Viruses

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 1415

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 834

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 669

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 802

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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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

Viewed by 2101

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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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

Viewed by 1289

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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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 468

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

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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 1 | Viewed by 961

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 1171

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 2 | Viewed by 1991

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 1445

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 1 | Viewed by 1927

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 2 | Viewed by 1142

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 1355

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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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

Viewed by 1709

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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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

Viewed by 902

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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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 1 | Viewed by 1461

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 1777

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 1647

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

Viewed by 1136

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 1234

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 833

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 2 | Viewed by 1917

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 4579

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 5 | Viewed by 13398

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 1 | Viewed by 10194

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 1 | Viewed by 8391

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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18 pages, 2584 KB

Open AccessEditor’s ChoiceArticle

Disease Tolerance in ‘Anaheim’ Pepper to PepGMV-D Strain Involves Complex Interactions Between the Movement Protein Putative Promoter Region and Unknown Host Factors

by Cecilia Hernández-Zepeda and Judith K. Brown

Viruses 2025, 17(2), 268; https://doi.org/10.3390/v17020268 - 15 Feb 2025

Viewed by 3872

Abstract

Pepper golden mosaic virus (PepGMV) is a bipartite begomovirus of pepper and tomato from North America. In ‘Anaheim’ pepper plants PepGMV-Mo strain (Mo) causes systemic yellow foliar mosaic symptoms, while PepGMV-D strain (D) causes distortion of 1st–6th expanding leaves, and asymptomatic infection of [...] Read more.

Pepper golden mosaic virus (PepGMV) is a bipartite begomovirus of pepper and tomato from North America. In ‘Anaheim’ pepper plants PepGMV-Mo strain (Mo) causes systemic yellow foliar mosaic symptoms, while PepGMV-D strain (D) causes distortion of 1st–6th expanding leaves, and asymptomatic infection of subsequently developing leaves, like other known ‘recovery’ phenotypes. Infections established with DNA-A Mo and D components expressing red-shifted green fluorescent protein in place of coat protein and in situ hybridization, showed PepGMV-Mo localized to phloem and mesophyll cells, while -D was mesophyll restricted. Alignment of PepGMV-Mo and -D DNA-B components revealed three indels upstream of the BC1 gene that encodes the movement protein (MP). To determine if this non-coding region (*BC1) D-strain MP putative promoter contributed to ‘recovery’, plants were inoculated with chimeric DNA-B Mo/D components harboring reciprocally exchanged *BC1, and wild-type DNA-A Mo and D components. Symptoms were reminiscent but not identical to wild-type -Mo or -D infection, respectively, suggesting ‘recovery’ cannot be attributed solely to the *BC1. Both BC1 and D*BC1 were targeted by post-transcriptional gene silencing; however, ‘recovered’ leaves accumulated fewer transcripts and 21–24 nt vsiRNAs. Thus, inefficient in planta movement of PepGMV-D is associated with a non-pepper-adapted ‘defective’ BC1 that facilitates hyper-efficient PTGS, leading to BC1 transcript degradation that in turn limits virus spread, thereby recapitulating disease ‘tolerance’. Full article

(This article belongs to the Special Issue Plant Virus Interactions with Hosts: Mechanisms and Applications)

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15 pages, 3034 KB

Open AccessEditor’s ChoiceArticle

Impacts of Antiretroviral Therapy on the Oral Microbiome and Periodontal Health of Feline Immunodeficiency Virus-Positive Cats

by Laura Bashor, Jennifer E. Rawlinson, Christopher P. Kozakiewicz, Elisa Behzadi, Craig Miller, Jeffrey Kim, Megan Cierzan, Mary Nehring, Scott Carver, Zaid Abdo and Sue VandeWoude

Viruses 2025, 17(2), 257; https://doi.org/10.3390/v17020257 - 13 Feb 2025

Cited by 2 | Viewed by 4718

Abstract

Feline immunodeficiency virus (FIV) is the domestic cat analogue of HIV infection in humans. Both viruses induce oral disease in untreated individuals, with clinical signs that include gingivitis and periodontal lesions. Oral disease manifestations in HIV patients are abated by highly effective combination [...] Read more.

Feline immunodeficiency virus (FIV) is the domestic cat analogue of HIV infection in humans. Both viruses induce oral disease in untreated individuals, with clinical signs that include gingivitis and periodontal lesions. Oral disease manifestations in HIV patients are abated by highly effective combination antiretroviral therapy (cART), though certain oral manifestations persist despite therapy. Microorganisms associated with oral cavity opportunistic infections in patients with HIV cause similar pathologies in cats. To further develop this model, we evaluated characteristics of feline oral health and the oral microbiome during experimental FIV infection over an 8-month period following cART. Using 16S rRNA sequencing, we evaluated gingival bacterial communities at four timepoints in uninfected and FIV-infected cats treated with either cART or placebo. Comprehensive oral examinations were also conducted by a veterinary dental specialist over the experimental period. Gingival inflammation was higher in FIV-infected cats treated with placebo compared to cART-treated cats and the controls at the study endpoint. Oral microbiome alpha diversity increased in all groups, while beta diversity differed among treatment groups, documenting a significant effect of cART therapy on microbiome community composition. This finding has not previously been reported, and indicates cART ameliorates immunodeficiency virus-associated oral disease via the preservation of oral mucosal microbiota. Further, this study illustrates the value of the FIV animal model for investigations of mechanistic associations and therapeutic interventions for HIV’s oral manifestations. Full article

(This article belongs to the Section Animal Viruses)

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35 pages, 2508 KB

Open AccessEditor’s ChoiceReview

Tobacco Mosaic Virus Movement: From Capsid Disassembly to Transport Through Plasmodesmata

by Amr Ibrahim, Nobumitsu Sasaki, James E. Schoelz and Richard S. Nelson

Viruses 2025, 17(2), 214; https://doi.org/10.3390/v17020214 - 31 Jan 2025

Cited by 2 | Viewed by 6126

Abstract

Determining mechanisms to establish an initial infection and form intracellular complexes for accumulation and movement of RNA plant viruses are important areas of study in plant virology. The impact of these findings on the basic understanding of plant molecular virology and its application [...] Read more.

