shows Higher HBsAg Isoform Levels than HBV Infection, Paralleling HDV Replicative Activity

by Stefano D’Anna, Lorenzo Piermatteo, Alessia Magnapera, Ilaria Grossi, Caterina Tramontozzi, Antonella Olivero, Leonardo Duca, Giulia Torre, Elisabetta Teti, Andrea Di Lorenzo, Vincenzo Malagnino, Marco Iannetta, Sandro Grelli, Pierpaolo Paba, Ada Bertoli, Francesca Ceccherini-Silberstein, Leonardo Baiocchi, Simona Francioso, Ilaria Lenci, Michele Milella, Annalisa Saracino, Alessia Ciancio, Giuseppina Brancaccio, Loredana Sarmati, Pietro Lampertico, Mario Rizzetto, Gian Paolo Caviglia, Romina Salpini and Valentina Svicher Show full author list Hide full author list

Viruses 2026, 18(5), 515; https://doi.org/10.3390/v18050515 - 30 Apr 2026

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Abstract

Background & Aim: The entry of Hepatitis D Virus (HDV) depends on HBV surface proteins (HBsAg) composed of three isoforms: large-, middle, and small HBsAg. Here, we investigate the levels of total HBsAg and HBsAg isoforms and their correlations with HDV-RNA, HBcrAg, and [...] Read more.

Background & Aim: The entry of Hepatitis D Virus (HDV) depends on HBV surface proteins (HBsAg) composed of three isoforms: large-, middle, and small HBsAg. Here, we investigate the levels of total HBsAg and HBsAg isoforms and their correlations with HDV-RNA, HBcrAg, and transaminases in the setting of untreated chronic hepatitis D (CHD). Methods: This study includes 316 HBeAg-negative patients: 192 CHD and 124 with chronic hepatitis B (CHB) as a control group. HBsAg isoforms were quantified by ad hoc-designed ELISAs. Results: The composition of HBsAg isoforms varied between the two groups of patients, with remarkably higher small HBsAg, middle-HBsAg, and large HBsAg in CHD than in CHB. This data was confirmed by multivariable analysis (p < 0.0001). Among CHD, HBsAg isoforms positively correlated with HDV-RNA (p < 0.0001) and HBcrAg (p < 0.0001) but not with HBV-DNA. The results were confirmed by stratifying patients according to HDV-RNA (< or >1000 IU/mL) and HBcrAg (< or >3 logU/mL). Furthermore, CHD patients with ALT > upper limit of normal presented significantly higher S-HBsAg and M-HBsAg levels. Conclusions: CHD is characterized by a more elevated HBsAg isoform production, paralleling HDV-RNA and HBcrAg release. This may suggest a preferential recruitment of HBsAg isoforms in HDV virions at the expense of HBV virions. The association of HBsAg isoforms with higher ALT also suggests their potential contribution in supporting HDV-induced pro-inflammatory stimuli. Full article

(This article belongs to the Special Issue Virology in Italy 2025—9th National Congress of the Italian Society for Virology)

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20 pages, 2724 KB

Open AccessEditor’s ChoiceArticle

CHIKV-Infected Human Dermal Fibroblasts Mount an IFNβ Transcriptional Response Independent of TBK1/IKKε Signaling That Fails to Prevent Lethal Infection

by Meagan M. Taylor, Rosemary W. Roberts and Jonathan O. Rayner

Viruses 2026, 18(5), 503; https://doi.org/10.3390/v18050503 - 28 Apr 2026

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Abstract

Chikungunya virus (CHIKV) is an alphavirus that infects dermal fibroblasts as a primary target cell during natural mosquito-borne transmission. While primary human dermal fibroblasts (hDFs) have been implicated as a key source of type I interferon (IFN-I) during CHIKV infection, the dynamics of [...] Read more.

Chikungunya virus (CHIKV) is an alphavirus that infects dermal fibroblasts as a primary target cell during natural mosquito-borne transmission. While primary human dermal fibroblasts (hDFs) have been implicated as a key source of type I interferon (IFN-I) during CHIKV infection, the dynamics of this response and its sufficiency for antiviral protection remain incompletely understood. Here, we systematically characterize in vitro CHIKV infection of primary hDFs, evaluating the effects of single-passage viral stock origin (mammalian- vs. mosquito-propagated), donor variability, and multiplicity of infection (MOI) on infection kinetics and innate immune induction. We demonstrate that hDFs support high-titered CHIKV replication at both MOI 1 and 0.01, resulting in universal cell death by 72 hpi despite robust IFNβ transcript induction—reaching up to ~2800-fold over mock—and secretion of pro-inflammatory cytokines, including IFNα2, TNFα, IL-1β, and IL-8. Notably, IFNβ protein levels remained below 10 pg/mL under all infection conditions, revealing a disconnect between transcriptional and translational responses, suggesting CHIKV-mediated translational suppression. Pharmacological inhibition of TBK1/IKKε via amlexanox did not suppress IFNβ transcript induction at any tested concentration, suggesting that canonical PRR signaling through this node—including both RIG-I/MAVS and TLR3/TRIF pathways—is not the major driver of the observed transcriptional response. In contrast, co-inoculation with exogenous IFNβ as low as 20 pg/mL activated IFNAR signaling, robustly upregulated interferon-stimulated genes (ISGs), and fully rescued hDFs from otherwise lethal infection. Together, these findings demonstrate that CHIKV-infected hDFs mount a transcriptionally robust but translationally insufficient innate immune response and that the transcriptional response appears to operate independently of TBK1/IKKε. These results have direct implications for understanding how the skin microenvironment may modulate early CHIKV pathogenesis and suggest that paracrine IFNβ signaling from neighboring cell types may be critical for fibroblast survival during natural infection. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 3rd Edition)

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19 pages, 5184 KB

Open AccessEditor’s ChoiceArticle

Heterologous Sequential mRNA Vaccination of Indian Rhesus Macaques Elicits Broad Binding and Neutralizing Antibody Responses Against Diverse Henipaviruses

by Thomas B. Voigt, Noor Ghosh, Brandon C. Rosen, Taylor Newbolt, Johan J. Louw, Aaron Yrizarry-Medina, Christakis Panayiotou, Jack T. Mauter, Giovana de Figueiredo Godoy, Joshua Terao, Eva G. Rakasz, Matthew R. Reynolds, Dawn M. Dudley, David I. Watkins and Michael J. Ricciardi

Viruses 2026, 18(5), 487; https://doi.org/10.3390/v18050487 - 23 Apr 2026

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Abstract

Henipaviruses (HNVs), including Nipah virus (NiV) and Hendra virus (HeV), are highly pathogenic and often lethal zoonotic viruses with broad species tropism and no approved human vaccines. The emergence of genetically divergent HNVs—including Ghana virus (GhV), Langya virus (LayV), and Mojiang virus (MojV)—emphasizes [...] Read more.

Henipaviruses (HNVs), including Nipah virus (NiV) and Hendra virus (HeV), are highly pathogenic and often lethal zoonotic viruses with broad species tropism and no approved human vaccines. The emergence of genetically divergent HNVs—including Ghana virus (GhV), Langya virus (LayV), and Mojiang virus (MojV)—emphasizes the need for broadly protective countermeasures. Here, we evaluated the antibody (Ab) responses to sequential mRNA vaccines encoding the membrane-bound attachment glycoprotein (gG) from NiV, GhV, and/or LayV in a pilot study with Indian rhesus macaques. Serum binding Ab responses were quantified by ELISA against five soluble gG antigens (NiV, HeV, GhV, LayV, MojV). Functional activity was assessed by neutralization assays using NiV, HeV, and GhV pseudoviruses, and by receptor-blocking ELISA. Sequential vaccination induced high-titer IgG binding against all five HNV gGs with increasing breadth after each dose. Pan-genus regimens elicited moderate neutralizing Ab titers against NiV, HeV, and GhV, whereas the NiV-only regimen elicited potent but narrow neutralization against NiV and HeV. Conversely, the GhV-LayV-GhV regimen elicited strong binding to GhV, LayV, and MojV gG and robust neutralization of GhV pseudovirus, but limited cross-reactivity to NiV and HeV. In this pilot study, we demonstrated that mRNA vaccination can elicit broadly reactive binding and neutralizing Ab responses across phylogenetically distant HNVs. Additionally, we show GhV pseudovirus neutralization for the first time. Collectively, these data provide a foundation for the development of next-generation pan-genus HNV vaccines capable of mitigating future HNV outbreaks. Full article

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15 pages, 3281 KB

Open AccessEditor’s ChoiceArticle

Functional Analysis of the Halastavi árva Virus (HalV) Internal Ribosome Entry Site

by Subash Chapagain, Lauren F. Woodburn, Natalie C. J. Strynadka and Eric Jan

Viruses 2026, 18(5), 492; https://doi.org/10.3390/v18050492 - 23 Apr 2026

Viewed by 1995

Abstract

Viral internal ribosome entry sites (IRESs) are specialized RNA structures that facilitate cap-independent translation as a strategy to usurp the host translational machinery. The Type 6 IRESs are the most streamlined mechanism to date, as they adopt a three pseudoknot RNA structure to [...] Read more.

Viral internal ribosome entry sites (IRESs) are specialized RNA structures that facilitate cap-independent translation as a strategy to usurp the host translational machinery. The Type 6 IRESs are the most streamlined mechanism to date, as they adopt a three pseudoknot RNA structure to initiate factorless translation initiation by directly recruiting the ribosome and drive translation. The Halastavi árva virus (HalV) IRES represents the most minimalistic subclass identified to date, whereby the IRES lacks specific pseudoknot domains that bind to the 40S subunit but instead recruits pre-assembled 80S ribosomes via a mechanism that is not fully understood. Here, we examined cellular conditions that can support HalV IRES translation. We demonstrated that the HalV IRES is translationally active in insect Sf21 lysates and Drosophila S2 cells, but inactive in mammalian RRL and wheat germ extract. Cells treated with heat shock or serum starvation suppressed HalV IRES activity, whereas virus infection robustly enhanced HalV IRES-mediated translation. Finally, the HalV IRES can support viral translation and replication using a heterologous viral replicon. These findings highlight the context-specific cellular conditions that allow ribosome assembly and translation by a factorless minimalist IRES. Full article

(This article belongs to the Special Issue Viral Strategies and Cellular Countermeasures That Regulate mRNA Access to the Translation Apparatus: 2nd Edition)

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17 pages, 1136 KB

Open AccessEditor’s ChoiceArticle

Polymorphisms for Defence and Virulence in the Arabidopsis thaliana–Cucumber mosaic virus Interaction Are Expressed in the Host’s Native Habitat

by Israel Pagán, Rafael de Andrés-Torán, Nuria Montes, Aurora Fraile and Fernando García-Arenal

Viruses 2026, 18(5), 494; https://doi.org/10.3390/v18050494 - 23 Apr 2026

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Abstract

Plant defences are assumed to evolve in response to the negative effects of virus infection on plant fitness (virulence), and to drive plant–virus coevolution. However, viruses are not always antagonistic symbionts of plants, and the expression of defence traits is environment-dependent. Thus, understanding [...] Read more.

