Viruses

12 pages, 1316 KiB

Open AccessArticle

Retinal Epithelial Neutralization Assay Optimizes AAV Serotype Selection for Ocular Gene Therapy

by Yao Li, Yujia Chen, Nan Huo, Zuyuan Jia, He Huang, Zhenghao Zhao, Shipo Wu and Lihua Hou

Viruses 2025, 17(7), 988; https://doi.org/10.3390/v17070988 (registering DOI) - 15 Jul 2025

Abstract

Adeno-associated virus (AAV) vectors face a critical translational challenge in ocular gene therapy due to pre-existing neutralizing antibodies (NAbs) whose seroprevalence limits patient eligibility. Standard NAb detection using non-ocular cell models (Human Embryonic Kidney 293T) may inadequately predict retinal transduction inhibition due to [...] Read more.

Adeno-associated virus (AAV) vectors face a critical translational challenge in ocular gene therapy due to pre-existing neutralizing antibodies (NAbs) whose seroprevalence limits patient eligibility. Standard NAb detection using non-ocular cell models (Human Embryonic Kidney 293T) may inadequately predict retinal transduction inhibition due to cell type-related variations in receptor usage and immunogenicity. This study established parallel NAb detection platforms utilizing human retinal pigment epithelial (ARPE-19) cells and standard 293T cells to systematically evaluate clinical serum samples against ophthalmologically relevant AAV serotypes (2, 5, 8, 9) via luciferase reporter-based transduction inhibition assays. Comparative analysis demonstrated ARPE-19 exhibited 42–48% higher NAb titers against AAV5/9 compared to 293T cells, with distinct serotype-biased neutralization hierarchies observed between cellular models. Furthermore, female-derived sera exhibited significantly elevated NAbs against particular serotypes in the ARPE-19 system. Critically, inter-serotype cross-neutralization correlation patterns differed substantially between cellular platforms. These findings demonstrate that physiologically relevant retinal cellular models provide essential immunological profiling data, revealing NAb characteristics obscured in standard assays. Consequently, employing retinal cell-based platforms is crucial for optimizing AAV serotype selection, patient stratification, and predicting clinical outcomes in ocular gene therapy. Full article

(This article belongs to the Section General Virology)

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25 pages, 5162 KiB

Open AccessPerspective

The Emerging Role of Omics-Based Approaches in Plant Virology

by Viktoriya Samarskaya, Nadezhda Spechenkova, Natalia O. Kalinina, Andrew J. Love and Michael Taliansky

Viruses 2025, 17(7), 986; https://doi.org/10.3390/v17070986 (registering DOI) - 15 Jul 2025

Abstract

Virus infections in plants are a major threat to crop production and sustainable agriculture, which results in significant yield losses globally. The past decade has seen the development and deployment of sophisticated high-throughput omics technologies including genomics, transcriptomics, proteomics, and metabolomics, in order [...] Read more.

Virus infections in plants are a major threat to crop production and sustainable agriculture, which results in significant yield losses globally. The past decade has seen the development and deployment of sophisticated high-throughput omics technologies including genomics, transcriptomics, proteomics, and metabolomics, in order to try to understand the mechanisms underlying plant–virus interactions and implement strategies to ameliorate crop losses. In this review, we discuss the current state-of-the-art applications of such key omics techniques, their challenges, future, and combinatorial use (e.g., single cell and spatial omics coupled with super-resolution high-throughput imaging methods and artificial intelligence-based predictive models) to obtain new mechanistic insights into plant–virus interactions, which could be exploited for more effective plant disease management and monitoring. Full article

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

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22 pages, 498 KiB

Open AccessReview

The XEC Variant: Genomic Evolution, Immune Evasion, and Public Health Implications

by Alaa A. A. Aljabali, Kenneth Lundstrom, Altijana Hromić-Jahjefendić, Nawal Abd El-Baky, Debaleena Nawn, Sk. Sarif Hassan, Alberto Rubio-Casillas, Elrashdy M. Redwan and Vladimir N. Uversky

Viruses 2025, 17(7), 985; https://doi.org/10.3390/v17070985 (registering DOI) - 15 Jul 2025

Abstract

Narrative review synthesizes the most current literature on the SARS-CoV-2 XEC variant, focusing on its genomic evolution, immune evasion characteristics, epidemiological dynamics, and public health implications. To achieve this, we conducted a structured search of the literature of peer-reviewed articles, preprints, and official [...] Read more.