Determining mechanisms to establish an initial infection and form intracellular complexes for accumulation and movement of RNA plant viruses are important areas of study in plant virology. The impact of these findings on the basic understanding of plant molecular virology and its application in agriculture is significant. Studies with tobacco mosaic virus (TMV) and related tobamoviruses often provide important foundational knowledge for studies involving other viruses. Topics discussed here include capsid disassembly, establishment of a virus replication complex (VRC), and transport of the VRCs or virus components within the cell to locations at the plasmodesmata for intercellular virus RNA (vRNA) movement. Seminal findings with TMV and related tobamoviruses include detecting co-translational disassembly of the vRNA from the virus rod, full sequencing of genomic vRNA and production of infectious transcript for genetic studies determining virus components necessary for intercellular movement, and biochemical and cell biological studies determining the host factors, protein and membrane, needed for replication and movement. This review highlights many of the studies through the years on TMV and selected tobamoviruses that have impacted not only our understanding of tobamovirus accumulation and movement but also that of other plant viruses. Full article

(This article belongs to the Special Issue Tobamoviruses: Molecular Aspects and Resistance Regulation—a Special Issue Commemorating 125 Years of Research on Tobamoviruses)

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39 pages, 7731 KB

Open AccessEditor’s ChoiceArticle

Role of the Psi Packaging Signal and Dimerization Initiation Sequence in the Organization of Rous Sarcoma Virus Gag-gRNA Co-Condensates

by Gregory S. Lambert, Rebecca J. Kaddis Maldonado and Leslie J. Parent

Viruses 2025, 17(1), 97; https://doi.org/10.3390/v17010097 - 13 Jan 2025

Cited by 2 | Viewed by 3407

Abstract

Retroviral genome selection and virion assembly remain promising targets for novel therapeutic intervention. Recent studies have demonstrated that the Gag proteins of Rous sarcoma virus (RSV) and human immunodeficiency virus type-1 (HIV-1) undergo nuclear trafficking, colocalize with nascent genomic viral RNA (gRNA) at [...] Read more.

Retroviral genome selection and virion assembly remain promising targets for novel therapeutic intervention. Recent studies have demonstrated that the Gag proteins of Rous sarcoma virus (RSV) and human immunodeficiency virus type-1 (HIV-1) undergo nuclear trafficking, colocalize with nascent genomic viral RNA (gRNA) at transcription sites, may interact with host transcription factors, and display biophysical properties characteristic of biomolecular condensates. In the present work, we utilized a controlled in vitro condensate assay and advanced imaging approaches to investigate the effects of interactions between RSV Gag condensates and viral and nonviral RNAs on condensate abundance and organization. We observed that the psi (Ψ) packaging signal and the dimerization initiation sequence (DIS) had stabilizing effects on RSV Gag condensates, while RNAs lacking these features promoted or antagonized condensation, depending on local protein concentration and condensate architecture. An RNA containing Ψ, DIS, and the dimerization linkage structure (DLS) that is capable of stable dimer formation was observed to act as a bridge between RSV Gag condensates. These observations suggest additional, condensate-related roles for Gag-Ψ binding, gRNA dimerization, and Gag dimerization/multimerization in gRNA selection and packaging, representing a significant step forward in our understanding of how these interactions collectively facilitate efficient genome packaging. Full article

(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)

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17 pages, 9817 KB

Open AccessEditor’s ChoiceArticle

Repurposing Drugs for Synergistic Combination Therapies to Counteract Monkeypox Virus Tecovirimat Resistance

by Haydar Witwit, Beatrice Cubitt, Roaa Khafaji, Esteban M. Castro, Miguel Goicoechea, Maria M. Lorenzo, Rafael Blasco, Luis Martinez-Sobrido and Juan C. de la Torre

Viruses 2025, 17(1), 92; https://doi.org/10.3390/v17010092 - 13 Jan 2025

Cited by 17 | Viewed by 4708

Abstract

The ongoing monkeypox (mpox) disease outbreak has spread to multiple countries in Central Africa and evidence indicates it is driven by a more virulent clade I monkeypox virus (MPXV) strain than the clade II strain associated with the 2022 global mpox outbreak, which [...] Read more.

The ongoing monkeypox (mpox) disease outbreak has spread to multiple countries in Central Africa and evidence indicates it is driven by a more virulent clade I monkeypox virus (MPXV) strain than the clade II strain associated with the 2022 global mpox outbreak, which led the WHO to declare this mpox outbreak a public health emergency of international concern. The FDA-approved small molecule antiviral tecovirimat (TPOXX) is recommended to treat mpox cases with severe symptoms, but the limited efficacy of TPOXX and the emergence of TPOXX resistant MPXV variants has challenged this medical practice of care and highlighted the urgent need for alternative therapeutic strategies. In this study we have used vaccinia virus (VACV) as a surrogate of MPXV to assess the antiviral efficacy of combination therapy of TPOXX together with mycophenolate mofetil (MMF), an FDA-approved immunosuppressive agent that we have shown to inhibit VACV and MPXV, or the N-myristoyltransferase (NMT) inhibitor IMP-1088. Both MMF and IMP-1088 drugs exhibited strong dose-dependent antiviral activity against VACV and mpox, and potent synergistic effects in conjunction with TPOXX. Our findings support combination therapy of direct-acting (TPOXX) and host-targeted (MMF and IMP-1088) antivirals as a promising approach to treat mpox and prevent the emergence and spread of TPOXX-resistant MPXV variants. Full article

(This article belongs to the Special Issue Mpox (Monkeypox): From Neglected Tropical Disease to Emerging Global Pathogen)

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22 pages, 15117 KB

Open AccessEditor’s ChoiceArticle

The Transcriptional Program of Staphylococcus aureus Phage K Is Affected by a Host rpoC Mutation That Confers Phage K Resistance

by Rohit Kongari, Melissa D. Ray, Susan M. Lehman, Roger D. Plaut, Deborah M. Hinton and Scott Stibitz

Viruses 2024, 16(11), 1773; https://doi.org/10.3390/v16111773 - 13 Nov 2024

Cited by 2 | Viewed by 8576

Abstract

To better understand host–phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these [...] Read more.

