Viruses

1 pages, 140 KiB

Open AccessCorrection

Correction: López-Ferber et al. Baculovirus Genetic Diversity and Population Structure. Viruses 2025, 17, 142

by Miguel López-Ferber, Primitivo Caballero and Trevor Williams

Viruses 2025, 17(5), 683; https://doi.org/10.3390/v17050683 - 7 May 2025

Abstract

In the original publication [...] Full article

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

20 pages, 2012 KiB

Open AccessReview

Multidimensional Regulatory Mechanisms and Targeting Strategies of the eEF1 Family in RNA Virus Infection

by Xin Wang, Kaituo Liu, Xiaoquan Wang and Xiufan Liu

Viruses 2025, 17(5), 682; https://doi.org/10.3390/v17050682 - 7 May 2025

Abstract

The eukaryotic translation elongation factor 1 (eEF1) family exhibits critical roles in RNA viral infection beyond its canonical function in protein synthesis. This review analyzes the structural characteristics of eEF1A and the eEF1B complex, and their regulatory mechanisms during viral infection. eEF1A impacts [...] Read more.

The eukaryotic translation elongation factor 1 (eEF1) family exhibits critical roles in RNA viral infection beyond its canonical function in protein synthesis. This review analyzes the structural characteristics of eEF1A and the eEF1B complex, and their regulatory mechanisms during viral infection. eEF1A impacts viral replication by stabilizing viral RNA-dependent RNA polymerase (RdRp) complexes, modulating genomic RNA synthesis, and facilitating viral assembly through cytoskeletal regulation. eEF1B subunits contribute through enhancing viral mRNA translation, regulating nuclear transport of viral components, and mediating post-translational modifications. The high conservation of eEF1 proteins across species and their involvement in multiple stages of viral replication establish them as promising broad-spectrum antiviral targets. Current eEF1-targeting compounds like plitidepsin demonstrate efficacy against diverse viral families, though therapeutic development faces challenges in balancing antiviral activity with host toxicity. This review provides a theoretical foundation for developing novel antiviral strategies targeting host–virus interaction interfaces and offers insights into addressing emerging infectious diseases. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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14 pages, 6054 KiB

Open AccessArticle

Virtual Screening and Molecular Dynamics Simulation Targeting the ATP Domain of African Swine Fever Virus Type II DNA Topoisomerase

by Rui Zhao, Lezi Hou, Weldu Tesfagaber, Linfei Song, Zhenjiang Zhang, Fang Li, Zhigao Bu and Dongming Zhao

Viruses 2025, 17(5), 681; https://doi.org/10.3390/v17050681 - 7 May 2025

Abstract

African Swine Fever Virus (ASFV) Topo II ATPase domain, resistant to conventional inhibitors (e.g., ICRF-187) due to M18/W19 steric clashes, was targeted via hierarchical virtual screening (Schrödinger) of the Chembridge library combined with MM/GBSA calculations. Five ligands (10012949, 40242484, 46712145, 15880207, and 33688815) [...] Read more.

African Swine Fever Virus (ASFV) Topo II ATPase domain, resistant to conventional inhibitors (e.g., ICRF-187) due to M18/W19 steric clashes, was targeted via hierarchical virtual screening (Schrödinger) of the Chembridge library combined with MM/GBSA calculations. Five ligands (10012949, 40242484, 46712145, 15880207, and 33688815) showed high affinity, with 46712145 adopting symmetrical π–π stacking, hydrogen bonds, and alkyl interactions to bypass steric hindrance. Molecular dynamics simulations (100 ns) revealed ligand-induced flexibility, evidenced by elevated RMSD/Rg values versus the free protein. DCCM analysis highlighted enhanced anti-correlated motions between GHKL motifs and sensor domains in chain B/C, suggesting stabilization of a non-catalytic conformation to inhibit ATP hydrolysis. Free energy landscape (FEL) analysis showed 46712145 occupying a broad, shallow energy basin, enabling conformational adaptability, contrasting the narrow deep well of the free protein. This study proposes a symmetric ligand design strategy and conformational capture mechanism to block ATPase activity. Compound 46712145 demonstrates stable binding and dynamic regulation, providing a novel lead scaffold for anti-ASFV drug development. These findings establish a structural framework for combating ASFV through targeted ATPase inhibition. Full article

(This article belongs to the Section Animal Viruses)

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18 pages, 2869 KiB

Open AccessHypothesis

A Model of Non-Homologous Recombination Mediated by HIV-1 Reverse Transcriptase Explaining Sequence Motif Duplications That Confer a Replication Fitness Advantage

by Arun Panchapakesan and Udaykumar Ranga

Viruses 2025, 17(5), 680; https://doi.org/10.3390/v17050680 - 7 May 2025

Abstract

The Reverse Transcriptase of the Human Immunodeficiency Virus (HIV) is distinguished by its high rate of homologous recombination. A less-studied consequence of this phenomenon is the increased occurrence of non-homologous recombination, which results in length polymorphism. While most of these genome-wide variations are [...] Read more.