Plant defences are assumed to evolve in response to the negative effects of virus infection on plant fitness (virulence), and to drive plant–virus coevolution. However, viruses are not always antagonistic symbionts of plants, and the expression of defence traits is environment-dependent. Thus, understanding plant–virus interactions requires analysing the expression of defence traits in the host’s native habitat. Here we analyse the effect of cucumber mosaic virus (CMV) infection, and the expression of resistance and tolerance in the native habitat of a wild Arabidopsis thaliana population. Plants from ten genotypes from that population, which have been shown to differ in resistance and tolerance to CMV in a greenhouse, were inoculated with an Arabidopsis isolate of CMV and transplanted to their habitat. Resistance was rated based on virus accumulation in leaves, and tolerance was rated based on the effect of infection on plant fecundity relative to virus accumulation. Consistent with the greenhouse assays, virulence depended on the host genotype, and polymorphisms for resistance and tolerance were expressed in the field, supporting the validity of the conclusions from the greenhouse assays. Our results also support theoretical predictions on the relationships between pathogen multiplication and virulence and between resistance and tolerance. Full article

(This article belongs to the Special Issue Plant Virus Resistance—2nd Edition)

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13 pages, 3491 KB

Open AccessEditor’s ChoiceArticle

Targeted and Effective Phage-Based Biocontrol of Black Rot Disease in Broccoli

by Miloud Sabri, Khaoula Mektoubi, Orges Cara, Roukia Bougheloum, Angelo De Stradis, Giuseppe Parrella and Toufic Elbeaino

Viruses 2026, 18(5), 484; https://doi.org/10.3390/v18050484 - 22 Apr 2026

Viewed by 674

Abstract

Xanthomonas species are Gram-negative bacterial pathogens responsible for diseases in over 400 plant hosts, including numerous economically important crops such as Brassica species. The limited efficacy and environmental concerns associated with chemical control strategies underscore the need for sustainable and targeted alternatives. In [...] Read more.

Xanthomonas species are Gram-negative bacterial pathogens responsible for diseases in over 400 plant hosts, including numerous economically important crops such as Brassica species. The limited efficacy and environmental concerns associated with chemical control strategies underscore the need for sustainable and targeted alternatives. In this study, we evaluated the suitability and biocontrol efficacy of phages Phi1 and Phi3 to combat Xanthomonas campestris pv. campestris (Xcc) in broccoli plants. Kill-curve assays demonstrated that both phages effectively suppressed Xcc growth across a range of multiplicities of infection. Transmission electron microscopy further confirmed their lytic activity, revealing pronounced structural damage to Xcc cells following phage treatment, accompanied by the subsequent release of phage progeny. To assess host specificity and biosafety, the phages were tested against 41 bacterial isolates that were isolated and taxonomically characterized from broccoli and cauliflower in this study. Neither Phi1 nor Phi3 exhibited lytic activity against any non-target isolate, indicating high host specificity and minimal risk to the native Brassica-associated microbiota. In planta assays demonstrated that the combined application of Phi1 and Phi3 reduced Xcc-induced symptom severity in broccoli plants by 80%. Collectively, these results demonstrate that phages Phi1 and Phi3 represent effective and biologically precise agents for the control of black rot disease in Brassica crops. Full article

(This article belongs to the Special Issue Phage Cocktails: Promising Approaches Against Infections)

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17 pages, 2294 KB

Open AccessEditor’s ChoiceArticle

In Vitro Antiviral Properties of Two Recombinant Sendai Virus Vectors Encoding ORFV 011 and ORFV 059 Genes

by Álex Gómez, Idoia Glaria, Irati Moncayola, Leonor Puzol, Laura Arriazu, Ainhoa Calero, Ignacio de Blas, Mikel Nazábal, Itziar Hualde, Benhur Lee, Lluís Luján, Ralf Amann, Irache Echeverría and Ramsés Reina

Viruses 2026, 18(4), 462; https://doi.org/10.3390/v18040462 - 13 Apr 2026

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Abstract

Orf virus (ORFV) is a globally distributed zoonotic parapoxvirus that causes a highly contagious mucocutaneous disease in small ruminants. Despite the urgent demand for vaccination-based control, no licensed vaccines are currently available universally. In this study, we generated two recombinant Sendai virus (SeV) [...] Read more.

Orf virus (ORFV) is a globally distributed zoonotic parapoxvirus that causes a highly contagious mucocutaneous disease in small ruminants. Despite the urgent demand for vaccination-based control, no licensed vaccines are currently available universally. In this study, we generated two recombinant Sendai virus (SeV) vectors expressing ORFV 011 (rSeV-GFP-B2L) and ORFV 059 (rSeV-GFP-059) genes and evaluated their ability to stimulate antiviral responses in vitro. Following the transduction, we assessed transgene expression, innate immune activation, induction of interferon-stimulated genes (A3Z1, OBST2, SAMHD1), and antiviral activity. Both vectors significantly upregulated pattern recognition receptors (TLRs, RIG-I) and type I interferon (IFN-β) genes, with rSeV-GFP-059 inducing the strongest response. Remarkably, OBST2 was robustly upregulated, suggesting a potential role in restricting ORFV replication. Antiviral activity assays revealed a marked reduction in ORFV DNA copies and a mild decrease in ORFV RNA transcription in rSeV-GFP-059-transduced cells, particularly at later time points, accompanied by complete abrogation of the typical cytopathic effect. Collectively, these results demonstrate that SeV-based vectors, particularly rSeV-GFP-059, efficiently prime antiviral immunity and suppress ORFV replication, establishing a promising platform for further in vivo vaccine evaluation in sheep. Full article

(This article belongs to the Special Issue Viral Diseases of Sheep and Goats)

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18 pages, 6880 KB

Open AccessEditor’s ChoiceArticle

Mitochondrial Antiviral Signaling (MAVS) Protein Modulates the Transition from Acute to Persistent Parainfluenza Virus Infection and Resistance to Complement-Mediated Cell Lysis

by Jenna R. Aquino and Griffith D. Parks

Viruses 2026, 18(4), 416; https://doi.org/10.3390/v18040416 - 27 Mar 2026

Viewed by 1384

Abstract

Parainfluenza virus 5 (PIV5) can establish persistent infections in host cells despite encountering innate immune defenses, including the complement (C′) system. The host determinants that enable persistently infected cells (PI) to evade C’-mediated clearance remain largely undefined. Here, we identify the mitochondrial antiviral [...] Read more.

Parainfluenza virus 5 (PIV5) can establish persistent infections in host cells despite encountering innate immune defenses, including the complement (C′) system. The host determinants that enable persistently infected cells (PI) to evade C’-mediated clearance remain largely undefined. Here, we identify the mitochondrial antiviral signaling (MAVS) protein, a central adaptor in double-stranded RNA-triggered antiviral and pro-survival signaling pathways, as a critical mediator of both PIV5 persistence and acquired resistance to C’ lysis. Wild-type (WT) PIV5-infected A549 cells were initially sensitive to C’-directed killing, but these cells rapidly establish a PI in culture with ~25% of the cell population becoming resistant to C’ lysis by day 2 and ~75% by day 4. In contrast, PIV5-infected A549 MAVS-deficient (MAVS KO) cells exhibited elevated viral gene expression, increased deposition of C3 and the membrane attack complex, and were more susceptible than WT cells to C′ killing. PIV5-infected MAVS KO cells showed rapid cytopathic effects and never established a stable PI. While pharmacological suppression of viral gene expression with ribavirin (RBV) restored the survival of PIV5-infected MAVS KO cells into a long-term PI-like state, these RBV-induced PI cells remained sensitive to C’ lysis. Collectively, these findings demonstrate a role of MAVS in modulating a PIV5 infection in culture, to facilitate both the conversion of a PIV5 acute infection to a PI and development of resistance to C’ killing. Full article

(This article belongs to the Special Issue RNA Viruses Replication and Innate Immunity)

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15 pages, 2971 KB

Open AccessEditor’s ChoiceArticle

Prior Infection with Torque Teno Virus Mitigates Influenza Pathology in Mice

by Md-Tariqul Islam, Brett Webb and Sheela Ramamoorthy

Viruses 2026, 18(3), 357; https://doi.org/10.3390/v18030357 - 15 Mar 2026

Viewed by 1748

Abstract

Respiratory infections caused by influenza viruses are frequently associated with coinfection by other infectious agents. Torque teno viruses (TTVs) are small DNA viruses that can function as opportunistic pathogens and are epidemiologically linked to influenza viruses as well as a broad spectrum of [...] Read more.

Respiratory infections caused by influenza viruses are frequently associated with coinfection by other infectious agents. Torque teno viruses (TTVs) are small DNA viruses that can function as opportunistic pathogens and are epidemiologically linked to influenza viruses as well as a broad spectrum of infectious and immune-mediated diseases. Among TTVs, swine torque teno viruses (TTSuVs) are unique in that they have been shown to act as primary pathogens. With the long-term objective of developing experimental tools to better understand inter-viral interactions, this study aimed to optimize a murine model of TTV and influenza virus coinfection. Experimental mice were inoculated with TTSuV1 on day 1 post infection (DPI 1), while phosphate-buffered saline (PBS)-treated mice served as negative controls. A subset of TTSuV1-infected mice was subsequently coinfected with the influenza A virus H1N1 (IAV) at either 12 or 27 days following TTSuV1 infection. An additional group of mice was maintained as an IAV only control. Mice infected with IAV were euthanized 72–84 h post-IAV infection, corresponding to DPI 15 and 30, respectively. Unexpectedly, gross and histopathological examination of lung tissues revealed that prior TTSuV1 infection significantly attenuated IAV-induced pathology in coinfected mice. Coinfected animals also exhibited a tendency toward reduced IAV replication in the lungs as measured by qPCR, TCID₅₀ and HAs compared to mice infected with IAV alone, accompanied by lower levels of virus-specific antibodies to IAV at DPI 30 and TTSuV1 at DPI 15 respectively. At DPI 30, TTSuV1 genomic DNA levels in lung tissue and whole blood were higher in coinfected mice, suggestive of prolonged viremia in the coinfected group. Collectively, these findings establish baseline parameters for a murine TTV and influenza coinfection model and provide a foundation for future studies aimed at elucidating the molecular and immunological mechanisms underlying viral coinfections. Full article

(This article belongs to the Special Issue Advancing Research of Anelloviruses, Second Edition)

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20 pages, 2565 KB

Open AccessEditor’s ChoiceArticle

Host Cell Central Carbon Metabolism and Cellular NAD⁺ Pool Regulate Efficient Replication of Vesicular Stomatitis Virus

by Kush K. Pandey, Bikash R. Sahoo, D. S. McVey and Asit K. Pattnaik

Viruses 2026, 18(3), 326; https://doi.org/10.3390/v18030326 - 6 Mar 2026

Viewed by 1434

Abstract

Vesicular stomatitis virus (VSV) is a promising oncolytic virus whose replication efficiency and tumor selectivity are strongly influenced by host cell metabolism. Cancer cells, including glioblastoma, exhibit profound rewiring of central carbon metabolism to sustain proliferation, redox balance, and biosynthetic demand, yet how [...] Read more.