Narrative review synthesizes the most current literature on the SARS-CoV-2 XEC variant, focusing on its genomic evolution, immune evasion characteristics, epidemiological dynamics, and public health implications. To achieve this, we conducted a structured search of the literature of peer-reviewed articles, preprints, and official surveillance data from 2023 to early 2025, prioritizing virological, clinical, and immunological reports related to XEC and its parent lineages. Defined by the distinctive spike protein mutations, T22N and Q493E, XEC exhibits modest reductions in neutralization in vitro, although current evidence suggests that mRNA booster vaccines, including those targeting JN.1 and KP.2, retain cross-protective efficacy against symptomatic and severe disease. The XEC strain of SARS-CoV-2 has drawn particular attention due to its increasing prevalence in multiple regions and its potential to displace other Omicron subvariants, although direct evidence of enhanced replicative fitness is currently lacking. Preliminary analyses also indicated that glycosylation changes at the N-terminal domain enhance infectivity and immunological evasion, which is expected to underpin the increasing prevalence of XEC. The XEC variant, while still emerging, is marked by a unique recombination pattern and a set of spike protein mutations (T22N and Q493E) that collectively demonstrate increased immune evasion potential and epidemiological expansion across Europe and North America. Current evidence does not conclusively associate XEC with greater disease severity, although additional research is required to determine its clinical relevance. Key knowledge gaps include the precise role of recombination events in XEC evolution and the duration of cross-protective T-cell responses. New research priorities include genomic surveillance in undersampled regions, updated vaccine formulations against novel spike epitopes, and long-term longitudinal studies to monitor post-acute sequelae. These efforts can be augmented by computational modeling and the One Health approach, which combines human and veterinary sciences. Recent computational findings (GISAID, 2024) point to the potential of XEC for further mutations in under-surveilled reservoirs, enhancing containment challenges and risks. Addressing the potential risks associated with the XEC variant is expected to benefit from interdisciplinary coordination, particularly in regions where genomic surveillance indicates a measurable increase in prevalence. Full article

(This article belongs to the Special Issue Translational Research in Virology)

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21 pages, 4817 KiB

Open AccessReview

Parvovirus RNA Processing: Compact Genomic Organization and Unique Alternative mRNA Processing Mechanisms

by Lisa K. Uhl and Olufemi O. Fasina

Viruses 2025, 17(7), 984; https://doi.org/10.3390/v17070984 (registering DOI) - 15 Jul 2025

Abstract

Parvoviruses have compact genomic organizations with overlapping open reading frames and thus utilize alternative RNA processing strategies, alternative splicing, alternative polyadenylation, and alternative translation mechanisms to generate a range of diverse proteins encoded within their genome. This comprehensive review provides an update on [...] Read more.

Parvoviruses have compact genomic organizations with overlapping open reading frames and thus utilize alternative RNA processing strategies, alternative splicing, alternative polyadenylation, and alternative translation mechanisms to generate a range of diverse proteins encoded within their genome. This comprehensive review provides an update on recent insights into the diverse mRNA processing mechanisms utilized by members of the Parvoviridae family, with emphasis on Bocaparvoviruses and Dependoparvoviruses to expand their protein repertoire and maintain their replicative advantage in infected host cells. It highlights the role of Bocaparvovirus ancillary nonstructural protein NP1; the first parvovirus protein involved in mRNA processing, specifically alternative splicing and alternative polyadenylation. Full article

(This article belongs to the Collection Parvoviridae)

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16 pages, 604 KiB

Open AccessReview

An Update on RNA Virus Discovery: Current Challenges and Future Perspectives

by Humberto Debat and Nicolas Bejerman

Viruses 2025, 17(7), 983; https://doi.org/10.3390/v17070983 (registering DOI) - 15 Jul 2025

Abstract

The relentless emergence of RNA viruses poses a perpetual threat to global public health, necessitating continuous efforts in surveillance, discovery, and understanding of these pathogens. This review provides a comprehensive update on recent advancements in RNA virus discovery, highlighting breakthroughs in technology and [...] Read more.