The Reverse Transcriptase of the Human Immunodeficiency Virus (HIV) is distinguished by its high rate of homologous recombination. A less-studied consequence of this phenomenon is the increased occurrence of non-homologous recombination, which results in length polymorphism. While most of these genome-wide variations are sporadic, some provide a replication advantage to variant strains, such as those in the Long Terminal Repeat (LTR) and p6-Gag regions. By analyzing sequences from these two regions in the HIV-1 databases, we categorize all types of non-homologous recombination into four groups based on the presence or absence of two molecular features. Additionally, drawing on established models of homologous recombination, we propose a model that describes the process of sequence duplication. This model can also be applied to explain non-homologous recombination in different types of HIV and other viruses. Full article

(This article belongs to the Special Issue Regulation of HIV-1 Transcription and Latency, 2nd Edition)

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22 pages, 11006 KiB

Open AccessArticle

Capsid Structure of the Fish Pathogen Syngnathus Scovelli Chapparvovirus Offers a New Perspective on Parvovirus Structural Biology

by Judit J. Penzes and Jason T. Kaelber

Viruses 2025, 17(5), 679; https://doi.org/10.3390/v17050679 - 6 May 2025

Abstract

Chapparvoviruses (ChPVs) comprise a divergent lineage of the Parvoviridae ssDNA virus family and evolved to infect vertebrate animals independently from the Parvovirinae subfamily. Despite being pathogenic and widespread in environmental samples and metagenomic assemblies, their structural characterization has proven challenging. Here, we report [...] Read more.

Chapparvoviruses (ChPVs) comprise a divergent lineage of the Parvoviridae ssDNA virus family and evolved to infect vertebrate animals independently from the Parvovirinae subfamily. Despite being pathogenic and widespread in environmental samples and metagenomic assemblies, their structural characterization has proven challenging. Here, we report the first structural analysis of a ChPV, represented by the fish pathogen, Syngnathus scovelli chapparvovirus (SsChPV). We show through the SsChPV structure that the lineage harbors a surface morphology, subunit structure, and multimer interactions that are unique among parvoviruses. The SsChPV capsid evolved a threefold-related depression of α-helices that is analogous to the β-annulus pore of denso- and hamaparvoviruses and may play a role in monomer oligomerization during assembly. As interacting β-strands are absent from the twofold symmetry axis, the viral particle lacks the typical stability and resilience of parvovirus capsids. Although all parvoviruses thus far rely on the threading of large, flexible N-terminal domains to the capsid surface for their intracellular trafficking, our results show that ChPVs completely lack any such N-terminal sequences. This led to the subsequent degradation of their fivefold channel, the site of N-terminus externalization. These findings suggest that ChPVs harbor an infectious pathway that significantly deviates from the rest of the Parvoviridae. Full article

(This article belongs to the Section Animal Viruses)

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23 pages, 4705 KiB

Open AccessArticle

Genetic Diversity, Population Structure, and Cross-Border Dispersal Patterns of Tomato Leaf Curl Palampur Virus in South and West Asia

by Muhammad Naeem Sattar, Biju V. Chellappan, Sherif M. ElGanainy, Mustafa I. Almaghaslah, Sallah A. Al Hashedi and Adil A. Al-Shoaibi

Viruses 2025, 17(5), 678; https://doi.org/10.3390/v17050678 - 6 May 2025

Abstract

Tomato leaf curl Palampur virus (ToLCPalV) is an economically important bipartite begomovirus in the agro-ecological regions in south and western Asia. This study was designed to investigate the sequence variation dynamics, regional delineation, genetic diversity, population structure, and cross-border dispersal patterns of ToLCPalV. [...] Read more.

Tomato leaf curl Palampur virus (ToLCPalV) is an economically important bipartite begomovirus in the agro-ecological regions in south and western Asia. This study was designed to investigate the sequence variation dynamics, regional delineation, genetic diversity, population structure, and cross-border dispersal patterns of ToLCPalV. The research revealed clear geographical structuring, with distinct Indo–Pak subcontinent and Middle Eastern clades, but no host-specific differentiation. Genetic diversity analysis indicated higher diversity in the Indo–Pak subcontinent, particularly in the DNA-B component, suggesting an older, more diverse population of ToLCPalV prevailing in this region. Neutrality tests and selection pressure analyses revealed predominantly purifying selection, with limited positive selection observed in BV1 of DNA-B. The primary source of dispersal of ToLCPalV progenitor was estimated in Varnasi, India in 1955, from where the virus was spread. No recombination events were detected, suggesting that mutation and selection are the primary drivers of ToLCPalV evolution. Furthermore, a detailed SDT-based nucleotide sequence comparison analysis also identified two potential strains of ToLCPalV. This study elucidates the spatiotemporal dynamics and evolutionary history of ToLCPalV, revealing its cross-border spread and adaptive evolution. These findings contribute to a more comprehensive understanding of begomovirus epidemiology and provide valuable insights into ToLCPalV’s phylogeography and evolutionary dynamics. Full article