To better understand host–phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host rpoC gene, which encodes the RNA polymerase β’ subunit. To examine the hypothesis that mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and rpoC_G17D mutant cultures infected with phage K, at different timepoints after infection. Infection of the WT host led to a steady increase of phage transcription relative to the host. Our analysis allowed us to define 53 transcriptional units and to categorize genes based on their temporal expression patterns. Predicted promoter sequences defined by conserved −35, −10, and, in some cases, extended −10 elements, were found upstream of early and middle genes. However, in many cases, sequences upstream of late genes did not contain clear, complete, canonical promoter sequences, suggesting that factors in addition to host RNA polymerase are required for their expression. Infection of the rpoC_G17D mutant host led to a transcriptional pattern that was similar to that of the WT at early timepoints. However, beginning at 20 min after infection, transcription of late genes (such as phage structural genes and host lysis genes) was severely reduced. Our data indicate that the rpoC_G17D mutation prevents the expression of phage late genes, resulting in a failed infection cycle for phage K. In addition to illuminating the global transcriptional landscape of phage K throughout the infection cycle, this study will inform our investigations into the basis of phage K’s control of its transcriptional program as well as mechanisms of phage resistance. Full article

(This article belongs to the Section Bacterial Viruses)

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21 pages, 6333 KB

Open AccessEditor’s ChoiceArticle

Multiplex Microscopy Assay for Assessment of Therapeutic and Serum Antibodies against Emerging Pathogens

by Nuno Sartingen, Vanessa Stürmer, Matthias Kaltenböck, Thorsten G. Müller, Paul Schnitzler, Anna Kreshuk, Hans-Georg Kräusslich, Uta Merle, Frauke Mücksch, Barbara Müller, Constantin Pape and Vibor Laketa

Viruses 2024, 16(9), 1473; https://doi.org/10.3390/v16091473 - 17 Sep 2024

Viewed by 4230

Abstract

The emergence of novel pathogens, exemplified recently by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need for rapidly deployable and adaptable diagnostic assays to assess their impact on human health and guide public health responses in future pandemics. In this [...] Read more.

The emergence of novel pathogens, exemplified recently by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need for rapidly deployable and adaptable diagnostic assays to assess their impact on human health and guide public health responses in future pandemics. In this study, we developed an automated multiplex microscopy assay coupled with machine learning-based analysis for antibody detection. To achieve multiplexing and simultaneous detection of multiple viral antigens, we devised a barcoding strategy utilizing a panel of HeLa-based cell lines. Each cell line expressed a distinct viral antigen, along with a fluorescent protein exhibiting a unique subcellular localization pattern for cell classification. Our robust, cell segmentation and classification algorithm, combined with automated image acquisition, ensured compatibility with a high-throughput approach. As a proof of concept, we successfully applied this approach for quantitation of immunoreactivity against different variants of SARS-CoV-2 spike and nucleocapsid proteins in sera of patients or vaccinees, as well as for the study of selective reactivity of monoclonal antibodies. Importantly, our system can be rapidly adapted to accommodate other SARS-CoV-2 variants as well as any antigen of a newly emerging pathogen, thereby representing an important resource in the context of pandemic preparedness. Full article

(This article belongs to the Special Issue Microscopy Methods for Virus Research)

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31 pages, 115227 KB

Open AccessEditor’s ChoiceArticle

Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes

by Yani Arhab, Tatyana V. Pestova and Christopher U. T. Hellen

Viruses 2024, 16(9), 1413; https://doi.org/10.3390/v16091413 - 4 Sep 2024

Cited by 4 | Viewed by 3718

Abstract

Caliciviruses have positive-sense RNA genomes, typically with short 5′-untranslated regions (5′UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5′UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. [...] Read more.

Caliciviruses have positive-sense RNA genomes, typically with short 5′-untranslated regions (5′UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5′UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200–300 codon-long ORF (designated ORF1*) that overlaps the 5′-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3′-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES’s 3′-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF₄₅, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1). Full article

(This article belongs to the Special Issue Viral Strategies and Cellular Countermeasures that Regulate mRNA Access to the Translation Apparatus)

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10 pages, 3633 KB

Open AccessEditor’s ChoiceCommunication

Resistance of the CRISPR-Cas13a Gene-Editing System to Potato Spindle Tuber Viroid Infection in Tomato and Nicotiana benthamiana

by Ying Wei Khoo, Qingsong Wang, Shangwu Liu, Binhui Zhan, Tengfei Xu, Wenxia Lv, Guangjing Liu, Shifang Li and Zhixiang Zhang

Viruses 2024, 16(9), 1401; https://doi.org/10.3390/v16091401 - 31 Aug 2024

Cited by 3 | Viewed by 2756

Abstract

Gene-editing technology, specifically the CRISPR-Cas13a system, has shown promise in breeding plants resistant to RNA viruses. This system targets RNA and, theoretically, can also combat RNA-based viroids. To test this, the CRISPR-Cas13a system was introduced into tomato plants via transient expression and into [...] Read more.