Vesicular stomatitis virus (VSV) is a promising oncolytic virus whose replication efficiency and tumor selectivity are strongly influenced by host cell metabolism. Cancer cells, including glioblastoma, exhibit profound rewiring of central carbon metabolism to sustain proliferation, redox balance, and biosynthetic demand, yet how these metabolic states regulate VSV replication remains incompletely defined. Here, we investigated the dependency of VSV replication on glycolysis, the pentose phosphate pathway (PPP), and glutamine metabolism in A172 human glioblastoma cells. Pharmacologic inhibition of glycolysis using 2-DG strongly suppressed VSV replication in a dose-dependent manner, highlighting a robust requirement for glycolytic flux and downstream intermediates. While inhibiting the PPP with 6-AN, a nicotinamide adenine dinucleotide (NAD) analog, markedly impaired viral replication, D-ribose was unable to rescue the inhibition, indicating that nucleotide precursor limitation alone was insufficient to explain this effect. Interestingly, depletion of glucose 6-phosphate dehydrogenase (G6PD), a key enzyme in the PPP, resulted in significant enhancement of VSV replication. Restoration of viral replication by NAD⁺ precursors in the presence of 6-AN or suppression of replication by the NAMPT inhibitor FK866 suggested NAD⁺ availability as a critical determinant of VSV replication. Additionally, blockade of glutaminase activity with BPTES reduced viral replication, underscoring the importance of anaplerotic pathways in glioblastoma cells. Collectively, these findings demonstrate that VSV replication is tightly coupled to metabolic programs, particularly those governing energy production and NAD(P)H balance. This work provides a metabolic framework for optimizing oncolytic VSV therapies and suggests that metabolic interventions in cancer treatment may influence oncolytic virus efficacy. Full article

(This article belongs to the Special Issue Virus Infections and Host Metabolism 2026)

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26 pages, 2135 KB

Open AccessEditor’s ChoiceReview

Inside the European Plant Viroid Scenario: Continental Distribution, Host Range, and Genetic Features of the Main Viroid Populations

by Athos Pedrelli, Marzia Vergine, Luigi De Bellis and Andrea Luvisi

Viruses 2026, 18(3), 325; https://doi.org/10.3390/v18030325 - 5 Mar 2026

Viewed by 1283

Abstract

Viroids are a serious threat to plant health due to their broad host range, high infectivity, and latent infections. Europe’s heterogeneous climate, ecology, and agriculture make it a key setting for viroid research. Despite numerous country- and host-specific reports, a continental synthesis has [...] Read more.

Viroids are a serious threat to plant health due to their broad host range, high infectivity, and latent infections. Europe’s heterogeneous climate, ecology, and agriculture make it a key setting for viroid research. Despite numerous country- and host-specific reports, a continental synthesis has been lacking. In this study, we systematically collected all available official records of plant viroids in Europe from 1972 to 2025. A total of 255 documents were analyzed, encompassing 35 countries of the European continent and 118 host plant species, classified by host use (cultivated, ornamental, wild) and growth habit. Nucleotide sequences of the most common European viroids were retrieved from the NCBI database to assess genetic diversity and recombination. Europe hosts 32 of the 45 recognized viroid species worldwide (~71%), representing all eight genera. Southern Europe emerged as the main hotspot (~70% of reports), largely associated with Mediterranean climates and intensive cultivation of woody crops. Cultivated plants were the dominant hosts across all regions, while ornamentals were particularly important in Northern and Western Europe. Population genetic analyses revealed heterogeneous patterns, quasispecies dynamics, and recombination, shaped by host and geography. This is the first integrated overview of viroids across Europe, highlighting the importance of surveillance, sequencing, and genomic research. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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31 pages, 5707 KB

Open AccessEditor’s ChoiceArticle

Identification of Receptor Binding Proteins of Yersinia Phage φR1-37 and Enterocoliticin That Use the Same Bacterial Surface Receptor

by Mikael Skurnik, Rahime Tetik, Muhammad Suleman Qasim, Jana Sachsenröder, Ralf Dieckmann, Carlos G. Leon-Velarde, Göran Widmalm, Eckhard Strauch and Arnab Bhattacharjee

Viruses 2026, 18(3), 291; https://doi.org/10.3390/v18030291 - 27 Feb 2026

Viewed by 2005

Abstract

The bacterium Yersinia enterocolitica serotype O:3 is targeted by two distinct agents, the bacteriophage φR1-37 and the bacteriocin-like enterocoliticin (a tailocin), which both utilize the lipopolysaccharide (LPS) outer core (OC) hexasaccharide as their primary host receptor. In order to understand this convergent recognition [...] Read more.

The bacterium Yersinia enterocolitica serotype O:3 is targeted by two distinct agents, the bacteriophage φR1-37 and the bacteriocin-like enterocoliticin (a tailocin), which both utilize the lipopolysaccharide (LPS) outer core (OC) hexasaccharide as their primary host receptor. In order to understand this convergent recognition mechanism, we first characterized the enterocoliticin system, reporting the complete sequence of its large, biosynthetic gene cluster. Most of the 42 predicted gene products were functionally annotated by homology to known gene products. We then focused on identifying the receptor-binding proteins (RBPs) responsible for host attachment of both agents in order to elucidate a possible shared mechanism of binding. For phage φR1-37, the receptor binding complex was identified as the inseparable Gp298 tail fiber protein and its Gp297 trimerization chaperone, confirming its function as the RBP. Based on sequence identity with Gp298, the Orf39 gene product of the enterocoliticin cluster was predicted to be its corresponding RBP. An analytical comparison of the predicted RBPs revealed a highly conserved homologous region spanning 80–85 amino acid residues, which presents the only structural explanation for their identical receptor specificity. To resolve the binding mechanism, we generated high-confidence trimeric structural models for the Gp298 and Orf39 proteins using AlphaFold3-multimer. These models validated the high structural similarity of the RBP domains, despite global dissimilarity of the complete trimeric structures. Further docking simulations with a pentasaccharide ligand (generated by CarbBuilder) provided suggestive molecular models for the protein-carbohydrate interactions within the OC region. Intriguingly, a database search using the identified binding site motif revealed their wide and diverse presence in various phage tail proteins, suggesting that this motif is a specialized, common structure for carbohydrate recognition. This work identifies a conserved, novel sugar-binding motif as the molecular basis of host recognition for these key anti-Yersinia biologics. Full article

(This article belongs to the Special Issue 15-Year Anniversary of Viruses)

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20 pages, 1264 KB

Open AccessEditor’s ChoiceReview

Advances in Plant Antiviral RNAi: From Host DCLs/RDRs to Diversified Viral Counteracting Strategies

by Xue Li, Fuan Pan, Xueping Zhou, Aiming Wang, Richard Kormelink and Fangfang Li

Viruses 2026, 18(2), 184; https://doi.org/10.3390/v18020184 - 29 Jan 2026

Cited by 1 | Viewed by 1950

Abstract

Plant RNA interference (RNAi) is a fundamental antiviral defense that relies on coordinated activities of DICER-like endonucleases (DCLs), Argonaute proteins (AGOs) and RNA-dependent RNA polymerases (RDRs). Over the past decades, studies using model and crop species have uncovered complex and often redundant roles [...] Read more.

Plant RNA interference (RNAi) is a fundamental antiviral defense that relies on coordinated activities of DICER-like endonucleases (DCLs), Argonaute proteins (AGOs) and RNA-dependent RNA polymerases (RDRs). Over the past decades, studies using model and crop species have uncovered complex and often redundant roles for DCLs and RDRs in generating and amplifying virus-derived small interfering RNAs (vsiRNAs), in addition to connections with transcriptional gene silencing (TGS) and epigenetic defenses against DNA viruses. Concurrently, plant viruses have evolved diverse counterstrategies—proteinaceous RNA silencing suppressors (RSSs), exoribonuclease (XRN)-resistant noncoding RNAs, and indirect manipulation of host pathways—to evade RNAi. Driven by the co-evolutionary arms race, plants have developed sophisticated counter-countermeasures that modulate or overcome viral anti-RNAi activity. Accumulated evidence suggests that plants encode host factor genes that are activated to degrade or sequester viral components such as RSSs against viral infection. On the other hand, plants have also evolved endogenous host modulators of antiviral RNAi that can either reinforce the antiviral response or be co-opted by viruses to antagonize it, representing a furious dynamic molecular battling mechanism. Here, we review recent advances in the molecular functions of DCLs and RDRs across species, summarize newly discovered viral counter-defenses (including RNA-based suppressors), and discuss host counter-countermeasures. We research key areas—such as the roles of RDRγ-class proteins, RTL1 (RNase three-like 1)-mediated competition with DCLs, and the mechanistic impact of viral noncoding RNAs—and outline translational opportunities for improving virus resistance in crops through breeding, biotechnological approaches, and RNA-based applications. Full article

(This article belongs to the Special Issue Plant Virus Research and Biotechnology-Based Resistance Strategies—In Honor of Professor Andrew Otis Jackson)

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17 pages, 2038 KB

Open AccessEditor’s ChoiceArticle

Diverse Temperate Coliphages of the Urinary Tract

by Haley Atkins, Natalie Stegman and Catherine Putonti

Viruses 2026, 18(2), 179; https://doi.org/10.3390/v18020179 - 29 Jan 2026

Viewed by 1121

Abstract

While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. [...] Read more.

While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract. Full article

(This article belongs to the Special Issue Bacteriophage Diversity, 2nd Edition)

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21 pages, 7298 KB

Open AccessEditor’s ChoiceArticle

Switchable Retargeting of Lentiviral Vectors Through a VSV-G-Binding Adapter Molecule

by Vladislav A. Zhuchkov, Marat P. Valikhov, Yulia E. Kravchenko, Elena I. Frolova and Stepan P. Chumakov

Viruses 2025, 17(12), 1563; https://doi.org/10.3390/v17121563 - 29 Nov 2025

Viewed by 3487

Abstract

Selective gene delivery to defined cell populations remains one of the key challenges in lentiviral vector-based gene therapy. The vesicular stomatitis virus glycoprotein (VSV-G) confers high infectivity but lacks cell-type specificity because of the ubiquitous expression of its receptor, LDLR. To enable modular, [...] Read more.

Selective gene delivery to defined cell populations remains one of the key challenges in lentiviral vector-based gene therapy. The vesicular stomatitis virus glycoprotein (VSV-G) confers high infectivity but lacks cell-type specificity because of the ubiquitous expression of its receptor, LDLR. To enable modular, receptor-specific targeting while retaining the production efficiency of VSV-G-pseudotyped vectors, we designed a bispecific adapter, 929-B6, comprising a VSV-G-binding nanobody and an ERBB2-binding DARPin 9.29. Anti-VSV-G nanobodies were isolated from an alpaca immune library and screened in cell-based pseudoreceptor assays to identify the optimal binder (VSVG-B6). The resulting adapter was evaluated with receptor-ablated (VSV-G_mut) and wild-type VSV-G-pseudotyped LVs across ERBB2-positive and -negative cell lines and in a mouse xenograft model. 929-B6 enabled efficient, receptor-specific transduction of ERBB2-expressing cells without increasing infection of ERBB2-negative controls. Pre-incubation of VSV-G_mut-pseudotyped LVs with 1–2 µg/mL 929-B6 increased transduction up to eight-fold in ERBB2⁺ cells, with similar but smaller effects for VSV-G and VSV-G_mut + 929R pseudotypes. Across breast cancer lines, transduction enhancement correlated with ERBB2 surface density, and co-culture experiments confirmed selective entry into ERBB2⁺ populations. In vivo imaging of ERBB2⁺ tumors revealed a visible tumor-localized luminescent signal following administration of 929-B6-treated vectors. The 929-B6 adapter provides a rapid, scalable means to retarget standard LV stocks toward chosen receptors without re-engineering the envelope or co-packaging pseudoreceptor plasmids. Its modularity suggests a generalizable platform for both gene therapy and oncolytic applications requiring flexible, receptor-defined tropism. Full article

(This article belongs to the Section General Virology)

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14 pages, 3070 KB

Open AccessEditor’s ChoiceArticle

Minimal Polymerase-Containing Precursor Required for Chikungunya Virus RNA Synthesis

by David Aponte-Diaz, Abha Jain, Jayden M. Harris, Jamie J. Arnold and Craig E. Cameron

Viruses 2025, 17(12), 1556; https://doi.org/10.3390/v17121556 - 28 Nov 2025

Cited by 1 | Viewed by 1751

Abstract

Alphaviruses pose a growing global health threat, with Chikungunya virus (CHIKV) epidemics ongoing. Although several CHIKV vaccine candidates have progressed to late-stage clinical evaluation, none have yet achieved licensure or widespread availability. The CHIKV nonstructural proteins nsP2 and nsP4 encode essential enzymatic activities [...] Read more.