(This article belongs to the Special Issue Plant Virus Spillovers)

16 pages, 10955 KiB

Open AccessArticle

Characterizations of Newly Isolated Erwinia amylovora Loessnervirus-like Bacteriophages from Hungary

by Elene Lomadze, György Schneider, Szilvia Papp, Dominika Bali, Roberta Princz-Tóth and Tamás Kovács

Viruses 2025, 17(5), 677; https://doi.org/10.3390/v17050677 - 6 May 2025

Abstract

This study explores alternative methods to combat bacterial infections like fire blight caused by Erwinia amylovora (Ea) using bacteriophages as potential antimicrobial agents. Two lytic phages, Ea PF 7 and Ea PF 9, were isolated from apple samples and classified as Loessnervirus-like based [...] Read more.

This study explores alternative methods to combat bacterial infections like fire blight caused by Erwinia amylovora (Ea) using bacteriophages as potential antimicrobial agents. Two lytic phages, Ea PF 7 and Ea PF 9, were isolated from apple samples and classified as Loessnervirus-like based on their genomes. Both phages showed strong efficacy, lysing 95% of the tested 37 Ea strains. They inhibited bacterial growth for up to 10 h, even at low infection rates. The phages had a short latent period of 10 min and produced high burst sizes of 108 and 125 phage particles per infected cell. Stability tests revealed that both phages were stable at moderate temperatures (37–45 °C) and within a pH range of 4–10. However, their viability decreased at higher temperatures and extreme pH levels. Both phages exhibited notable desiccation tolerance and moderate resistance to UV-B radiation during UV testing. The phages were exposed to carefully controlled irradiation, considering factors like lamp type, radiation intensity, exposure time, and object distance. This method introduces a complex approach to research, ensuring repeatable and comparable results. These findings suggest that Ea PF 7 and Ea PF 9 hold promise as antimicrobial agents for therapeutic and biotechnological applications, potentially helping to combat antibiotic resistance in the future. Full article

(This article belongs to the Special Issue Recent Advances in Phage-Plant Interactions)

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20 pages, 2992 KiB

Open AccessArticle

Survey and Associated Risk Factors for the Presence of Ruminant Pestiviruses in Domestic Ovine and Caprine Populations from Kazakhstan

by Andrey V. Zhigailov, Yuliya V. Perfilyeva, Angelina A. Malysheva, Alena S. Cherusheva, Zhanna A. Berdygulova, Dinara A. Naizabayeva, Karina R. Ivanova, Saltanat A. Kuatbekova, Zhaniya M. Dosmagambet, Anzhelika V. Lushova, Sofiya A. Kan, Artyom V. Kuligin, Akerke O. Bissenbay, Moldir M. Kuatbek, Akzhigit S. Mashzhan, Nurshat Abdolla, Anna S. Nizkorodova, Elina R. Maltseva, Aralbek S. Rsaliyev, Yergali O. Abduraimov, Ainur A. Zhaksylykova, Aida M. Abdybekova, Seidigapbar M. Mamadaliyev, Yuriy A. Skiba and Yekaterina O. Ostapchuk Show full author list Hide full author list

Viruses 2025, 17(5), 676; https://doi.org/10.3390/v17050676 - 6 May 2025

Abstract

Pestiviruses, particularly bovine viral diarrhea virus (BVDV), cause significant economic losses worldwide. While cattle are the primary hosts for BVDV, sheep and goats can also be affected. This nationwide survey aimed to assess the prevalence, genetic characteristics, and risk factors associated with pestiviruses [...] Read more.

Pestiviruses, particularly bovine viral diarrhea virus (BVDV), cause significant economic losses worldwide. While cattle are the primary hosts for BVDV, sheep and goats can also be affected. This nationwide survey aimed to assess the prevalence, genetic characteristics, and risk factors associated with pestiviruses in sheep and goats in Kazakhstan. A one-off cross-sectional study was conducted to estimate the prevalence of pestiviruses in sheep and goats across 58 districts in 17 oblasts of Kazakhstan. A total of 2028 animals were examined using antibody ELISA, and RT-qPCR was performed on 2056 samples. Logistic regression models were used to identify potential risk factors linked to pestiviral infection. The overall prevalence of pestiviral infection in small ruminants was estimated to be 53.7% by ELISA and 2.5% by RT-qPCR. Regression analysis revealed that age, farm type, and geographic location were risk factors for pestiviral infections in small ruminants in Kazakhstan. Partial sequence analysis of the 5′-untranslated region confirmed the presence of BVDV2. Phylogenetic analysis revealed two distinct clusters of Kazakhstani BVDV2 strains, which were significantly different from known BVDV2 genotypes. No other ruminant pestiviruses were identified. The results highlight the importance of integrating small ruminants into BVDV infection control strategies to mitigate risks to livestock. Full article