Gene-editing technology, specifically the CRISPR-Cas13a system, has shown promise in breeding plants resistant to RNA viruses. This system targets RNA and, theoretically, can also combat RNA-based viroids. To test this, the CRISPR-Cas13a system was introduced into tomato plants via transient expression and into Nicotiana benthamiana through transgenic methods, using CRISPR RNAs (crRNAs) targeting the conserved regions of both sense and antisense genomes of potato spindle tuber viroid (PSTVd). In tomato plants, the expression of CRISPR-Cas13a and crRNAs substantially reduced PSTVd accumulation and alleviated disease symptoms. In transgenic N. benthamiana plants, the PSTVd levels were lower as compared to wild-type plants. Several effective crRNAs targeting the PSTVd genomic RNA were also identified. These results demonstrate that the CRISPR-Cas13a system can effectively target and combat viroid RNAs, despite their compact structures. Full article

(This article belongs to the Special Issue Crop Resistance to Viral Infections)

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16 pages, 3588 KB

Open AccessEditor’s ChoiceArticle

Parainfluenza Virus 5 V Protein Blocks Interferon Gamma-Mediated Upregulation of NK Cell Inhibitory Ligands and Improves NK Cell Killing of Neuroblastoma Cells

by Elisabeth M. Shiffer, Jeremiah L. Oyer, Alicja J. Copik and Griffith D. Parks

Viruses 2024, 16(8), 1270; https://doi.org/10.3390/v16081270 - 9 Aug 2024

Cited by 2 | Viewed by 2904

Abstract

Natural killer (NK) cells can be effective immunotherapeutic anti-cancer agents due to their ability to selectively target and kill tumor cells. This activity is modulated by the interaction of NK cell receptors with inhibitory ligands on the surface of target cells. NK cell [...] Read more.

Natural killer (NK) cells can be effective immunotherapeutic anti-cancer agents due to their ability to selectively target and kill tumor cells. This activity is modulated by the interaction of NK cell receptors with inhibitory ligands on the surface of target cells. NK cell inhibitory ligands can be upregulated on tumor cell surfaces in response to interferon-gamma (IFN-γ), a cytokine which is produced by activated NK cells. We hypothesized that the resistance of tumor cells to NK cell killing could be overcome by expression of the parainfluenza virus 5 (PIV5) V protein, which has known roles in blocking IFN-γ signaling. This was tested with human PM21-NK cells produced through a previously developed particle-based method which yields superior NK cells for immunotherapeutic applications. Infection of human SK-N-SH neuroblastoma cells with PIV5 blocked IFN-γ-mediated upregulation of three NK cell inhibitory ligands and enhanced in vitro killing of these tumor cells by PM21-NK cells. SK-N-SH cells transduced to constitutively express the V protein alone were resistant to IFN-γ-mediated increases in cell surface expression of NK cell inhibitory ligands. Real-time in vitro cell viability assays demonstrated that V protein expression in SK-N-SH cells was sufficient to increase PM21-NK cell-mediated killing. Toward a potential therapeutic application, transient lentiviral delivery of the V gene also enhanced PM21-NK cell killing in vitro. Our results provide the foundation for novel therapeutic applications of V protein expression in combination with ex vivo NK cell therapy to effectively increase the killing of tumor cells. Full article

(This article belongs to the Special Issue Viruses 2024—A World of Viruses)

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13 pages, 1551 KB

Open AccessEditor’s ChoiceArticle

Challenges in the Diagnosis of SARS-CoV-2 Infection in the Nervous System

by Samya Jezine Da Silva, Mauro Jorge Cabral-Castro, Cássia Cristina Alves Gonçalves, Diana Mariani, Orlando Ferreira, Amílcar Tanuri and Marzia Puccioni-Sohler

Viruses 2024, 16(8), 1247; https://doi.org/10.3390/v16081247 - 3 Aug 2024

Cited by 2 | Viewed by 3425

Abstract

Neurological involvement has been widely reported in SARS-CoV-2 infection. However, viral identification in the cerebrospinal fluid (CSF) is rarely found. The aim of this study is to evaluate the accuracy of virological and immunological biomarkers in CSF for the diagnosis of neuroCOVID-19. We [...] Read more.

Neurological involvement has been widely reported in SARS-CoV-2 infection. However, viral identification in the cerebrospinal fluid (CSF) is rarely found. The aim of this study is to evaluate the accuracy of virological and immunological biomarkers in CSF for the diagnosis of neuroCOVID-19. We analyzed 69 CSF samples from patients with neurological manifestations: 14 with suspected/confirmed COVID-19, with 5 additional serial CSF samples (group A), and as a control, 50 non-COVID-19 cases (group B—26 with other neuroinflammatory diseases; group C—24 with non-inflammatory diseases). Real-time reverse-transcription polymerase chain reaction (real-time RT-PCR) was used to determine SARS-CoV-2, and specific IgG, IgM, neopterin, and protein 10 induced by gamma interferon (CXCL-10) were evaluated in the CSF samples. No samples were amplified for SARS-CoV-2 by real-time RT-PCR. The sensitivity levels of anti-SARS-CoV-2 IgG and IgM were 50% and 14.28%, respectively, with 100% specificity for both tests. CXCL-10 showed high sensitivity (95.83%) and specificity (95.83%) for detection of neuroinflammation. Serial CSF analysis showed an association between the neuroinflammatory biomarkers and outcome (death and hospital discharge) in two cases (meningoencephalitis and rhombencephalitis). The detection of SARS-CoV-2 RNA and specific immunoglobulins in the CSF can be used for neuroCOVID-19 confirmation. Additionally, CXCL-10 in the CSF may contribute to the diagnosis and monitoring of neuroCOVID-19. Full article

(This article belongs to the Special Issue Molecular Biomarkers for Viral Infection)

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23 pages, 3415 KB

Open AccessEditor’s ChoiceArticle

Temporal Dynamics of Purinergic Receptor Expression in the Lungs of Marek’s Disease (MD) Virus-Infected Chickens Resistant or Susceptible to MD

by Haji Akbar and Keith W. Jarosinski

Viruses 2024, 16(7), 1130; https://doi.org/10.3390/v16071130 - 14 Jul 2024

Viewed by 2763

Abstract

Marek’s disease virus (MDV) is an economic concern for the poultry industry due to its poorly understood pathophysiology. Purinergic receptors (PRs) are potential therapeutic targets for viral infections, including herpesviruses, prompting our investigation into their role in MDV pathogenesis. The current study is [...] Read more.