Alphaviruses pose a growing global health threat, with Chikungunya virus (CHIKV) epidemics ongoing. Although several CHIKV vaccine candidates have progressed to late-stage clinical evaluation, none have yet achieved licensure or widespread availability. The CHIKV nonstructural proteins nsP2 and nsP4 encode essential enzymatic activities that represent key targets for antiviral development, yet the biochemical basis of nsP4 RNA-dependent RNA polymerase (RdRp) activity remains poorly understood. Here, we identify a minimal, functional precursor form of nsP4 derived from the nsP3–nsP4 polyprotein (P34) that is active in a cell-based RNA replicon system. Using synthetic, capped mRNAs, we show that cleavage of P34 by the nsP2 protease is required for robust reporter expression, and that a truncated form retaining only the C-terminal 50 residues of nsP3 (CT50-P34) supports near-wild-type replication. Unexpectedly, ubiquitin–nsP4 fusions failed to substitute for P34, likely reflecting the transient expression supported by our RNA-based system. We propose that precursor forms of nsP4 interact with the nsP1 dodecamer at the site of genome replication, where cleavage activates the RdRp and localization within the nsP1 dodecamer maintains nsP4 in its active conformation. Dissociation from the nsP1 dodecamer triggers a conformational switch to an inactive state. Together, these findings establish a tractable framework for interrogation of the assembly, activation, and regulation of the alphavirus polymerase. Full article

(This article belongs to the Special Issue 15-Year Anniversary of Viruses)

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20 pages, 1732 KB

Open AccessEditor’s ChoiceArticle

Molecular Determinants of Species-Specific Interactions Between Protein Kinase R and Poxvirus K3 Orthologs

by Chorong Park, Greg Brennan, Chen Peng, Chi Zhang, Jingxin Cao, Loubna Tazi and Stefan Rothenburg

Viruses 2025, 17(12), 1550; https://doi.org/10.3390/v17121550 - 26 Nov 2025

Viewed by 1415

Abstract

Protein kinase R (PKR) is an antiviral protein that is involved in molecular “arms races” with viral antagonists. As a result, some PKR inhibitors, including the vaccinia virus (VACV) protein K3 and its orthologs from other poxviruses only inhibit PKRs of selected species. [...] Read more.

Protein kinase R (PKR) is an antiviral protein that is involved in molecular “arms races” with viral antagonists. As a result, some PKR inhibitors, including the vaccinia virus (VACV) protein K3 and its orthologs from other poxviruses only inhibit PKRs of selected species. We previously reported contrasting inhibition patterns of human, sheep, and cow PKRs by VACV K3 and the sheeppox virus (SPPV) K3 ortholog, SPPV 011. Here we show that the differential sensitivities of cow and sheep PKRs to VACV K3 were mediated by only two residues in PKR helix αG. In contrast, SPPV 011 sensitivities were governed by additional residues and regions. Analysis of the PKR sensitivities from 20 mammalian species to VACV K3 and SPPV 011 revealed four different sensitivity patterns: some PKRs were inhibited by only one K3 ortholog, as previously reported, whereas other PKRs were either resistant or sensitive to both inhibitors. Furthermore, we characterized a residue (K45) in VACV K3 that is involved in the species-specific inhibition of PKR. Mutating this residue increased the inhibition of sheep but not human PKR, whereas it decreased the inhibition of mouse PKR, highlighting that a single mutation in a viral protein can result in distinct species-dependent inhibition changes. Full article

(This article belongs to the Special Issue Viral Strategies and Cellular Countermeasures That Regulate mRNA Access to the Translation Apparatus: 2nd Edition)

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20 pages, 5948 KB

Open AccessEditor’s ChoiceArticle

The Viruses of Botrytis cinerea and Beyond: Molecular Characterization of RNA Viruses and Retroplasmids

by Huang Huang, Jiasen Cheng, Yanping Fu, Qing Cai, Yang Lin, Tao Chen, Bo Li, Xiao Yu, Xueqiong Xiao, Daohong Jiang and Jiatao Xie

Viruses 2025, 17(12), 1527; https://doi.org/10.3390/v17121527 - 21 Nov 2025

Cited by 1 | Viewed by 1384

Abstract

Over the past five years, research has progressively revealed a rich diversity of RNA viruses in Botrytis cinerea. In this study, we identified nine RNA viruses from the viromes of three B. cinerea strains, including five mitoviruses, one umbra-like virus, and three [...] Read more.

Over the past five years, research has progressively revealed a rich diversity of RNA viruses in Botrytis cinerea. In this study, we identified nine RNA viruses from the viromes of three B. cinerea strains, including five mitoviruses, one umbra-like virus, and three partitiviruses. Among these, Sclerotinia sclerotiorum partitivirus 1 (SsPV1) was artificially introduced in a previous study. Excluding SsPV1, we cloned the other two partitiviruses and confirmed that both belong to Gammapartitivirus and contain three genomic segments, with dsRNA3 as an RNA satellite. In addition to RNA viruses, we discovered 12 retroplasmids in the three B. cinerea strains. These retroplasmids utilize the mitochondrial genetic codes and only encode a single open reading frame, which is predicted to produce a reverse transcriptase. It is also well known that mitoviruses use the mitochondrial genetic codes to encode their RNA-dependent RNA polymerase. Given the similarities between mitoviruses and retroplasmids in several aspects, we suggest that the mycovirus community could consider whether retroplasmids should be included within the conceptual scope of viruses. Furthermore, this study calls on researchers to pay attention to mobile genetic elements beyond typical RNA viruses, such as the retroplasmids reported here. Additionally, it underscores the importance of using single-spore or single-protoplast isolation methods in mycoviral studies to maintain a consistent genetic and viral background when investigating viral effects on the fungal host. Full article

(This article belongs to the Collection Mycoviruses)

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23 pages, 2988 KB

Open AccessEditor’s ChoiceArticle

Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.

by Emily A. Morgese, Barbra D. Ferrell, Spencer C. Toth, Shawn W. Polson, K. Eric Wommack and Jeffry J. Fuhrmann

Viruses 2025, 17(11), 1474; https://doi.org/10.3390/v17111474 - 4 Nov 2025

Cited by 1 | Viewed by 1781

Abstract

Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing [...] Read more.

Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts’ genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. diazoefficiens strain USDA110 and B. elkanii strains USDA94 and USDA31. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ~70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens had a podophage-like morphology, exhibited greater genetic diversity, and divided into two distinct species. Although no phages were recovered against the B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware Bradyrhizobium isolates showed susceptibility in a host range assay. The phage genomes demonstrated features predicting phenotypes. The phage terminase genes predicted headful packaging which promotes generalized transduction. The B. elkanii phages all carried tmRNA genes capable of rescuing stalled ribosomes, and all but one of the phages isolated against the two host species carried DNA polymerase A indicating greater phage control of genome replication. State-of-the-art structural annotation of a hypothetical gene shared by the B. diazoefficiens phages, having a mean amino acid identity of ~25% and similarity of ~35%, predicted a putative tail fiber function. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics. Full article

(This article belongs to the Section Bacterial Viruses)

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19 pages, 4474 KB

Open AccessEditor’s ChoiceArticle

Multivalent Interactions Between the Picornavirus 3C(D) Main Protease and RNA Oligonucleotides Induce Liquid–Liquid Phase Separation

by Somnath Mondal, Saumyak Mukherjee, Kevin E. W. Namitz, Neela H. Yennawar and David D. Boehr

Viruses 2025, 17(11), 1473; https://doi.org/10.3390/v17111473 - 4 Nov 2025

Cited by 1 | Viewed by 3113

Abstract

The picornavirus 3CD protein is a precursor to the 3C main protease and the 3D RNA-dependent RNA polymerase. In addition to its functions in proteolytic processing of the virus polyprotein and cleavage of key host factors, the 3C domain interacts with cis-acting replication [...] Read more.

The picornavirus 3CD protein is a precursor to the 3C main protease and the 3D RNA-dependent RNA polymerase. In addition to its functions in proteolytic processing of the virus polyprotein and cleavage of key host factors, the 3C domain interacts with cis-acting replication elements (CREs) within the viral genome to regulate replication and translation events. We investigated the molecular determinants of RNA binding to 3C using a wide range of biophysical and computational methods. These studies showed that 3C binds to a broad spectrum of RNA oligonucleotides, displaying minimal sequence and structure dependence, at least for these shorter RNAs. However, they also uncovered a novel aspect of these interactions, that is, 3C-RNA binding can induce liquid–liquid phase separation (LLPS), with 3CD–RNA interactions likewise leading to LLPS. This may be a general phenomenon for other 3C and 3C-like proteases and polyproteins incorporating 3C domains. These findings have potential implications in understanding virally induced apoptosis and the control of stress granules, which involve LLPS and include other proteins with known interactions with 3C/3CD. Full article

(This article belongs to the Section General Virology)

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11 pages, 3281 KB

Open AccessEditor’s ChoiceArticle

Identification of Reassortment of Orthotospovirus citrullomaculosi in Jiangxi Province, China

by Bin Peng, Xinlong Zhang, Na Cao, Chengpu Yan, Fangshu Li and Fanghong Zhu

Viruses 2025, 17(11), 1448; https://doi.org/10.3390/v17111448 - 31 Oct 2025

Viewed by 817

Abstract

Watermelon silver mottle virus (WSMoV) is a thrips-transmitted Orthotospovirus that severely impacts cucurbits production across Asia. Although previous diversity studies focused on the nucleocapsid (N) gene, genome-level evolutionary analyses are lacking. In 2023 and 2024, symptomatic watermelon in Jiangxi Province, China, [...] Read more.

Watermelon silver mottle virus (WSMoV) is a thrips-transmitted Orthotospovirus that severely impacts cucurbits production across Asia. Although previous diversity studies focused on the nucleocapsid (N) gene, genome-level evolutionary analyses are lacking. In 2023 and 2024, symptomatic watermelon in Jiangxi Province, China, was analyzed by RT-PCR and high-throughput sequencing, yielding complete genomes of two WSMoV isolates, FZNC and THBC. Multiple-sequence alignment and phylogenetic analysis of the complete sequences of L, M, and S RNAs defined two phylogenetic clades (O and N). However, the Jiangxi isolates clustered in different clades for the L segment versus the M and S segments, suggesting a potential reassortment event. This conclusion was confirmed by RDP4 and RT-PCR analysis, which identified a significant reassortment event involving an L RNA segment derived from a Guangdong isolate (Clade N) and the M and S segments from a Taiwan isolate (Clade O). This study provides the first evidence of natural reassortment in WSMoV, underscoring its potential for rapid evolution. It also constitutes the first report of WSMoV in Jiangxi Province, in East China, marking a concerning expansion of its geographic range into inland China and raising the risk of cucurbit production. Full article

(This article belongs to the Special Issue Biosecurity and Plant Viruses: A Call to Action for a Sustainable Future)

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15 pages, 2242 KB

Open AccessEditor’s ChoiceArticle

Historical and Contemporary Evidence Confirms a Higrevirus as the Causal Agent of Citrus Zonate Chlorosis in Brazil

by Laura R. Pereira, Mariane C. Rodrigues, Camila Chabi-Jesus, Pedro L. Ramos-González, Cristiane J. Barbosa, Magno G. Santos, Helcio Costa, Luana C. Maro, Aline D. Tassi, Elliot W. Kitajima, Ricardo Harakava and Juliana Freitas-Astúa

Viruses 2025, 17(11), 1428; https://doi.org/10.3390/v17111428 - 28 Oct 2025

Cited by 2 | Viewed by 1372

Abstract

Citrus leprosis (CL) and citrus zonate chlorosis (ZC) were first described in Brazil in the 1930s. Both diseases, which caused non-systemic lesions primarily characterized by chlorotic and/or necrotic spots, were associated with the presence of Brevipalpus mites. While CL has since been well [...] Read more.