(This article belongs to the Section Animal Viruses)

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16 pages, 3274 KiB

Open AccessArticle

Long-Term Dynamics of SARS-CoV-2 Variant-Specific Neutralizing Antibodies Following mRNA Vaccination and Infection

by Veronika Vaňová, Jana Náhliková, Martina Ličková, Monika Sláviková, Ivana Kajanová, Ľubomíra Lukáčiková, Miroslav Sabo, Žofia Rádiková, Silvia Pastoreková and Boris Klempa

Viruses 2025, 17(5), 675; https://doi.org/10.3390/v17050675 - 6 May 2025

Abstract

Understanding the long-term dynamics of SARS-CoV-2 neutralizing antibodies is critical for evaluating vaccine-induced protection and informing booster strategies. In this longitudinal study, we analyzed 114 serum samples from 19 individuals across six time points over a three-year period following mRNA vaccination (Comirnaty) and [...] Read more.

Understanding the long-term dynamics of SARS-CoV-2 neutralizing antibodies is critical for evaluating vaccine-induced protection and informing booster strategies. In this longitudinal study, we analyzed 114 serum samples from 19 individuals across six time points over a three-year period following mRNA vaccination (Comirnaty) and natural SARS-CoV-2 infection. Using pseudotype-based neutralization assays against nine SARS-CoV-2 variants, including major Omicron subvariants (BA.1–BA.5, BQ.1.1, XBB), and anti-S1 IgG ELISA, we observed that antibody levels peaked after the third vaccine dose and remained relatively stable two years later. Neutralization titers rose markedly after the second and third doses, with the highest neutralization observed at two years post-booster. Strong correlations were found between anti-S1 IgG levels and mean neutralization titers for pre-Omicron variants (r = 0.79–0.93; p < 0.05), but only moderate for Omicron subvariants (r ≈ 0.50–0.64). Notably, hybrid immunity (vaccination plus infection) resulted in higher neutralization titers at the final time point compared to vaccine-only participants. The lowest neutralization was observed against XBB, underscoring the immune evasiveness of emerging variants. These findings support the importance of booster vaccination and highlight the added durability of hybrid immunity in long-term protection. Full article

(This article belongs to the Special Issue SARS-CoV-2 Neutralizing Antibodies 3rd Edition)

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13 pages, 1104 KiB

Open AccessArticle

The Individual and Combined Entomopathogenic Activity of a Spodoptera frugiperda Multiple Nucleopolyhedrovirus and a Type I Spodoptera frugiperda Granulovirus on S. frugiperda Larvae

by Magali Ordóñez-García, Juan Carlos Bustillos-Rodríguez, José de Jesús Ornelas-Paz, Miguel Ángel Salas-Marina, Octavio Jhonathan Cambero-Campos, Carlos Horacio Acosta-Muñiz, David Ignacio Berlanga-Reyes and Claudio Rios-Velasco

Viruses 2025, 17(5), 674; https://doi.org/10.3390/v17050674 - 5 May 2025

Abstract

The bioinsecticidal activity of several doses of a Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV-CH-32; LD₁₀, LD₅₀, and LD₉₀) and a Type I Spodoptera frugiperda granulovirus (SfGV-CH13; LD₅₀ and LD₉₀), alone and in co-infection, was evaluated [...] Read more.

The bioinsecticidal activity of several doses of a Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV-CH-32; LD₁₀, LD₅₀, and LD₉₀) and a Type I Spodoptera frugiperda granulovirus (SfGV-CH13; LD₅₀ and LD₉₀), alone and in co-infection, was evaluated on S. frugiperda larvae. In the co-infection assays, one virus was applied at 0 h, and then the second virus was supplied at different times (0, 12, and 24 h) in order to test the effect of the co-infection time on the insecticidal activity of the viruses. The symptoms observed in the co-infected larvae depended on the viral dose supplied at 0 h. The larvae treated with the highest dose (LD₉₀) of SfMNPV-CH32 and co-infected with SfGV-CH13 at LD₅₀ showed symptoms of nucleopolyhedrovirus infection at 14 days post-infection. The larvae initially infected with the highest dose of SfGV-CH13 (LD₉₀) and subsequently co-infected with SfMNPV-CH32 (LD₅₀ and LD₁₀) showed infection symptoms characteristic of both viruses. The insecticidal activity of SfGV-CH13 and SfMNPV-CH32 alone or in combination depended on the viral doses and the time elapsed between the first and second inoculation. An antagonistic effect was observed for most of the treatments tested. A synergistic effect was observed only in treatment 10, where the larvae were first infected with SfMNPV-CH32 at a high dose (LD₉₀) and inoculated 24 h later with SfGV-CH13 (LD₅₀). Full article

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

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6 pages, 428 KiB

Open AccessCommunication

Return of the Biennial Circulation of Enterovirus D68 in Colorado Children in 2024 Following the Large 2022 Outbreak

by Hai Nguyen-Tran, Molly Butler, Dennis Simmons, Samuel R. Dominguez and Kevin Messacar

Viruses 2025, 17(5), 673; https://doi.org/10.3390/v17050673 - 5 May 2025

Abstract

Enterovirus D68 (EV-D68) caused large biennial cyclical outbreaks of respiratory disease and cases of acute flaccid myelitis from 2014 to 2018 in the USA. An anticipated outbreak did not occur in 2020, likely due to non-pharmaceutical interventions targeting the COVID-19 pandemic. A large [...] Read more.