The relentless emergence of RNA viruses poses a perpetual threat to global public health, necessitating continuous efforts in surveillance, discovery, and understanding of these pathogens. This review provides a comprehensive update on recent advancements in RNA virus discovery, highlighting breakthroughs in technology and methodologies that have significantly enhanced our ability to identify novel viruses across diverse host organisms. We explore the expanding landscape of viral diversity, emphasizing the discovery of previously unknown viral families and the role of zoonotic transmissions in shaping the viral ecosystem. Additionally, we discuss the potential implications of RNA virus discovery on disease emergence and pandemic preparedness. Despite remarkable progress, current challenges in sample collection, data interpretation, and the characterization of newly identified viruses persist. Our ability to anticipate and respond to emerging respiratory threats relies on virus discovery as a cornerstone for understanding RNA virus evolution. We address these challenges and propose future directions for research, emphasizing the integration of multi-omic approaches, advanced computational tools, and international collaboration to overcome barriers in the field. This comprehensive overview aims to guide researchers, policymakers, and public health professionals in navigating the intricate landscape of RNA virus discovery, fostering a proactive and collaborative approach to anticipate and mitigate emerging viral threats. Full article

(This article belongs to the Special Issue Evolutionary Challenges of RNA Viruses: Insights from SARS-CoV-2 Variants and Emerging Respiratory Diseases)

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15 pages, 1884 KiB

Open AccessArticle

Adrenomedullin Therapy for Moderate-to-Severe COVID-19 Pneumonia: Double-Blind Placebo-Controlled Phase 2a Trial

by Toshihiro Kita, Norio Ohmagari, Sho Saito, Hiroshi Mukae, Takahiro Takazono, Taka-Aki Nakada, Tadanaga Shimada, Yuji Hirai, Yuichiro Shindo, Kosaku Komiya, Atsushi Saito, Masaya Yamato, Koichiro Homma, Masaki Okamoto, Yoshihiro Yamamoto, Yoshikazu Mutoh, Chihiro Hasegawa, Nobuaki Mori, Fukumi Nakamura-Uchiyama, Mitsuru Honda, Keisuke Tomii, Hiroshi Ishii, Ichiro Takajo, Koji Watanabe and Kazuo Kitamura Show full author list Hide full author list

Viruses 2025, 17(7), 982; https://doi.org/10.3390/v17070982 (registering DOI) - 14 Jul 2025

Abstract

Adrenomedullin (AM) is a bioactive peptide that is strongly induced during severe inflammation, including pneumonia and sepsis, and serves as an organ-protective factor. The plasma concentration of AM is markedly increased in the novel coronavirus disease COVID-19 and is closely related to the [...] Read more.

Adrenomedullin (AM) is a bioactive peptide that is strongly induced during severe inflammation, including pneumonia and sepsis, and serves as an organ-protective factor. The plasma concentration of AM is markedly increased in the novel coronavirus disease COVID-19 and is closely related to the severity of the disease and prognosis of patients. We performed two investigator-initiated trials to evaluate the efficacy and safety of AM in patients with moderate-to-severe COVID-19. This multicenter, double-blind, placebo-controlled phase-2a trial evaluated COVID-19 patients with severe (n = 33) and moderate (n = 31) pneumonia in Japan. Patients were randomly assigned to receive either 15 ng/kg/min AM or placebo. The primary endpoint was the duration of mechanical ventilation (MV) for severe pneumonia and oxygen support for moderate pneumonia. The main secondary endpoint was clinical status up to 30 days after the intervention. No differences in primary or secondary endpoints were observed between the AM and placebo groups in patients with severe or moderate pneumonia. In the severe pneumonia group, three patients in the placebo group died due to respiratory failure, and one patient in the AM group died due to respiratory failure. The respiratory function test at 30 days in the moderate pneumonia group tended to be better than that in the AM group and approached significance (p = 0.073). Although mild adverse events caused by the vasodilatory effects of AM were noted, the safety of AM for treating pneumonia was confirmed. In these trials, we did not observe a definitive efficacy of AM in moderate to severe pneumonia. Alternative strategies for the treatment of AM in pneumonia require further research. Full article