Citrus leprosis (CL) and citrus zonate chlorosis (ZC) were first described in Brazil in the 1930s. Both diseases, which caused non-systemic lesions primarily characterized by chlorotic and/or necrotic spots, were associated with the presence of Brevipalpus mites. While CL has since been well characterized as being caused by viruses of the genera Cilevirus (family Kitaviridae) and Dichorhavirus (family Rhabdoviridae) and transmitted by several species of Brevipalpus mites, the causal agent of ZC remained unknown. In this study, we analyzed Citrus spp. samples exhibiting typical ZC symptoms using high-throughput sequencing (HTS) to determine the etiology of ZC. We examined historical herbarium specimens collected between 1933 and 1965 alongside fresh samples collected from 2016 to 2022. Our results identified the higrevirus hibiscus green spot virus 2 (HGSV2, Higrevirus waimanalo) as the causal agent of ZC. In addition, we report for the first time the presence of a higrevirus in continental America, expand the diversity of known kitaviruses infecting citrus in Brazil, and demonstrate the transmission of an higrevirus by Brevipalpus yothersi and B. papayensis. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)

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22 pages, 3777 KB

Open AccessEditor’s ChoiceArticle

Comparative Transcriptomics Reveals Novel and Differential Circular RNA Responses Underlying Interferon-Mediated Antiviral Regulation in Porcine Alveolar Macrophages

by Jiuyi Li, Oluwaseun Adeyemi, Laura C. Miller and Yongming Sang

Viruses 2025, 17(10), 1307; https://doi.org/10.3390/v17101307 - 27 Sep 2025

Cited by 2 | Viewed by 1429

Abstract

Porcine Reproductive and Respiratory Syndrome (PRRS) causes significant economic losses in the swine industry. Circular RNAs (circRNAs), a class of stable non-coding RNAs, are increasingly recognized as regulators in immune responses and host–virus interactions. This study investigated the genome-wide circRNA responses in porcine [...] Read more.

Porcine Reproductive and Respiratory Syndrome (PRRS) causes significant economic losses in the swine industry. Circular RNAs (circRNAs), a class of stable non-coding RNAs, are increasingly recognized as regulators in immune responses and host–virus interactions. This study investigated the genome-wide circRNA responses in porcine alveolar macrophages (PAMs), key cell targets of PRRSV, following treatment with a modified live virus (MLV) vaccine or two interferon (IFN) subtypes (IFN-α1, IFN-ω5). Using RNA sequencing, we identified over 1000 differentially expressed circRNAs across treatment groups, revealing both conserved and distinct expression profiles. Gene Ontology and KEGG pathway analyses indicated that circRNA-associated genes are significantly enriched in immune-related processes and pathways, including cytokine signaling and antiviral defense. Notably, IFN-ω5 treatment induced a pronounced circRNA response, aligning with its potent antiviral activity. We further explored the regulatory potential of these circRNAs by predicting miRNA binding sites, revealing complex circRNA-miRNA interaction networks. Additionally, we assessed the coding potential of differentially expressed circRNAs by identifying open reading frames (ORFs), internal ribosome entry sites (IRESs), and N6-methyladenosine (m⁶A) modification sites, suggesting a subset may undergo non-canonical translation. These findings provide a comprehensive landscape of circRNA expression in PAMs under different antiviral conditions, highlighting their potential roles as immune regulators and novel players in interferon-mediated antiviral responses, particularly downstream of IFN-ω5. This work contributes to understanding the non-coding RNA landscape in the PRRSV-swine model and suggests circRNAs as potential targets for future antiviral strategies. Full article

(This article belongs to the Special Issue Host Cell-Virus Interaction, 4th Edition)

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14 pages, 3998 KB

Open AccessEditor’s ChoiceArticle

Dysregulation of microRNAs in the Brains of Mice Infected with Powassan Virus

by Amany Elsharkawy, Komal Arora, Hamid Reza Jahantigh and Mukesh Kumar

Viruses 2025, 17(10), 1288; https://doi.org/10.3390/v17101288 - 23 Sep 2025

Viewed by 1537

Abstract

microRNAs (miRNAs) are known to play critical roles in the regulation of gene expression during neurodegenerative diseases and neurotropic viral infections. However, their specific contribution to the pathogenesis of Powassan virus (POWV) infection in the brain remains poorly understood. Understanding miRNA dynamics in [...] Read more.

microRNAs (miRNAs) are known to play critical roles in the regulation of gene expression during neurodegenerative diseases and neurotropic viral infections. However, their specific contribution to the pathogenesis of Powassan virus (POWV) infection in the brain remains poorly understood. Understanding miRNA dynamics in the brain during POWV infection may reveal novel insights into viral neuropathogenesis and host antiviral responses. Therefore, in the present study, we analyzed miRNA expression profiles in the mouse brain at different time points following a peripheral POWV infection. A total of 599 miRNAs were examined at day 3, 6, and 9 post-infection. Infection with POWV resulted in the modulation of several miRNAs in the brain at all time points. There was a progressive increase in the number of dysregulated miRNAs over the course of infection. This correlated with POWV dissemination into the brain with a progressive increase in viral RNA levels that peaked at day 9 post-infection. There was an early upregulation of miR-1983, miR-19a, and miR-216b that persisted until day 9 post-infection. POWV infection also resulted in the downregulation of miR-500 at all examined time points. Using IPA, we determined the significant canonical pathways affected by miRNA dysregulation. POWV infection modulated the activation of the thyroid hormone receptor and retinoid X receptor (TR/RXR) and the regulation of the phosphatase and tensin homolog (PTEN). Additionally, macrophage classical activation and growth arrest and DNA damage-inducible 45 (GADD45) signaling were activated as early as day 3 post-infection and persisted until day 9 post-infection. Furthermore, our analysis revealed the activation of cell death pathways such as necrosis and apoptosis and the inhibition of cell cycle progression, as well as leukopoiesis. To our knowledge, this is the first study to evaluate the modulation of miRNAs in the brain following POWV infection. Full article

(This article belongs to the Special Issue Tick-Borne Viruses 2026)

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19 pages, 3052 KB

Open AccessEditor’s ChoiceArticle

Genome-Wide Variation Profile of the Genus Tobamovirus

by Amany E. Gomaa and Hernan Garcia-Ruiz

Viruses 2025, 17(9), 1284; https://doi.org/10.3390/v17091284 - 22 Sep 2025

Cited by 5 | Viewed by 2829

Abstract

The genus Tobamovirus belongs to the family Virgaviridae, and the genome consists of monopartite, positive, single-strand RNA. Most species contain four open reading frames encoding four essential proteins. Transmission occurs primarily through mechanical contact between plants, and in some cases, via seed [...] Read more.

The genus Tobamovirus belongs to the family Virgaviridae, and the genome consists of monopartite, positive, single-strand RNA. Most species contain four open reading frames encoding four essential proteins. Transmission occurs primarily through mechanical contact between plants, and in some cases, via seed dispersal. Tobamovirus fructirugosum (tomato brown rugose fruit virus, ToBRFV), the most recently described species in the genus, was first reported in 2015. It overcame genetic resistance that had been effective in tomato for sixty years, causing devastating losses in tomato production worldwide, and highlights the importance of understanding Tobamovirus genomic variation and evolution. In this study, we measured and characterized nucleotide variation for the entire genome and for all species in the genus Tobamovirus. Additionally, we measured the selection pressure acting on each open reading frame. Results showed that low nucleotide diversity and negative selection pressure are general features of tobamoviruses, with values that are approximately the same across open reading frames and without hypervariable areas. A comparison of nucleotide diversity between T. fructirugosum and its close relatives, T. tomatotessellati (tomato mosaic virus, ToMV) and T. tabaci (tobacco mosaic virus, TMV), showed low nucleotide diversity in the movement protein region harboring the resistance-breaking mutation. Furthermore, phylogenetic and diversity analyses showed that T. fructirugosum continues to evolve, and geographical distribution and host influence genomic diversity. Full article

(This article belongs to the Special Issue Plant Viral Pathogens: Innovations in Detection, Genetic Diversity, and Evolutionary Dynamics)

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16 pages, 2280 KB

Open AccessEditor’s ChoiceArticle

Modification of H1N1 Influenza Luciferase Reporter Viruses Using StopGo Translation and/or Mouse-Adapted Mutations

by Po-Ling Chen, Guohua Yang, Chet Ojha, Balaji Banoth and Charles J. Russell

Viruses 2025, 17(9), 1211; https://doi.org/10.3390/v17091211 - 5 Sep 2025

Viewed by 1879

Abstract

Reporter viruses are valuable tools for studying infections at the cellular level and in living animals. They also enable rapid, high-throughput antiviral drug screening and serological studies. We previously developed a bioluminescence-based reporter virus, rTN09-PA-Nluc, derived from influenza A/Tennessee/1-560/2009 (TN09, pH1N1) in which [...] Read more.

Reporter viruses are valuable tools for studying infections at the cellular level and in living animals. They also enable rapid, high-throughput antiviral drug screening and serological studies. We previously developed a bioluminescence-based reporter virus, rTN09-PA-Nluc, derived from influenza A/Tennessee/1-560/2009 (TN09, pH1N1) in which a NanoLuc (Nluc) reporter protein was fused to the PA protein. Reduced growth of rTN09-PA-Nluc in MDCK cells and mice was restored by mutations arising from mouse adaptation. Here, to test the hypothesis that the growth defect resulted from the PA-Nluc protein fusion, we generated the luciferase reporter virus rTN09-PA-Nluc/SG, which undergoes StopGo translation to yield separate PA and NLuc proteins along with a proportion of the PA-Nluc fusion. The rTN09-PA-Nluc/SG virus had greater protein expression and increased replication in MDCK cells compared to rTN09-PA-Nluc. The reporter virus encoding StopGo translation was superior to the virus without it in bioluminescence-based virus neutralization assays in vitro, providing results in 24 h as opposed to 3 days using unmodified influenza virus and standard neutralization assay protocols. However, the reporter virus encoding StopGo translation remained attenuated in mice. Mouse-adaptive mutations were needed for full virulence and efficient non-invasive imaging in mice. Overall, these findings demonstrate the benefit of incorporating StopGo translation into influenza reporter viruses for in vitro assays, yet mouse-adapted mutations appeared superior in mice. Full article

(This article belongs to the Section Animal Viruses)

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15 pages, 1201 KB

Open AccessEditor’s ChoiceArticle

Immune Responses and Replication of Rescued Torque Teno Virus (TTSuV1) in Mice

by Md-Tariqul Islam, Brett Webb and Sheela Ramamoorthy

Viruses 2025, 17(8), 1105; https://doi.org/10.3390/v17081105 - 12 Aug 2025

Cited by 3 | Viewed by 2452

Abstract

Although Torque Teno Viruses (TTVs) were initially considered to be ubiquitous members of the mammalian virome, the finding that swine TTVs (TTSuV) can act as primary pathogens elevates the possible status of swine TTVs (TTSuVs) to an emerging swine pathogen. Since their discovery, [...] Read more.