Enterovirus D68 (EV-D68) caused large biennial cyclical outbreaks of respiratory disease and cases of acute flaccid myelitis from 2014 to 2018 in the USA. An anticipated outbreak did not occur in 2020, likely due to non-pharmaceutical interventions targeting the COVID-19 pandemic. A large respiratory disease outbreak occurred again in 2022, but uncertainty remained regarding if circulation of EV-D68 would return to the pre-pandemic patterns. We conducted prospective active surveillance of clinical respiratory specimens from Colorado children for EV-D68 in 2023 and 2024. A subset of residual specimens positive for rhinovirus/enterovirus (RV/EV) were tested for EV-D68 via a validated in-house EV-D68 reverse transcription–PCR assay. During epi weeks 18–44 in 2023, 525 residual specimens positive for RV/EV all tested negative for EV-D68. In 2024, during epi weeks 18–44, 10 (1.8%) of the 546 RV/EV-positive specimens were EV-D68-positive. The EV-D68-positive cases were predominantly young children (median age 4.8 years) receiving treatment with asthma medications. Following the 2022 EV-D68 outbreak, an anticipated outbreak did not occur in 2023. While EV-D68 was detected in 2024, the number of cases was not as significant as in prior outbreak years. Continued surveillance for EV-D68 will be important to understand the future dynamics of EV-D68 circulation and prepare for future outbreaks. Full article

(This article belongs to the Special Issue An Update on Enterovirus Research, 2nd Edition)

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16 pages, 1218 KiB

Open AccessArticle

Evaluating Population Normalization Methods Using Chemical Data for Wastewater-Based Epidemiology: Insights from a Site-Specific Case Study

by Marco Verani, Ileana Federigi, Alessandra Angori, Alessandra Pagani, Francesca Marvulli, Claudia Valentini, Nebiyu Tariku Atomsa, Beatrice Conte and Annalaura Carducci

Viruses 2025, 17(5), 672; https://doi.org/10.3390/v17050672 - 4 May 2025

Abstract

Wastewater-based epidemiology (WBE) has been widely employed to track the spread of human pathogens; however, correlating wastewater data with clinical surveillance remains challenging due to population variability and environmental factors affecting wastewater composition. This study evaluated different SARS-CoV-2 normalization methods, comparing static population [...] Read more.

Wastewater-based epidemiology (WBE) has been widely employed to track the spread of human pathogens; however, correlating wastewater data with clinical surveillance remains challenging due to population variability and environmental factors affecting wastewater composition. This study evaluated different SARS-CoV-2 normalization methods, comparing static population estimates with dynamic normalization based on common physicochemical parameters: chemical oxygen demand (COD), biochemical oxygen demand (BOD₅), and ammonia (NH₄-N). Wastewater samples were collected from four urban wastewater treatment plants (WWTPs) in northwestern Tuscany (Italy) from February 2021 to March 2023. The correlations between normalized viral loads and clinical COVID-19 cases were highest for static normalization (ρ = 0.405), followed closely by dynamic normalization using COD and BOD₅ (ρ = 0.378 each). Normalization based on NH₄-N was less effective. These findings suggest that chemical parameters, particularly COD and BOD₅, offer a valid alternative for viral normalization when population estimates or flow rate measurements are unavailable. These parameters provide a cost-effective and practical approach for improving WBE reliability, particularly in resource-limited settings. Our results reinforce the importance of normalization in WBE to enhance its representativeness and applicability for public health surveillance. Full article

(This article belongs to the Section General Virology)

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19 pages, 3675 KiB

Open AccessArticle

KRT6A Restricts Influenza A Virus Replication by Inhibiting the Nuclear Import and Assembly of Viral Ribonucleoprotein Complex

by Yu Chang, Zhibo Shan, Wenjun Shi, Qibing Li, Yihan Wang, Bo Wang, Guangwen Wang, Hualan Chen, Li Jiang and Chengjun Li

Viruses 2025, 17(5), 671; https://doi.org/10.3390/v17050671 - 4 May 2025

Abstract

The transcription and replication of the genome of influenza A virus (IAV) take place in the nucleus of infected cells, which is catalyzed by the viral ribonucleoprotein (vRNP) complex. The nuclear import of the vRNP complex and its component proteins is essential for [...] Read more.