(This article belongs to the Section Coronaviruses)

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21 pages, 4582 KiB

Open AccessArticle

Modeling the Complete Dynamics of the SARS-CoV-2 Pandemic of Germany and Its Federal States Using Multiple Levels of Data

by Yuri Kheifetz, Holger Kirsten, Andreas Schuppert and Markus Scholz

Viruses 2025, 17(7), 981; https://doi.org/10.3390/v17070981 (registering DOI) - 14 Jul 2025

Abstract

Background/Objectives: Epidemiological modeling is a vital tool for managing pandemics, including SARS-CoV-2. Advances in the understanding of epidemiological dynamics and access to new data sources necessitate ongoing adjustments to modeling techniques. In this study, we present a significantly expanded and updated version [...] Read more.

Background/Objectives: Epidemiological modeling is a vital tool for managing pandemics, including SARS-CoV-2. Advances in the understanding of epidemiological dynamics and access to new data sources necessitate ongoing adjustments to modeling techniques. In this study, we present a significantly expanded and updated version of our previous SARS-CoV-2 model formulated as input–output non-linear dynamical systems (IO-NLDS). Methods: This updated framework incorporates age-dependent contact patterns, immune waning, and new data sources, including seropositivity studies, hospital dynamics, variant trends, the effects of non-pharmaceutical interventions, and the dynamics of vaccination campaigns. Results: We analyze the dynamics of various datasets spanning the entire pandemic in Germany and its 16 federal states using this model. This analysis enables us to explore the regional heterogeneity of model parameters across Germany for the first time. We enhance our estimation methodology by introducing constraints on parameter variation among federal states to achieve this. This enables us to reliably estimate thousands of parameters based on hundreds of thousands of data points. Conclusions: Our approach is adaptable to other epidemic scenarios and even different domains, contributing to broader pandemic preparedness efforts. Full article

(This article belongs to the Special Issue Multiscale Modeling and Forecasting of COVID-19 and Respiratory Virus Dynamics)

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20 pages, 3297 KiB

Open AccessArticle

Streptococcus equi subsp. zooepidemicus Supernatant Containing Streptolysin S Alters the Equine Nasal and Vaginal Mucosa, Modulating Equine Herpesvirus 1, 3 and 4 Infections

by Eslam Mohamed, Jolien Van Cleemput, Burak Şahin, Wim Van den Broeck, Filip Boyen and Hans Nauwynck

Viruses 2025, 17(7), 980; https://doi.org/10.3390/v17070980 (registering DOI) - 14 Jul 2025

Abstract

The equine respiratory and reproductive tract microbiomes are complex and subject to constant fluctuations. Among the microbial inhabitants, Streptococcus equi subsp. zooepidemicus (SEZ) is recognized as the dominant bacterium. It is an opportunistic pathogen that may occasionally lead to various types of infections. [...] Read more.

The equine respiratory and reproductive tract microbiomes are complex and subject to constant fluctuations. Among the microbial inhabitants, Streptococcus equi subsp. zooepidemicus (SEZ) is recognized as the dominant bacterium. It is an opportunistic pathogen that may occasionally lead to various types of infections. A key virulence factor of SEZ is the streptolysin S (SLS) toxin, which is responsible for the characteristic β-hemolysis on blood agar and tissue damage. Viruses and bacteria may interact and aggravate lesions and disease. This study aimed to evaluate the impact of an SLS-containing supernatant from SEZ on the nasal and vaginal mucosa and the subsequent replication of equine herpesviruses. The SLS-containing supernatant was prepared, and three 10-fold dilutions (optical density “OD” 10⁻², 10⁻³, 10⁻⁴) were applied to equine nasal and vaginal explants. Untreated and EGTA-treated explants served as controls. Epithelial integrity was assessed by measuring the thickness and intercellular spaces. Nasal explants were inoculated with EHV-1 and EHV-4, while vaginal explants received EHV-1 and EHV-3. Viral replication was estimated via immunofluorescence staining and confocal microscopy. SLS-containing supernatants 10⁻² and 10⁻³ compromised epithelial integrity. Viral replication increased in explants treated with SLS 10⁻³, demonstrating SLS’s damaging effects on the epithelium, facilitating equine herpesvirus replication. Full article