Marek’s disease virus (MDV) is an economic concern for the poultry industry due to its poorly understood pathophysiology. Purinergic receptors (PRs) are potential therapeutic targets for viral infections, including herpesviruses, prompting our investigation into their role in MDV pathogenesis. The current study is part of an experimental series analyzing the expression of PRs during MDV infection. To address the early or short-acting P2 PR responses during natural MDV infection, we performed an “exposure” experiment where age-matched chickens were exposed to experimentally infected shedders to initiate natural infection. In addition, select non-PR regulatory gene responses were measured. Two groups of naïve contact chickens (n = 5/breed/time point) from MD-resistant (White Leghorns: WL) and -susceptible (Pure Columbian) chicken lines were housed separately with experimentally infected PC (×PC) and WL (×WL) chickens for 6 or 24 h. Whole lung lavage cells (WLLC) were collected, RNA was extracted, and RT-qPCR assays were used to measure specific PR responses. In addition, other potentially important markers in pathophysiology were measured. Our study revealed that WL chickens exhibited higher P1 PR expression during natural infection. WL chickens also showed higher expression of P1A3 and P2X3 at 6 and 24 h when exposed to PC-infected chickens. P2X5 and P2Y1 showed higher expression at 6 h, while P2Y5 showed higher expression at 6 and 24 h; regardless of the chicken line, PC chickens exhibited higher expression of P2X2, P2Y8, P2Y10, P2Y13, and P2Y14 when exposed to either group of infected chickens. In addition, MDV infection altered the expression of DDX5 in both WL and PC groups exposed to PC-infected birds only. However, irrespective of the source of exposure, BCL2 and ANGPTL4 showed higher expression in both WL and PC. The expression of STAT1A and STAT5A was influenced by time and breed, with major changes observed in STAT5A. CAT and SOD1 expression significantly increased in both WL and PC birds, regardless of the source of infection. GPX1 and GPX2 expression also increased in both WL and PC, although overall lower expression was observed in PC chickens at 24 h compared to 6 h. Our data suggest systemic changes in the host during early infection, indicated by the altered expression of PRs, DDX5, BCL2, ANGPTL4, and other regulatory genes during early MDV infection. The relative expression of these responses in PC and WL chickens suggests they may play a key role in their response to natural MDV infection in the lungs and long-term pathogenesis and survival. Full article

(This article belongs to the Special Issue Marek's Disease Virus)

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11 pages, 1523 KB

Open AccessEditor’s ChoiceArticle

Transovarial Transmission of Cell-Fusing Agent Virus in Naturally Infected Aedes aegypti Mosquitoes

by Dilip K. Nag and Kathryn J. Efner

Viruses 2024, 16(7), 1116; https://doi.org/10.3390/v16071116 - 11 Jul 2024

Cited by 2 | Viewed by 7929

Abstract

Mosquito-borne arboviruses include several pathogens that are responsible for many diseases of significant public health burden. Mosquitoes also host many insect-specific viruses that cannot replicate in vertebrate cells. These insect-specific viruses persist in nature predominantly via vertical transmission (VT), and they exhibit high [...] Read more.

Mosquito-borne arboviruses include several pathogens that are responsible for many diseases of significant public health burden. Mosquitoes also host many insect-specific viruses that cannot replicate in vertebrate cells. These insect-specific viruses persist in nature predominantly via vertical transmission (VT), and they exhibit high VT rates (VTRs). Cell-fusing agent virus (CFAV), an insect-specific orthoflavivirus, shows high VTRs in naturally infected mosquitoes but not in artificially infected mosquitoes. To determine whether the high VTRs are due to transovarial transmission, we investigated VT and ovary infection patterns in naturally CFAV-infected Aedes aegypti (Bangkok) mosquitoes. VT was monitored by detecting CFAV among the progeny by reverse-transcription polymerase chain reaction and ovary infection was determined by in situ hybridization using a virus-specific probe. We showed that in CFAV-positive mosquitoes, ovarian follicles were infected, suggesting that VT occurs by transovarial transmission in naturally infected mosquitoes. Additionally, mosquitoes harbored dormant, non-replicative CFAV that remained below the detection level. These results suggested that CFAV persists via VT in nature and has the potential to remain dormant in diapausing mosquitoes during unfavorable conditions. Understanding this VT mechanism is crucial for comprehending the persistence of insect-specific viruses (and potentially dual-host arboviruses) in their natural environment. Full article

(This article belongs to the Section Invertebrate Viruses)

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22 pages, 6191 KB

Open AccessEditor’s ChoiceArticle

Toward the Development of a Pan-Lyssavirus Vaccine

by Sabrine Ben Hamed, Jacob F. Myers, Anisha Chandwani, Christoph Wirblich, Drishya Kurup, Nir Paran and Matthias J. Schnell

Viruses 2024, 16(7), 1107; https://doi.org/10.3390/v16071107 - 10 Jul 2024

Cited by 3 | Viewed by 4114

Abstract

In addition to the rabies virus (RABV), 16 more lyssavirus species have been identified worldwide, causing a disease similar to RABV. Non-rabies-related human deaths have been described, but the number of cases is unknown, and the potential of such lyssaviruses causing human disease [...] Read more.