The transcription and replication of the genome of influenza A virus (IAV) take place in the nucleus of infected cells, which is catalyzed by the viral ribonucleoprotein (vRNP) complex. The nuclear import of the vRNP complex and its component proteins is essential for the efficient replication of IAV and is therefore prone to be targeted by host restriction factors. Herein, we found that host cellular protein keratin 6A (KRT6A) is a negative regulator of IAV replication because siRNA-mediated knockdown of KRT6A expression increased the growth titers of IAV, whereas exogenous overexpression of KRT6A reduced viral yields. The nuclear import of incoming vRNP complexes and newly synthesized nucleoprotein (NP) was significantly impaired when KRT6A was overexpressed. Further studies showed that KRT6A interacts with the four vRNP complex proteins—polymerase basic protein 1 (PB1), polymerase basic protein 2 (PB2), polymerase acidic protein (PA), and NP. Notably, the interaction between KRT6A and vRNP complex proteins had no effect on the nuclear import of PB2 or the PB1-PA heterodimer but impaired the interaction between NP and the nuclear import adaptor importin α3, thereby inhibiting the nuclear import of incoming vRNP complexes and newly synthesized NP. Moreover, KRT6A was further shown to suppress the assembly of the vRNP complex and consequently reduce viral polymerase activity. Together, our data uncover a novel role of KRT6A in counteracting the nuclear import and functions of the vRNP complex, thereby restricting the replication of IAV. Full article

(This article belongs to the Section Animal Viruses)

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16 pages, 255 KiB

Open AccessArticle

Optimization and Validation of Universal Real-Time RT-PCR Assay to Detect Virulent Newcastle Disease Viruses

by Ellen Ruth Alexander Morris, Megan E. Schroeder, Phelue N. Anderson, Lisa J. Schroeder, Nicholas Monday, Gabriel Senties-Cue, Martin Ficken, Pamela J. Ferro, David L. Suarez and Kiril M. Dimitrov

Viruses 2025, 17(5), 670; https://doi.org/10.3390/v17050670 - 3 May 2025

Abstract

Newcastle disease, caused by virulent strains of avian paramyxovirus 1 (APMV-1), occurs globally and has significant social and economic impact. APMV-1 is a rapidly evolving RNA virus and is genetically divided into class I and class II with almost all virulent viruses being [...] Read more.

Newcastle disease, caused by virulent strains of avian paramyxovirus 1 (APMV-1), occurs globally and has significant social and economic impact. APMV-1 is a rapidly evolving RNA virus and is genetically divided into class I and class II with almost all virulent viruses being of class II. The considerable genetic diversity of the virus adds complexity to maintaining the high sensitivity and specificity of molecular detection assays. The current USDA’s fusion gene rRT-PCR assay was designed for class II APMV-1 isolates with an emphasis on early-2000s US strains. Assessment with globally circulating genotypes confirmed previously described lower sensitivity (sub-genotypes VII.1.1, VII.2) and identified absence of detection (genotype XIV). An additional forward primer and two probes were designed using a comprehensive complete fusion gene sequence database. The optimized multiplex assay detected genotype XIV and improved sensitivity for sub-genotypes VII.1.1 and VII.2, with maintained sensitivity for the remaining genotypes. No near-neighbors or APMV-1 of low virulence were detected. Using field and experimental clinical samples, both the specificity and sensitivity were determined to be 100%, compared to the current assay with 100% and 93%, respectively. The new assay identifies all known chicken virulent APMV-1 genotypes with the benefit of using an exogenous internal positive control, which monitors extraction efficiency and inhibitors. Full article

(This article belongs to the Special Issue Newcastle Disease and Other Avian Orthoavulaviruses 1)

22 pages, 17763 KiB

Open AccessArticle

Plasmid-Based Reverse Genetics System Enabling One-Step Generation of Genotype 3 Hepatitis E Virus

by Tominari Kobayashi, Takashi Nishiyama, Kentaro Yamada, Kazumoto Murata and Hiroaki Okamoto

Viruses 2025, 17(5), 669; https://doi.org/10.3390/v17050669 - 3 May 2025

Abstract

Hepatitis E virus (HEV) is a positive-sense, single-stranded RNA virus that poses a significant public health risk, yet its study is hindered by the complexity of conventional RNA-based reverse genetics systems. These systems require multiple steps, including genome cloning, in vitro transcription, and [...] Read more.

Hepatitis E virus (HEV) is a positive-sense, single-stranded RNA virus that poses a significant public health risk, yet its study is hindered by the complexity of conventional RNA-based reverse genetics systems. These systems require multiple steps, including genome cloning, in vitro transcription, and capping, making them labor-intensive and susceptible to RNA degradation. In this study, we developed a single-step, plasmid-based HEV expression system that enabled direct intracellular transcription of the full-length HEV genome under a cytomegalovirus immediate-early (CMV-IE) promoter. The viral genome was flanked by hammerhead (HH) and hepatitis delta virus (HDV) ribozymes to ensure precise self-cleavage and the generation of authentic 5′ and 3′ termini. This system successfully supported HEV genome replication, viral protein expression, and progeny virion production at levels comparable to those obtained using in vitro-transcribed, capped HEV RNA. Additionally, a genetic marker introduced into the plasmid construct was stably retained in progeny virions, demonstrating the feasibility of targeted genetic modifications. However, plasmid-derived HEV exhibited delayed replication kinetics, likely due to the absence of an immediate 5′ cap. Attempts to enhance capping efficiency through co-expression of the vaccinia virus capping enzyme failed to improve HEV replication, suggesting that alternative strategies, such as optimizing the promoter design for capping, may be required. This plasmid-based HEV reverse genetics system simplifies the study of HEV replication and pathogenesis and provides a versatile platform for the genetic engineering of the HEV genome. Full article