Although Torque Teno Viruses (TTVs) were initially considered to be ubiquitous members of the mammalian virome, the finding that swine TTVs (TTSuV) can act as primary pathogens elevates the possible status of swine TTVs (TTSuVs) to an emerging swine pathogen. Since their discovery, the molecular mechanisms of TTV–host interactions remain largely unknown as robust in vitro culture systems and in vivo animal models have not been available. This study was undertaken to address some of these long-standing gaps. Recombinant TTSuV1 rescued from an infectious clone was used to infect C57BL/J6 mice. Infected mice seroconverted within 15 days post-infection and mounted virus neutralizing antibody responses. Viral DNA was detected in blood and lung tissue for the duration of the study. TTSuV1 isolated from the lung tissue of infected mice productively and serially infected PK-15 cells in vitro, indicating that the treatment produced viable, replicative viral particles in the host. TTSuV1 antigen was also detected by flow cytometry in lymphocytes, including the T and B lymphocyte subsets. Infected mice exhibited mild splenic hyperplasia and lymphopenia. The ability to respond to mitogenic stimuli was highly diminished in infected mice and a striking lack of virus-specific recall responses was observed for the 30-day duration of the study. Therefore, this study is the first to provide experimental evidence that recombinant TTSuV1 rescued from an infectious clone is infective and induces immune responses in laboratory mice. This model provides a critical tool for advancing research on TTV immunopathogenesis. Full article

(This article belongs to the Special Issue Viral Infections and Immune Dysregulation 2024–2025)

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18 pages, 5221 KB

Open AccessEditor’s ChoiceArticle

New Isolates of Betachloroviruses Shed Light on the Diversity and Biological Complexity of an Unexplored Group of Giant Algal Viruses

by Júlia W. Souza, Lethícia R. Henriques, Roger M. Carlson, Bruna B. F. Botelho, João Victor R. P. Carvalho, João Pedro N. Santos, Eric R. G. R. Aguiar, Irina V. Agarkova, James L. Van Etten, David D. Dunigan and Rodrigo A. L. Rodrigues

Viruses 2025, 17(8), 1096; https://doi.org/10.3390/v17081096 - 8 Aug 2025

Cited by 4 | Viewed by 1517

Abstract

The majority of giant algal viruses belong to the family Phycodnaviridae, class Algavirales, phylum Nucleocytoviricota. Among them, the genus Chlorovirus is the most studied, with three recognized groups based on genomics and host range, although many fundamental questions remain to [...] Read more.

The majority of giant algal viruses belong to the family Phycodnaviridae, class Algavirales, phylum Nucleocytoviricota. Among them, the genus Chlorovirus is the most studied, with three recognized groups based on genomics and host range, although many fundamental questions remain to be elucidated, particularly regarding their diversity. In this study, we focus on betachloroviruses, a poorly explored subgroup that infects the alga Micractinium conductrix Pbi. Here, we describe the isolation and genomic analysis of 11 new betachloroviruses from water samples collected in Nebraska, USA. With 25 fully sequenced genomes now available, we assessed the genomic diversity of these viruses. They have double-stranded DNA genomes ranging from 295 to 374 kbp, encoding hundreds of ORFs, of which a large number (~40%) lack known function. Comparative genomics and phylogenetic analyses revealed three species of betachlorovirus, each with high intra-species genomic identity. Notably, some isolates with over 99.5% genomic identity display markedly different plaque phenotypes, which led us to propose the use of the term genomovar among giant algal viruses, a concept potentially applicable to other giant viral groups yet to be explored. Altogether, this work advances our understanding of betachloroviruses and highlights the importance of linking viral genotype to phenotype, opening new avenues for exploring the diversity of giant algal viruses. Full article

(This article belongs to the Special Issue Cyanophage and Algal Virus)

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18 pages, 3120 KB

Open AccessEditor’s ChoiceArticle

Měnglà Virus VP40 Localizes to the Nucleus and Impedes the RIG-I Signaling Pathway

by Joyce Sweeney Gibbons, Naveen Thakur, Emma Komers, Olivia A. Vogel, Poushali Chakraborty, JoAnn M. Tufariello and Christopher F. Basler

Viruses 2025, 17(8), 1082; https://doi.org/10.3390/v17081082 - 5 Aug 2025

Viewed by 1828

Abstract

Měnglà virus (MLAV) is a member of the genus Dianlovirus in the family Filoviridae, which also includes Ebola virus (EBOV) and Marburg virus (MARV). Whether MLAV poses a threat to human health is uncertain. However, the MLAV VP35 and VP40 proteins can impair [...] Read more.

Měnglà virus (MLAV) is a member of the genus Dianlovirus in the family Filoviridae, which also includes Ebola virus (EBOV) and Marburg virus (MARV). Whether MLAV poses a threat to human health is uncertain. However, the MLAV VP35 and VP40 proteins can impair IFNα/β gene expression and block IFNα/β-induced Jak-STAT signaling, respectively, suggesting the capacity to counteract human innate immune defenses. In this study, MLAV VP40 is demonstrated to impair the Sendai virus (SeV)-induced activation of the IFNβ promoter. Inhibition is independent of the MLAV VP40 PPPY late-domain motif that interacts with host proteins possessing WW-domains to promote viral budding. Similar IFNβ promoter inhibition was not detected for EBOV or MARV VP40. MLAV VP40 exhibited lesser capacity to inhibit TNFα activation of an NF-κB reporter gene. MLAV VP40 impaired IFNβ promoter activation by an over-expressed, constitutively active form of RIG-I and by the over-expressed IRF3 kinases TBK1 and IKKε. However, MLAV VP40 did not inhibit IFNβ promoter activation by constitutively active IRF3 5D. Consistent with these findings, MLAV VP40 inhibited SeV-induced IRF3 phosphorylation. Although IRF3 phosphorylation occurs in the cytoplasm, MLAV VP40 exhibits substantial nuclear localization, accumulating in foci in HeLa cell nuclei. In contrast, the VP40 of EBOV and MARV exhibited lower degrees of nuclear localization and did not accumulate in foci. MLAV VP40 interacts with importin alpha-1 (IMPα1), suggesting entry via the IMPα/IMPβ nuclear import pathway. Cumulatively, these data identify novel features that distinguish MLAV VP40 from its homologues in EBOV and MARV. Full article

(This article belongs to the Section Animal Viruses)

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17 pages, 3720 KB

Open AccessEditor’s ChoiceArticle

High-Throughput Sequencing Reveals the Mycoviral Diversity of the Pathogenic Grape Fungus Penicillium astrolabium During Postharvest

by Rui Wang, Guoqin Wen, Xiaohong Liu, Yingqing Luo, Yanhua Chang, Guoqi Li and Tingfu Zhang

Viruses 2025, 17(8), 1053; https://doi.org/10.3390/v17081053 - 28 Jul 2025

Cited by 1 | Viewed by 1241

Abstract

Penicillium astrolabium is a primary pathogenic fungus that causes grape blue mold during postharvest, leading to substantial losses in the grape industry. Nevertheless, hypovirulence-associated mycoviruses can attenuate the virulence of postharvest grape-rot pathogens, thereby offering a promising biocontrol tool. Characterizing the mycovirus repertoire [...] Read more.

Penicillium astrolabium is a primary pathogenic fungus that causes grape blue mold during postharvest, leading to substantial losses in the grape industry. Nevertheless, hypovirulence-associated mycoviruses can attenuate the virulence of postharvest grape-rot pathogens, thereby offering a promising biocontrol tool. Characterizing the mycovirus repertoire of P. astrolabium is imperative for grape protection, yet remains largely unexplored. Here, we screened six strains harboring viruses in 13 P. astrolabium isolates from rotted grapes. Using high-throughput sequencing, four novel dsRNA viruses and two +ssRNA viruses were identified from the six P. astrolabium strains. The dsRNA viruses belonged to two families—Chrysoviridae and Partitiviridae—and were designated to Penicillium astrolabium chrysovirus 1 (PaCV1), Penicillum astrolabium partitivirus 1′ (PaPV1′), Penicillum astrolabium partitivirus 2 (PaPV2), and Penicillum astrolabium partitivirus 3 (PaPV3). For the +ssRNA viruses, one was clustered into the Alphaflexiviridae family, while the other one was clustered into the Narnaviridae family. The two +ssRNA viruses were named Penicillium astrolabium alphaflexivirus 1 (PaAFV1) and Penicillium astrolabium narnavirus 1 (PaNV1), respectively. Moreover, several viral genomic contigs with non-overlapping and discontinuous sequences were identified in this study, which were probably representatives of five viruses from four families, including Discoviridae, Peribunyaviridae, Botourmiaviridae, and Picobirnaviridae. Taken together, our findings could expand the diversity of mycoviruses, advance the understanding of mycovirus evolution in P. astrolabium, and provide both potential biocontrol resources and a research system for dissecting virus–fungus–plant interactions. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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27 pages, 7908 KB

Open AccessEditor’s ChoiceArticle

Deciphering Cowpea Resistance to Potyvirus: Assessment of eIF4E Gene Mutations and Their Impact on the eIF4E-VPg Protein Interaction

by Fernanda Alves de Andrade, Madson Allan de Luna-Aragão, José Diogo Cavalcanti Ferreira, Fernanda Freitas Souza, Ana Carolina da Rocha Oliveira, Antônio Félix da Costa, Francisco José Lima Aragão, Carlos André dos Santos-Silva, Ana Maria Benko-Iseppon and Valesca Pandolfi

Viruses 2025, 17(8), 1050; https://doi.org/10.3390/v17081050 - 28 Jul 2025

Cited by 1 | Viewed by 2346

Abstract

Cowpea (Vigna unguiculata) is a crop of significant socioeconomic importance, particularly in the semi-arid regions of Africa and America. However, its productivity has been adversely affected by viral diseases, including the cowpea aphid-borne mosaic virus (CABMV), a single-stranded RNA virus. It [...] Read more.

Cowpea (Vigna unguiculata) is a crop of significant socioeconomic importance, particularly in the semi-arid regions of Africa and America. However, its productivity has been adversely affected by viral diseases, including the cowpea aphid-borne mosaic virus (CABMV), a single-stranded RNA virus. It is known that the VPg protein interacts with the host’s translation initiation factor (eIF4E), promoting viral replication. This study aimed to investigate the relationship between mutations in the cowpea eIF4E gene and resistance to CABMV. Twenty-seven cultivars were screened by PCR and bioassays for presence/absence of mutations associated with resistance or susceptibility to Potyviruses. Of the cultivars with mutations previously associated with susceptibility, 88.24% exhibited viral symptoms, while 62.5% associated with resistance remained asymptomatic. The in silico analyses revealed that non-synonymous mutations (Pro68Arg, Gly109Arg) alter the structure of the eIF4E protein, reducing its affinity to VPg. Molecular dynamics simulations also pointed to an enhanced structural stability of eIF4E in resistant cultivars and reinforced, for the first time, key mutations and the functional role of the eIF4E gene in resistance to CABMV in cowpea. Our results offer valuable insights for virus disease management and for genetic improvement programs for this important crop. Full article

(This article belongs to the Special Issue Viral Manipulation of Plant Stress Responses)

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16 pages, 2780 KB

Open AccessEditor’s ChoiceArticle

Impact of Wheat Resistance Genes on Wheat Curl Mite Fitness and Wheat Streak Mosaic Dynamics Under Single and Mixed Infections

by Saurabh Gautam and Kiran R. Gadhave

Viruses 2025, 17(7), 1010; https://doi.org/10.3390/v17071010 - 18 Jul 2025

Cited by 3 | Viewed by 1855

Abstract

The wheat curl mite (WCM, Aceria tosichella Keifer), a complex of eriophyid mite species, transmits wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV), which in single or mixed infections cause wheat streak mosaic (WSM) disease—a major threat to wheat production across [...] Read more.