In addition to the rabies virus (RABV), 16 more lyssavirus species have been identified worldwide, causing a disease similar to RABV. Non-rabies-related human deaths have been described, but the number of cases is unknown, and the potential of such lyssaviruses causing human disease is unpredictable. The current rabies vaccine does not protect against divergent lyssaviruses such as Mokola virus (MOKV) or Lagos bat virus (LBV). Thus, a more broad pan-lyssavirus vaccine is needed. Here, we evaluate a novel lyssavirus vaccine with an attenuated RABV vector harboring a chimeric RABV glycoprotein (G) in which the antigenic site I of MOKV replaces the authentic site of rabies virus (RABVG-cAS1). The recombinant vaccine was utilized to immunize mice and analyze the immune response compared to homologous vaccines. Our findings indicate that the vaccine RABVG-cAS1 was immunogenic and induced high antibody titers against both RABVG and MOKVG. Challenge studies with different lyssaviruses showed that replacing a single antigenic site of RABV G with the corresponding site of MOKV G provides a significant improvement over the homologous RABV vaccine and protects against RABV, Irkut virus (IRKV), and MOKV. This strategy of epitope chimerization paves the way towards a pan-lyssavirus vaccine to safely combat the diseases caused by these viruses. Full article

(This article belongs to the Special Issue Advances in Rabies Research 2023)

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17 pages, 17312 KB

Open AccessEditor’s ChoiceArticle

The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae

by Mario Mietzsch, Shweta Kailasan, Antonette Bennett, Paul Chipman, Bentley Fane, Juha T. Huiskonen, Ian N. Clarke and Robert McKenna

Viruses 2024, 16(7), 1103; https://doi.org/10.3390/v16071103 - 9 Jul 2024

Cited by 3 | Viewed by 6777

Abstract

Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy [...] Read more.

Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy to a resolution of 2.5 Å. A striking feature of the SpV4 capsid is the mushroom-like protrusions at the 3-fold axes, which is common among all members of the subfamily Gokushovirinae. While the function of the protrusion is currently unknown, this feature varies widely in this subfamily and is therefore possibly an adaptation for host recognition. Furthermore, on the interior of the SpV4 capsid, the location of DNA-binding protein VP8 was identified and shown to have low structural conservation to the capsids of other viruses in the family. The structural characterization of SpV4 will aid future studies analyzing the virus–host interaction, to understand disease mechanisms at a molecular level. Furthermore, the structural comparisons in this study, including a low-resolution structure of the chlamydia phage 2, provide an overview of the structural repertoire of the viruses in this family that infect various bacterial hosts, which in turn infect a wide range of animals and plants. Full article

(This article belongs to the Special Issue Structural Biology of Bacteriophages)

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22 pages, 2290 KB

Open AccessEditor’s ChoiceArticle

Evolution of RNA Viruses: Reasons for the Existence of Separate Plus, Minus, and Double-Strand Replication Strategies

by Hyunjin Park and Paul G. Higgs

Viruses 2024, 16(7), 1081; https://doi.org/10.3390/v16071081 - 5 Jul 2024

Viewed by 4454

Abstract

Plus, minus, and double-strand RNA viruses are all found in nature. We use computational models to study the relative success of these strategies. We consider translation, replication, and virion assembly inside one cell, and transmission of virions between cells. For viruses which do [...] Read more.

Plus, minus, and double-strand RNA viruses are all found in nature. We use computational models to study the relative success of these strategies. We consider translation, replication, and virion assembly inside one cell, and transmission of virions between cells. For viruses which do not incorporate a polymerase in the capsid, transmission of only plus strands is the default strategy because virions containing minus strands are not infectious. Packaging only plus strands has a significant advantage if the number of RNA strands produced per cell is larger than the number of capsids. In this case, by not packaging minus strands, the virus produces more plus-strand virions. Therefore, plus-strand viruses are selected at low multiplicity of infection. However, at high multiplicity of infection, it is preferable to package both strands because the additional minus virions produced are helpful when there are multiple infections per cell. The fact that plus-strand viruses are widespread while viruses that package both strands are not seen in nature suggests that RNA strands are indeed produced in excess over capsids, and that the multiplicity of infection is not sufficiently high to favor the production of both kinds of virions. For double-strand viruses, we show that it is advantageous to produce only plus strands from the double strand within the cell, as is observed in real viruses. The reason for the success of minus-strand viruses is more puzzling initially. For viruses that incorporate a polymerase in the virion, minus virions are infectious. However, this is not sufficient to explain the success of minus-strand viruses, because in this case, viruses that package both strands outcompete those that package only minus or only plus. Real minus-strand viruses make use of replicable strands that are coated by a nucleoprotein, and separate translatable plus strands that are uncoated. Here we show that when there are distinct replicable and translatable strands, minus-strand viruses are selected. Full article

(This article belongs to the Section General Virology)

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32 pages, 4747 KB

Open AccessEditor’s ChoiceArticle

Phage-Mediated Digestive Decolonization in a Gut-On-A-Chip Model: A Tale of Gut-Specific Bacterial Prosperity

by Brieuc Van Nieuwenhuyse, Maya Merabishvili, Nathalie Goeders, Kevin Vanneste, Bert Bogaerts, Mathieu de Jode, Joachim Ravau, Jeroen Wagemans, Leïla Belkhir and Dimitri Van der Linden

Viruses 2024, 16(7), 1047; https://doi.org/10.3390/v16071047 - 28 Jun 2024

Cited by 2 | Viewed by 5365

Abstract

Infections due to antimicrobial-resistant bacteria have become a major threat to global health. Some patients may carry resistant bacteria in their gut microbiota. Specific risk factors may trigger the conversion of these carriages into infections in hospitalized patients. Preventively eradicating these carriages has [...] Read more.