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

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54 pages, 9812 KiB

Open AccessReview

Australian Cool-Season Pulse Seed-Borne Virus Research: 2. Bean Yellow Mosaic Virus

by Roger A. C. Jones

Viruses 2025, 17(5), 668; https://doi.org/10.3390/v17050668 - 3 May 2025

Abstract

Here, research on seed-borne virus diseases of cool-season pulses caused by bean yellow mosaic virus (BYMV) in Australia’s grain cropping regions since the 1940s is reviewed. A historical approach is taken towards all past studies involving the main cool-season pulse crops grown, lupin, [...] Read more.

Here, research on seed-borne virus diseases of cool-season pulses caused by bean yellow mosaic virus (BYMV) in Australia’s grain cropping regions since the 1940s is reviewed. A historical approach is taken towards all past studies involving the main cool-season pulse crops grown, lupin, faba bean, field pea, lentil and chickpea, and the minor ones, narbon bean, vetches and Lathyrus species. The main emphasis adopted is on describing what these studies revealed concerning BYMV biology, epidemiology and management. The field and glasshouse experimentation that enabled the development of effective phytosanitary, cultural and host resistance control strategies, supported by many image illustrations from past investigations, is emphasized. This review commences by providing brief background information and describing past studies on BYMV symptom and sequence variants, and alternative BYMV hosts. Next, as the lupin/BYMV pathosystem has been investigated in much greater depth than any other cool season pulse/BYMV pathosystem combination in Australia, what past studies using it have found is covered considerable detail under a series of nine different sub-headings. Finally, what is known about the less thoroughly investigated cool-season pulse/BYMV pathosystems, especially those involving faba bean, field pea and lentil, is reviewed under seven different sub-headings. Recommendations are provided concerning future research priorities. Full article

(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)

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Graphical abstract

12 pages, 738 KiB

Open AccessArticle

Comprehensive Diagnosis of Viral Hepatitis in Spain: Bases for Implementation

by Joaquin Cabezas, Antonio Aguilera, Federico García, Raquel Domínguez-Hernández, Araceli Casado-Gómez, Nataly Espinoza-Cámac, Miguel Ángel Casado and Javier Crespo

Viruses 2025, 17(5), 667; https://doi.org/10.3390/v17050667 - 3 May 2025

Abstract

In 2022, scientific societies agreed on a document with recommendations for a comprehensive diagnosis of viral hepatitis (B, C, and D). The aim was to evaluate the situation in Spain regarding the comprehensive diagnosis of viral hepatitis in a single blood draw before [...] Read more.

In 2022, scientific societies agreed on a document with recommendations for a comprehensive diagnosis of viral hepatitis (B, C, and D). The aim was to evaluate the situation in Spain regarding the comprehensive diagnosis of viral hepatitis in a single blood draw before it is recommended. A panel of experts prepared a structured survey directed at hospitals (public or private with teaching accreditation) with ≥200 beds (sent 20 October 2022, closed 1 December 2022). The response rate was 61% (79/129; 52 hospitals with >500 beds). Among the participating hospitals, all could perform tests for HBsAg, anti-HCV, and HIV serology; 94% could perform PCR testing for HCV, 63% could test for anti-HDV, and 28% could test for HDV-RNA (67% [53/79] outsourced this testing). Point-of-care (POC) testing availability was low (24%), with 84% of these tests being supervised by the reference microbiological laboratory and the results being registered in the patients’ medical history. Ninety percent of the centers carried out the diagnosis in a single step (99% HCV, 70% HBV, 48% HDV, and 44% HBV-HDV). In addition, 77% used some communication strategy when an active infection was encountered (100% HCV, 49% HBV, and 31% HDV). Only 20% had an automated system for scheduling a specialist physician appointment. Most hospitals had the means for a comprehensive diagnosis of viral hepatitis in a single sample, but <50% could test for HBV/HDV. Alerts for continuity of care were available for HCV, but not HBV or HDV. POC device implementation is important for decentralized testing. Full article

(This article belongs to the Special Issue Advancing Hepatitis Elimination: HBV, HDV, and HCV)