The wheat curl mite (WCM, Aceria tosichella Keifer), a complex of eriophyid mite species, transmits wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV), which in single or mixed infections cause wheat streak mosaic (WSM) disease—a major threat to wheat production across the U.S. Great Plains. Resistant wheat cultivars bearing Cmc3 and Cmc4 (targeting WCM), Wsm1 and Wsm2 (targeting WSMV), and Wsm1 (targeting TriMV) are widely used to manage this pest–pathogen complex. However, comprehensive studies investigating how these resistance mechanisms influence both vector biology and virus transmission remain scarce. To address this gap, we evaluated disease development and WCM fitness across nine wheat cultivars with differential resistance profiles under single and mixed infections of WSMV and TriMV. We found strong viral synergy in co-infected plants, with TriMV accumulation markedly enhanced during mixed infections, irrespective of host genotype. Symptom severity and virus titers (both WSMV and TriMV) were highest in the cultivars carrying Wsm2, suggesting a potential trade-off in resistance effectiveness under mixed infection pressure. While mite development time (egg to adult) was unaffected by host genotype or infection status, mite fecundity was significantly reduced on infected plants carrying Wsm1 or Wsm2, but not on those with Cmc3 and Cmc4. Notably, virus accumulation in mites was reduced on the cultivars with Cmc3 and Cmc4, correlating with virus titers in the host tissues. Our findings highlight the complex interplay between host resistance, virus dynamics, and vector performance. Cultivars harboring Cmc3 and Cmc4 may offer robust field-level protection by simultaneously suppressing mite reproduction and limiting virus accumulation in both plant and vector. Full article

(This article belongs to the Special Issue Molecular and Biological Virus-Plant-Insect Vector Interactions)

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23 pages, 2511 KB

Open AccessEditor’s ChoiceArticle

The Role of Prion Protein in Reelin/Dab1 Signaling: Implications for Neurodegeneration

by Irene Giulia Rolle, Anna Burato, Merve Begüm Bacınoğlu, Fabio Moda and Giuseppe Legname

Viruses 2025, 17(7), 928; https://doi.org/10.3390/v17070928 - 29 Jun 2025

Viewed by 2256

Abstract

The cellular prion protein (PrP^C) is studied in prion diseases, where its misfolded isoform (PrP^Sc) leads to neurodegeneration. PrP^C has also been implicated in several physiological functions. The protein is abundant in the nervous system, and it is [...] Read more.

The cellular prion protein (PrP^C) is studied in prion diseases, where its misfolded isoform (PrP^Sc) leads to neurodegeneration. PrP^C has also been implicated in several physiological functions. The protein is abundant in the nervous system, and it is critical for cell signaling in cellular communication, where it acts as a scaffold for various signaling molecules. The Reelin signaling pathway, implicated both in Alzheimer’s and prion diseases, engages Dab1, an adaptor protein influencing APP processing and amyloid beta deposition. Here, we show, using Prnp knockout models (Prnp^0/0), that PrP^C modulates Reelin signaling, affecting Dab1 activation and downstream phosphorylation in both neuronal cultures and mouse brains. Notably, Prnp^0/0 mice showed reduced responsiveness to Reelin, associated with altered Dab1 phosphorylation and Fyn kinase activity. Even though no direct interaction between PrP^C and Reelin/ApoER2 was found, Prnp^0/0 neurons showed lower NCAM levels, a well-established PrP^C interactor. Prion infection further disrupted the Reelin signaling pathway, thus downregulating Dab1 and Reelin receptors and altering Reelin processing, like Alzheimer’s disease pathology. These findings emphasize PrP^C indirect role in Dab1 signaling via the NCAM and Fyn pathways, which influence synaptic function and neurodegeneration in prion diseases. Full article

(This article belongs to the Special Issue 15-Year Anniversary of Viruses)

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15 pages, 1340 KB

Open AccessEditor’s ChoiceArticle

Intersegment Recombination During Influenza A Virus Replication Gives Rise to a Novel Class of Defective Viral Genomes

by Soraya Anisi, George Noble, Rory Williams, Jack Hales, Hannah E. Bridgewater, Andrew Easton, William Collier and Phillip Gould

Viruses 2025, 17(6), 856; https://doi.org/10.3390/v17060856 - 16 Jun 2025

Viewed by 2164

Abstract

Influenza A virus (IAV) is a highly diverse pathogen with genetic variability primarily driven by mutation and reassortment. Using next-generation sequencing (NGS), we characterised defective viral genomes (DVGs) generated during the serial passaging of influenza A/Puerto Rico/8/1934 (H1N1) virus in embryonated chicken eggs. [...] Read more.

Influenza A virus (IAV) is a highly diverse pathogen with genetic variability primarily driven by mutation and reassortment. Using next-generation sequencing (NGS), we characterised defective viral genomes (DVGs) generated during the serial passaging of influenza A/Puerto Rico/8/1934 (H1N1) virus in embryonated chicken eggs. Deletions were the most abundant DVG type, predominantly accumulating in the polymerase-encoding segments. Notably, we identified and validated a novel class of multisegment DVGs arising from intersegment recombination events, providing evidence that the IAV RNA polymerase can detach from one genomic template and resume synthesis on another. Multisegment recombination primarily involved segments 1–3 but also occurred between other segment pairings. In specific lineages, certain multisegment DVGs reached high frequencies and persisted through multiple passages, suggesting they are not transient by-products of recombination but may possess features that support stable maintenance. Furthermore, multisegment DVGs were shown to be encapsidated within virions, similar to deletion DVGs. The observation of recombination between segments with limited sequence homology underscores the potential for complex recombination to expand IAV genetic diversity. These findings suggest recombination-driven DVGs represent a previously underappreciated mechanism in influenza virus evolution. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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16 pages, 3994 KB

Open AccessEditor’s ChoiceArticle

Antagonism in Orthotospoviruses Is Reflected in Plant Small RNA Profile

by Md Tariqul Islam, Kaixi Zhao, Nathan Johnson, Michael Axtell and Cristina Rosa

Viruses 2025, 17(6), 789; https://doi.org/10.3390/v17060789 - 30 May 2025

Cited by 1 | Viewed by 1622

Abstract

Mixed infections of plant viruses are commonly found in natural patho-systems and present a valuable opportunity to understand how multiple viruses can co-infect the same host. Tomato spotted wilt orthotospovirus (TSWV) and impatiens necrotic spot orthotospovirus (INSV) are present in the same geographic [...] Read more.

Mixed infections of plant viruses are commonly found in natural patho-systems and present a valuable opportunity to understand how multiple viruses can co-infect the same host. Tomato spotted wilt orthotospovirus (TSWV) and impatiens necrotic spot orthotospovirus (INSV) are present in the same geographic areas and are closely related. More mixed infections of TSWV and INSV have been reported in recent years, and the INSV host range has been reported to be increasing. In a previous study, we isolated and characterized one strain of INSV and one of TSWV and found that they have an antagonistic relationship in their vectors. However, we were unable to determine whether this antagonism extends to the host plant or to uncover the underlying mechanisms and the host’s contribution. Here, we show that TSWV and INSV exhibit antagonistic interactions in the host plant, as evidenced by a lower viral titer in mixed infections compared to single infections. Using small RNA sequencing, we identified that the host plant contributes to this antagonism through differential small RNA processing, which appears to regulate viral replication and the success of infection. This research advances our understanding of virus–virus and virus-host interactions and presents opportunities for leveraging these dynamics in integrated pest management strategies. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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18 pages, 9413 KB

Open AccessEditor’s ChoiceArticle

Primary Cells from a CD46-Edited Bovine Heifer Have Reduced BVDV Susceptibility Despite Viral Adaptation to Heparan Sulfate

by Alexandria C. Krueger, Brian L. Vander Ley, Michael P. Heaton, Tad S. Sonstegard and Aspen M. Workman

Viruses 2025, 17(5), 634; https://doi.org/10.3390/v17050634 - 28 Apr 2025

Cited by 2 | Viewed by 1614

Abstract

A precision genome edit in the bovine CD46 gene (A₈₂LPTFS₈₇) dramatically reduced bovine viral diarrhea virus (BVDV) susceptibility in a cloned heifer. However, pathogen evolution threatens the long-term efficacy of such interventions. Here, our aim is two-fold: first, to [...] Read more.

A precision genome edit in the bovine CD46 gene (A₈₂LPTFS₈₇) dramatically reduced bovine viral diarrhea virus (BVDV) susceptibility in a cloned heifer. However, pathogen evolution threatens the long-term efficacy of such interventions. Here, our aim is two-fold: first, to determine whether BVDV can adapt in vitro to use the edited CD46 receptor to infect Madin–Darby bovine kidney (MDBK) cells, and second, to evaluate the ex vivo infectivity of culture-adapted viruses in cells from the CD46-edited heifer. Serial passage of BVDV on CD46-edited MDBK cells selected for virus variants capable of CD46-independent infection. Virus genome sequencing revealed mutations in the viral E^RNS gene predicted to enhance HS-mediated entry. HS adaptation was confirmed by inhibiting virus infection with heparin or Heparinase I/III treatment. A naturally occurring HS-adapted field isolate from a persistently infected calf showed similar results. However, when tested on primary cells from the CD46-edited heifer, HS-adapted viruses showed reduced infectivity in skin fibroblasts, monocytes, and lymphocytes in a manner that correlated with HS expression. Thus, although BVDV can adapt to use HS as an alternative entry receptor, HS adaptation does not overcome the protection conferred by the CD46 edit in all relevant cell types. Full article

(This article belongs to the Special Issue Bovine Viral Diarrhea Viruses and Other Pestiviruses)

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18 pages, 10644 KB

Open AccessEditor’s ChoiceArticle

Investigation of HCPro-Mediated Ethylene Synthesis Pathway Through RNA-Seq Approaches

by Xinpeng Jiang, Lan Dong, Renjing Wan, Changli Zeng and Ting Yang

Viruses 2025, 17(5), 602; https://doi.org/10.3390/v17050602 - 23 Apr 2025

Cited by 1 | Viewed by 1225

Abstract

Chilli veinal mottle virus (ChiVMV) severely compromises the quality and yield of solanaceous crops. The helper component protease (HCPro) of ChiVMV functions as a multifunctional RNA silencing suppressor that subverts host antiviral defenses through diverse strategies, However, the underlying mechanisms remain mechanistically unresolved. [...] Read more.