Infections due to antimicrobial-resistant bacteria have become a major threat to global health. Some patients may carry resistant bacteria in their gut microbiota. Specific risk factors may trigger the conversion of these carriages into infections in hospitalized patients. Preventively eradicating these carriages has been postulated as a promising preventive intervention. However, previous attempts at such eradication using oral antibiotics or probiotics have led to discouraging results. Phage therapy, the therapeutic use of bacteriophage viruses, might represent a worthy alternative in this context. Taking inspiration from this clinical challenge, we built Gut-On-A-Chip (GOAC) models, which are tridimensional cell culture models mimicking a simplified gut section. These were used to better understand bacterial dynamics under phage pressure using two relevant species: Pseudomonas aeruginosa and Escherichia coli. Model mucus secretion was documented by ELISA assays. Bacterial dynamics assays were performed in GOAC triplicates monitored for 72 h under numerous conditions, such as pre-, per-, or post-bacterial timing of phage introduction, punctual versus continuous phage administration, and phage expression of mucus-binding properties. The potential genomic basis of bacterial phage resistance acquired in the model was investigated by variant sequencing. The bacterial “escape growth” rates under phage pressure were compared to static in vitro conditions. Our results suggest that there is specific bacterial prosperity in this model compared to other in vitro conditions. In E. coli assays, the introduction of a phage harboring unique mucus-binding properties could not shift this balance of power, contradicting previous findings in an in vivo mouse model and highlighting the key differences between these models. Genomic modifications were correlated with bacterial phage resistance acquisition in some but not all instances, suggesting that alternate ways are needed to evade phage predation, which warrants further investigation. Full article

(This article belongs to the Special Issue Phage-Bacteria Interplay in Health and Disease, Second Edition)

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20 pages, 1082 KB

Open AccessEditor’s ChoiceReview

Engineered Resistance to Tobamoviruses

by John Peter Carr

Viruses 2024, 16(7), 1007; https://doi.org/10.3390/v16071007 - 22 Jun 2024

Cited by 8 | Viewed by 5998

Abstract

Tobacco mosaic virus (TMV) was the first virus to be studied in detail and, for many years, TMV and other tobamoviruses, particularly tomato mosaic virus (ToMV) and tobamoviruses infecting pepper (Capsicum spp.), were serious crop pathogens. By the end of the twentieth [...] Read more.

Tobacco mosaic virus (TMV) was the first virus to be studied in detail and, for many years, TMV and other tobamoviruses, particularly tomato mosaic virus (ToMV) and tobamoviruses infecting pepper (Capsicum spp.), were serious crop pathogens. By the end of the twentieth and for the first decade of the twenty-first century, tobamoviruses were under some degree of control due to introgression of resistance genes into commercial tomato and pepper lines. However, tobamoviruses remained important models for molecular biology, biotechnology and bio-nanotechnology. Recently, tobamoviruses have again become serious crop pathogens due to the advent of tomato brown rugose fruit virus, which overcomes tomato resistance against TMV and ToMV, and the slow but apparently inexorable worldwide spread of cucumber green mottle mosaic virus, which threatens all cucurbit crops. This review discusses a range of mainly molecular biology-based approaches for protecting crops against tobamoviruses. These include cross-protection (using mild tobamovirus strains to ‘immunize’ plants against severe strains), expressing viral gene products in transgenic plants to inhibit the viral infection cycle, inducing RNA silencing against tobamoviruses by expressing virus-derived RNA sequences in planta or by direct application of double-stranded RNA molecules to non-engineered plants, gene editing of host susceptibility factors, and the transfer and optimization of natural resistance genes. Full article

(This article belongs to the Special Issue Tobamoviruses: Molecular Aspects and Resistance Regulation—a Special Issue Commemorating 125 Years of Research on Tobamoviruses)

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15 pages, 2537 KB

Open AccessEditor’s ChoiceArticle

Bacteriophages and Green Synthesized Zinc Oxide Nanoparticles in Combination Are Efficient against Biofilm Formation of Pseudomonas aeruginosa

by Elaheh Alipour-Khezri, Amin Moqadami, Abolfazl Barzegar, Majid Mahdavi, Mikael Skurnik and Gholamreza Zarrini

Viruses 2024, 16(6), 897; https://doi.org/10.3390/v16060897 - 31 May 2024

Cited by 8 | Viewed by 5942

Abstract

Bacteriophages (phages) are viruses that infect the bacteria within which their reproduction cycle takes place, a process that ends in the lysis and death of the bacterial cell. Some phages are also able to destroy bacterial biofilms. Due to increased antibiotics resistance, Pseudomonas [...] Read more.

Bacteriophages (phages) are viruses that infect the bacteria within which their reproduction cycle takes place, a process that ends in the lysis and death of the bacterial cell. Some phages are also able to destroy bacterial biofilms. Due to increased antibiotics resistance, Pseudomonas aeruginosa, another biofilm-forming pathogen, is a problem in many parts of the world. Zinc oxide (ZnO) and other metal nanoparticles (NPs) are biologically active and also possess anti-biofilm properties. ZnO-NPs were prepared by the green synthesis method using orange peels. The vibrational peaks of the ZnO-NPs were analyzed using FTIR analysis, and their size and morphological properties were determined using scanning electron microscopy (SEM). The ability of the ZnO-NPs to reduce or eliminate P. aeruginosa biofilm alone or in combination with phages PB10 and PA19 was investigated. The P. aeruginosa cells were effectively killed in the preformed 48 h biofilms during a 24 h incubation with the ZnO-NP–phage combination, in comparison with the control or ZnO-NPs alone. The treatments on growing biofilms were most efficient in the final stages of biofilm development. All five treatment groups showed a significant biofilm reduction compared to the control group (p < 0.0001) at 48 h of incubation. The influence of the ZnO-NPs and phages on the quorum sensing system of P. aeruginosa was monitored by quantitative real-time PCR (qRT-PCR) of the autoinducer biosynthesis gene lasI. While the ZnO-NPs repressed the lasI gene transcription, the phages slightly activated it at 24 and 48 h of incubation. Also, the effect of the ZnO-NPs and phage PA19 on the viability of HFF2 cells was investigated and the results showed that the combination of NPs with PA19 reduced the toxic effect of ZnO-NPs and also stimulated the growth in normal cells. Full article

(This article belongs to the Special Issue Bacteriophages and Biofilms 2.0)

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10 pages, 1191 KB

Open AccessEditor’s ChoiceArticle

Phage–Bacterial Interaction Alters Phenotypes Associated with Virulence in Acinetobacter baumannii

by Greater Kayode Oyejobi, Xiaoxu Zhang, Dongyan Xiong, Heng Xue, Mengjuan Shi, Hang Yang and Hongping Wei

Viruses 2024, 16(5), 743; https://doi.org/10.3390/v16050743 - 8 May 2024

Cited by 2 | Viewed by 5202

Abstract

Bacteriophages exert strong selection on their bacterial hosts to evolve resistance. At the same time, the fitness costs on bacteria following phage resistance may change their virulence, which may affect the therapeutic outcomes of phage therapy. In this study, we set out to [...] Read more.