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16 pages, 4518 KiB

Open AccessArticle

Impact of Vaccine-Elicited Anti-Spike IgG4 Antibodies on Fc-Effector Functions Against SARS-CoV-2

by Katrina Dionne, Alexandra Tauzin, Étienne Bélanger, Yann Desfossés, Mehdi Benlarbi, Ling Niu, Guillaume Beaudoin-Bussières, Halima Medjahed, Catherine Bourassa, Josée Perreault, Marzena Pazgier, Renée Bazin and Andrés Finzi

Viruses 2025, 17(5), 666; https://doi.org/10.3390/v17050666 - 3 May 2025

Abstract

mRNA vaccines have demonstrated considerable efficacy and safety against SARS-CoV-2, limiting the pandemic burden worldwide. The emergence of new variants of concern and the decline in neutralizing activity observed several weeks post-vaccination reinforced the call for repeated mRNA vaccination. We and others have [...] Read more.

mRNA vaccines have demonstrated considerable efficacy and safety against SARS-CoV-2, limiting the pandemic burden worldwide. The emergence of new variants of concern and the decline in neutralizing activity observed several weeks post-vaccination reinforced the call for repeated mRNA vaccination. We and others have shown that vaccine efficacy does not exclusively rely on antibody neutralizing activites; Fc-effector functions play an important role as well. However, it is well known that long-term exposure and repeated antigen stimulation elicit the IgG4 subclass of antibodies, which are inefficient at mediating Fc-effector functions. In this regard, recent studies highlighted concerns about IgG4 induction by mRNA vaccines. Here, we explored the impact of repeated mRNA vaccination on IgG4 induction and its impact on Fc-effector functions. We observed anti-Spike IgG4 elicitation after three doses of mRNA vaccine; the antibody levels further increased with additional doses. Vaccine-elicited IgG4 preferentially bound the ancestral D614G Spike. We also observed that Breakthrough Infection (BTI) after several doses of vaccine strongly increased IgG1 levels but had no impact on IgG4 levels, thereby improving Fc-effector functions. Finally, we observed that elderly donors vaccinated with Moderna mRNA vaccines elicited higher IgG4 levels and presented lower Fc-effector functions than donors vaccinated with the Pfizer mRNA vaccine. Altogether, our results highlight the importance of monitoring the IgG subclasses elicited by vaccination. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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16 pages, 2598 KiB

Open AccessArticle

Noncanonical Poly(A) Polymerase TENT4 Drives Expression of Subgenomic Hepatitis A Virus RNAs in Infected Cells

by You Li, Ankit Gupta, Brian N. Papas, David Aponte-Diaz, Jayden M. Harris, Ichiro Misumi, Jason K. Whitmire, Craig E. Cameron, Marcos Morgan and Stanley M. Lemon

Viruses 2025, 17(5), 665; https://doi.org/10.3390/v17050665 - 2 May 2025

Abstract

Both hepatitis B virus (HBV), an hepadnavirus with a DNA genome, and hepatitis A virus (HAV), a picornavirus, require the TRAMP-like host ZCCHC14-TENT4 complex for efficient replication. However, whereas HBV requires the nucleotidyltransferase activity of TENT4 to extend and stabilize the 3′ poly(A) [...] Read more.

Both hepatitis B virus (HBV), an hepadnavirus with a DNA genome, and hepatitis A virus (HAV), a picornavirus, require the TRAMP-like host ZCCHC14-TENT4 complex for efficient replication. However, whereas HBV requires the nucleotidyltransferase activity of TENT4 to extend and stabilize the 3′ poly(A) tails of mRNA transcribed from its genome, the role played by TENT4 in HAV replication is uncertain. HAV proteins are synthesized directly from its genomic RNA, which possesses a 3′ poly(A) tail, with its length and composition presumably maintained by 3D^pol-catalyzed RNA transcription during its replicative cycle. Using nanopore long-read sequencing of RNA from infected cells, we confirm here that the length of the HAV 3′ poly(A) tail is not altered by treating infected cells with RG7834, a small molecule TENT4 inhibitor with potent anti-HAV activity. Despite this, TENT4 catalytic activity is essential for HAV replication. Surprisingly, nanopore sequencing revealed a low abundance of HAV subgenomic RNAs (hsRNAs) that extend from the 5′ end of the genome to a site within the 5′ untranslated RNA (5′UTR) immediately downstream of a stem-loop to which the ZCCHC14-TENT4 complex is recruited. These hsRNAs are polyadenylated, and their abundance is sharply reduced by RG7834 treatment, implying they are likely products of TENT4. Similar subgenomic RNAs were not identified in poliovirus-infected cells. hsRNAs are present not only in HAV-infected cell culture but also in the liver of HAV-infected mice, where they represent 1–3% of all HAV transcripts, suggesting their physiological relevance. However, transfecting exogenous hsRNA into TENT4-depleted cells failed to rescue HAV replication, leaving the functional role of hsRNA unresolved. These findings reveal a novel picornaviral subgenomic RNA species while highlighting mechanistic differences in the manner in which HAV and HBV exploit the host ZCCHC4-TENT4 complex for their replication. Full article

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

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