Chilli veinal mottle virus (ChiVMV) severely compromises the quality and yield of solanaceous crops. The helper component protease (HCPro) of ChiVMV functions as a multifunctional RNA silencing suppressor that subverts host antiviral defenses through diverse strategies, However, the underlying mechanisms remain mechanistically unresolved. In this study, HCPro-overexpressing (HCPro-OX) and wild-type (WT) plants were inoculated with ChiVMV to monitor the physiological and molecular changes. Transcriptome analysis identified 11,815 differentially expressed genes (DEGs) under viral infection, among which 1115 genes were specifically regulated by HCPro. KEGG enrichment analysis revealed that the DEGs were significantly associated with plant hormone signal transduction pathways, indicating their crucial role in host–virus interactions. Furthermore, functional clustering of HCPro-regulated DEGs specifically identified key components in ethylene biosynthesis pathways. GO analysis of DEGs between virus-inoculated WT and HCPro-OX plants annotated ethylene biosynthesis-related genes NtACO and NtACS. qPCR validation confirmed that the expression of ethylene biosynthesis-related genes was suppressed by HCPro. Exogenous treatments with the ethylene precursor ACC demonstrated that ethylene suppressed viral accumulation, enhanced POD activity, and reduced the ROS accumulation induced by viral infection. In conclusion, our results demonstrate that HCPro promotes viral infection by suppressing ethylene biosynthesis, which in turn attenuates peroxidase activity, leading to ROS accumulation. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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17 pages, 256 KB

Open AccessEditor’s ChoiceOpinion

On the Trail of the Longest Plant RNA Virus: Citrus Tristeza Virus

by Moshe Bar-Joseph

Viruses 2025, 17(4), 508; https://doi.org/10.3390/v17040508 - 31 Mar 2025

Cited by 5 | Viewed by 2760

Abstract

The devastating tristeza epidemic swept through South American citrus groves in the 1930s and subsequently spread to most citrus-growing regions worldwide, causing varying degrees of damage and prompting significant changes in citrus cultivation practices. The causal agent of the disease, citrus tristeza virus [...] Read more.

The devastating tristeza epidemic swept through South American citrus groves in the 1930s and subsequently spread to most citrus-growing regions worldwide, causing varying degrees of damage and prompting significant changes in citrus cultivation practices. The causal agent of the disease, citrus tristeza virus (CTV), belongs to the genus Closterovirus in the family Closteroviridae. CTV virions are approximately two microns long and possess the largest known positive-strand RNA genome in plants, spanning 19.3 kb. The history of tristeza disease and CTV’s molecular biology and taxonomic relationships have been extensively reviewed in the scientific literature. This paper primarily focuses on the author’s personal experiences with tristeza disease and its causal agent over the past six decades. The journey began during a period when biological indexing was the primary diagnostic tool. It later progressed through the isolation of purified CTV particles, which served as a practical diagnostic tool for CTV suppression efforts in Israel during the 1970s. However, biological indexing was first replaced by electron microscopy, followed by ELISA procedures; both were eventually abandoned after it was discovered that many ELISA-positive infections were caused by symptomless CTV isolates, even on trees grafted onto sour orange rootstocks. In retrospect, my work on CTV can be categorized into three main phases. It began with the biological phase, inherited from earlier generations of citrus virologists, followed by the isolation and partial characterization of CTV virions, and culminated in the genomic era. While we live in an age of remarkable biotechnological achievements, my recommendation for future CTV research is to integrate both biological and genomic approaches rather than viewing them as mutually exclusive. This is particularly important for economically significant pathogens such as CTV, which should be studied continuously as both biological agents and molecular pathogens. Full article

(This article belongs to the Special Issue Citrus Viral Diseases: Advances in Knowledge and Technologies and Their Containment Measures)

13 pages, 2250 KB

Open AccessEditor’s ChoiceArticle

La Jolla Virus: The Pathology and Transmission in Its Host Drosophila suzukii

by Ibrahim Abdelhafiz, Tobias Kessel, Andreas Vilcinskas and Kwang-Zin Lee

Viruses 2025, 17(3), 408; https://doi.org/10.3390/v17030408 - 13 Mar 2025

Cited by 2 | Viewed by 5440

Abstract

Drosophila suzukii, commonly known as spotted-wing drosophila, has emerged as a highly destructive pest in global fruit and wine production. The effectiveness of chemical control is significantly compromised by rapid resistance development and a limited range of insecticide options. Biological control presents [...] Read more.

Drosophila suzukii, commonly known as spotted-wing drosophila, has emerged as a highly destructive pest in global fruit and wine production. The effectiveness of chemical control is significantly compromised by rapid resistance development and a limited range of insecticide options. Biological control presents a promising sustainable alternative. Our previous work suggested the La Jolla Virus (LJV) as a suitable candidate for the development of an insect virus-based control option. Here, we characterized the natural transmission and pathology of the virus. We tested various modes of horizontal transmission, including airborne, venereal and oral, and fecal routes. To understand LJV pathology in infected flies, we studied feeding behavior and demonstrated changes in food absorption compared to non-infected flies. We also investigated the impact on fecundity and egg-to-adult success rate. Altogether, these results collectively improve our understanding of LJV transmission in natural populations and the implication of infected flies in food ingestion and overall fitness. Full article

(This article belongs to the Special Issue Insect Viruses and Pest Management, the Third Edition)

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20 pages, 5726 KB

Open AccessEditor’s ChoiceArticle

Targeting Latent HIV Reservoirs: Effectiveness of Combination Therapy with HDAC and PARP Inhibitors

by Hasset Tibebe, Dacia Marquez, Aidan McGraw, Sophia Gagliardi, Cailyn Sullivan, Grace Hillmer, Kedhar Narayan, Coco Izumi, Adleigh Keating and Taisuke Izumi

Viruses 2025, 17(3), 400; https://doi.org/10.3390/v17030400 - 12 Mar 2025

Cited by 7 | Viewed by 15190

Abstract

The “Kick and Kill” strategy, which aims to reactivate latent HIV reservoirs and facilitate the clearance of reactivated HIV-infected cells, has yet to achieve a functional cure due to the limited efficacy of current latency reversal agents. This study evaluates the combination efficacy [...] Read more.

The “Kick and Kill” strategy, which aims to reactivate latent HIV reservoirs and facilitate the clearance of reactivated HIV-infected cells, has yet to achieve a functional cure due to the limited efficacy of current latency reversal agents. This study evaluates the combination efficacy of histone deacetylase (HDAC) inhibitor with poly(ADP-ribose) polymerase (PARP) inhibitor in latency reversal and immune-mediated clearance. Latently infected J-Lat cells and dual-fluorescent HIV-infected primary CD4 T cells were treated with the HDAC inhibitor (vorinostat) and one of four PARP inhibitors (olaparib, rucaparib, niraparib, or talazoparib). PARP inhibitors, when administered alone, showed no latency reversal activity. However, when combined with vorinostat, their efficacy increased threefold compared to vorinostat alone. This effect was mediated by the inhibition of tankyrase, a PARP superfamily member, which modulates the Hippo signaling pathway. In HIV_GR670-infected primary cells, the combination reduced the reservoir size by 67%. In addition, talazoparib alone significantly reduced actively infected cells by 50%. Talazoparib-treated peripheral blood mononuclear cells co-cultured with K562 cells demonstrated enhanced NK-cell-mediated cytotoxicity, with a 10% reduction in K562 cell viability. These findings demonstrate that combining HDAC and PARP inhibitors augments latency reversal and reservoir reduction. With both the HDAC inhibitors and PARP inhibitors used in this study approved by the FDA for cancer treatment, this combination therapy holds strong potential for rapid clinical integration, contingent upon the confirmation of efficacy and safety in ongoing in vivo studies. Full article

(This article belongs to the Special Issue Novel Strategies to Identify and Eliminate Latent HIV Cells)

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16 pages, 5313 KB

Open AccessEditor’s ChoiceArticle

The In Situ Structure of T-Series T1 Reveals a Conserved Lambda-Like Tail Tip

by Yuan Chen, Hao Xiao, Junquan Zhou, Zeng Peng, Yuning Peng, Jingdong Song, Jing Zheng and Hongrong Liu

Viruses 2025, 17(3), 351; https://doi.org/10.3390/v17030351 - 28 Feb 2025

Cited by 7 | Viewed by 11408

Abstract

It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of siphophages remain scarce. Using cryo-EM, we resolved the structures of T-series siphophage T1, encompassing its head, [...] Read more.

It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of siphophages remain scarce. Using cryo-EM, we resolved the structures of T-series siphophage T1, encompassing its head, connector complex, tail tube, and tail tip, at near-atomic resolution. The density maps enabled us to build the atomic models for the majority of T1 proteins. The T1 head comprises 415 copies of the major capsid protein gp47, arranged into an icosahedron with a triangulation number of seven, decorated with 80 homologous trimers and 60 heterotrimers along the threefold and quasi-threefold axes of the icosahedron. The T1 connector complex is composed of two dodecamers (a portal and an adaptor) and two hexamers (a stopper and a tail terminator). The flexible tail tube comprises approximately 34 hexameric rings of tail tube. The extensive disulfide bond network along the successive tail rings may mediate the flexible bending. The distal tip of T1, which is cone-shaped and assembled by proteins gp33, gp34, gp36, gp37, and gp38, displays structural similarity to that of phage lambda. In conjunction with previous studies of lambda-like siphophages, our structure will facilitate further exploration of the structural and mechanistic aspects of lambda-like siphophages. Full article

(This article belongs to the Section Bacterial Viruses)

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16 pages, 2806 KB

Open AccessEditor’s ChoiceArticle

Molecular Dissection of Symptom Determinants in Tomato Leaf Curl New Delhi Virus in Zucchini Through Mechanical Transmission

by Thuy T. B. Vo, Eui-Joon Kil, Marjia Tabassum, Bupi Nattanong, Muhammad Amir Qureshi, Hyo-Jin Im, Giuseppe Parrella, Taek-Kyun Lee and Sukchan Lee

Viruses 2025, 17(3), 294; https://doi.org/10.3390/v17030294 - 20 Feb 2025

Cited by 3 | Viewed by 9288

Abstract

Among begomovirus species, tomato leaf curl New Delhi virus (ToLCNDV) is significant and stands out as a mechanically transmissible bipartite begomovirus originating from the Old World. However, the mechanisms underlying the mechanical transmission of different ToLCNDV strains remain understudied, as their natural transmission [...] Read more.

Among begomovirus species, tomato leaf curl New Delhi virus (ToLCNDV) is significant and stands out as a mechanically transmissible bipartite begomovirus originating from the Old World. However, the mechanisms underlying the mechanical transmission of different ToLCNDV strains remain understudied, as their natural transmission occurs via insect vectors. In this study, we investigated the mechanical transmissibility of two ToLCNDVs, one from Italy and another from Pakistan, in host plants. Several cucurbit species were screened, and symptom differences between the two ToLCNDV clones were observed only in zucchini when subjected to rubbing inoculation. The Italian isolate (ToLCNDV-ES) induced typical disease symptoms such as leaf curling, yellow mosaic, and internode stunting, whereas a normal phenotype was observed in zucchini mechanically infected with ToLCNDV-In (Pakistani isolate). Subsequently, a gene-swapping experiment between the two ToLCNDVs was conducted, and ToLCNDV-ES DNA-B was identified as a crucial factor in mechanical transmission. We then constructed chimeric mutant clones based on the DNA-B sequence and assessed their ability to induce symptoms in zucchini. These results indicated that the nuclear shuttle protein is a determinant of symptom development during ToLCNDV mechanical transmission. Moreover, several defense-related host genes showed significant changes in relative expression in different ToLCNDV clones, indicating their potential role in disease symptom development through the mechanical transmission of ToLCNDV. This is the first report comparing the mechanical transmissibility of two isolates of different ToLCNDV strains from the Mediterranean region and the Indian subcontinent in the same host plant, providing new insights into the virus’s pathogenicity across different geographic regions. Full article

(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)

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