Bacteriophages exert strong selection on their bacterial hosts to evolve resistance. At the same time, the fitness costs on bacteria following phage resistance may change their virulence, which may affect the therapeutic outcomes of phage therapy. In this study, we set out to assess the costs of phage resistance on the in vitro virulence of priority 1 nosocomial pathogenic bacterium, Acinetobacter baumannii. By subjecting phage-resistant variant Ev5-WHG of A. baumannii WHG40004 to several in vitro virulence profiles, we found that its resistance to phage is associated with reduced fitness in host microenvironments. Also, the mutant exhibited impaired adhesion and invasion to mammalian cells, as well as increased susceptibility to macrophage phagocytosis. Furthermore, the whole-genome sequencing of the mutant revealed that there exist multiple mutations which may play a role in phage resistance and altered virulence. Altogether, this study demonstrates that resistance to phage can significantly alter phenotypes associated with virulence in Acinetobacter baumannii. Full article

(This article belongs to the Special Issue Phage-Bacteria Interplay in Health and Disease, Second Edition)

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12 pages, 1245 KB

Open AccessEditor’s ChoiceArticle

Host Barriers Limit Viral Spread in a Spillover Host: A Study of Deformed Wing Virus in the Bumblebee Bombus terrestris

by Tabea Streicher, Pina Brinker, Simon Tragust and Robert J. Paxton

Viruses 2024, 16(4), 607; https://doi.org/10.3390/v16040607 - 15 Apr 2024

Cited by 6 | Viewed by 4869

Abstract

The transmission of pathogens from reservoir to recipient host species, termed pathogen spillover, can profoundly impact plant, animal, and public health. However, why some pathogens lead to disease emergence in a novel species while others fail to establish or do not elicit disease [...] Read more.

The transmission of pathogens from reservoir to recipient host species, termed pathogen spillover, can profoundly impact plant, animal, and public health. However, why some pathogens lead to disease emergence in a novel species while others fail to establish or do not elicit disease is often poorly understood. There is strong evidence that deformed wing virus (DWV), an (+)ssRNA virus, spills over from its reservoir host, the honeybee Apis mellifera, into the bumblebee Bombus terrestris. However, the low impact of DWV on B. terrestris in laboratory experiments suggests host barriers to virus spread in this recipient host. To investigate potential host barriers, we followed the spread of DWV genotype B (DWV-B) through a host’s body using RT-PCR after experimental transmission to bumblebees in comparison to honeybees. Inoculation was per os, mimicking food-borne transmission, or by injection into the bee’s haemocoel, mimicking vector-based transmission. In honeybees, DWV-B was present in both honeybee faeces and haemolymph within 3 days of inoculation per os or by injection. In contrast, DWV-B was not detected in B. terrestris haemolymph after inoculation per os, suggesting a gut barrier that hinders DWV-B’s spread through the body of a B. terrestris. DWV-B was, however, detected in B. terrestris faeces after injection and feeding, albeit at a lower abundance than that observed for A. mellifera, suggesting that B. terrestris sheds less DWV-B than A. mellifera in faeces when infected. Barriers to viral spread in B. terrestris following oral infection may limit DWV’s impact on this spillover host and reduce its contribution to the community epidemiology of DWV. Full article

(This article belongs to the Section Invertebrate Viruses)

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32 pages, 407 KB

Open AccessEditor’s ChoiceArticle

The Medicinal Phage—Regulatory Roadmap for Phage Therapy under EU Pharmaceutical Legislation

by Timo Faltus

Viruses 2024, 16(3), 443; https://doi.org/10.3390/v16030443 - 12 Mar 2024

Cited by 39 | Viewed by 8803

Abstract

Bacteriophage therapy is a promising approach to treating bacterial infections. Research and development of bacteriophage therapy is intensifying due to the increase in antibiotic resistance and the faltering development of new antibiotics. Bacteriophage therapy uses bacteriophages (phages), i.e., prokaryotic viruses, to specifically target [...] Read more.

Bacteriophage therapy is a promising approach to treating bacterial infections. Research and development of bacteriophage therapy is intensifying due to the increase in antibiotic resistance and the faltering development of new antibiotics. Bacteriophage therapy uses bacteriophages (phages), i.e., prokaryotic viruses, to specifically target and kill pathogenic bacteria. The legal handling of this type of therapy raises several questions. These include whether phage therapeutics belong to a specially regulated class of medicinal products, and which legal framework should be followed with regard to the various technical ways in which phage therapeutics can be manufactured and administered. The article shows to which class of medicinal products phage therapeutics from wild type phages and from genetically modified (designer) phages do or do not belong. Furthermore, the article explains which legal framework is relevant for the manufacture and administration of phage therapeutics, which are manufactured in advance in a uniform, patient-independent manner, and for tailor-made patient-specific phage therapeutics. For the systematically coherent, successful translation of phage therapy, the article considers pharmaceutical law and related legal areas, such as genetic engineering law. Finally, the article shows how the planned legislative revisions of Directive 2001/83/EC and Regulation (EC) No 726/2004 may affect the legal future of phage therapy. Full article

(This article belongs to the Section Bacterial Viruses)

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