(This article belongs to the Section Animal Viruses)

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17 pages, 2042 KiB

Open AccessArticle

Comprehensive Virome Profiling of Apple Mosaic Disease-Affected Trees in Iran Using RT-PCR and Next-Generation Sequencing

by Anahita Hamedi, Farshad Rakhshandehroo, Mohammad Reza Safarnejad, Gholamreza Salehi Jouzani, Amani Ben Slimen and Toufic Elbeaino

Viruses 2025, 17(7), 979; https://doi.org/10.3390/v17070979 (registering DOI) - 13 Jul 2025

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Abstract

Apples (Malus domestica), one of Iran’s oldest cultivated fruit crops, hold considerable economic importance. In this study, 170 apple leaf samples representing various commercial cultivars were collected across the country. RT-PCR screening targeted five common apple-infecting viruses and two viroids: apple [...] Read more.

Apples (Malus domestica), one of Iran’s oldest cultivated fruit crops, hold considerable economic importance. In this study, 170 apple leaf samples representing various commercial cultivars were collected across the country. RT-PCR screening targeted five common apple-infecting viruses and two viroids: apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), apple stem grooving virus (ASGV), apple green crinkle-associated virus (AGCaV), apple mosaic virus (ApMV), apple scar skin viroid (ASSVd), and hop stunt viroid (HSVd). To identify additional or novel agents, 40 RT-PCR-negative samples were pooled into two composite groups and analyzed using next-generation sequencing (NGS). NGS was also performed on individual samples with mixed infections to retrieve full genomes. RT-PCR confirmed the presence of ACLSV, ASPV, ASGV, AGCaV, ApMV, and HSVd. NGS further revealed three additional pathogens: citrus concave gum-associated virus (CCGaV), apple hammerhead viroid (AHVd), and apricot vein clearing-associated virus (AVCaV), which were subsequently detected across the collection by RT-PCR. AGCaV was most prevalent (47.6%), followed by ACLSV (45.8%), HSVd (27.6%), AVCaV (20.5%), ASGV (17%), AHVd (15.2%), ASPV (14.1%), CCGaV (4.7%), and ApMV (3.5%). Mixed infections occurred in 67% of samples. Phylogenetic analysis based on CP genes (ACLSV, ASGV, AGCaV) and full genomes (AVCaV, AHVd) clustered Iranian isolates together, suggesting a common origin. This is the first report in Iran of AGCaV, CCGaV, ApMV, and AVCaV in apple, and notably, the first global report of AVCaV in a non-Prunus host. The findings provide the first comprehensive assessment of the sanitary status of apple trees in Iran. Full article

(This article belongs to the Special Issue Viral Diseases of Major Crops)

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17 pages, 5856 KiB

Open AccessArticle

Characterization of Gene Expression Suppression by Bovine Coronavirus Non-Structural Protein 1

by Takehiro Ohkami, Ichika Kitashin, Riko Kawashima, Aimi Yoshida, Taizo Saito, Yasuhiro Takashima, Wataru Kamitani and Keisuke Nakagawa

Viruses 2025, 17(7), 978; https://doi.org/10.3390/v17070978 (registering DOI) - 13 Jul 2025

Viewed by 87

Abstract

Coronavirus non-structural protein 1 (nsp1) is a pathogenic determinant of Betacoronaviruses. Previous studies demonstrated that the nsp1 of various coronaviruses induces host shutoff through a variety of mechanisms; however, there is little information on the function of bovine coronavirus (BCoV) nsp1. We [...] Read more.

Coronavirus non-structural protein 1 (nsp1) is a pathogenic determinant of Betacoronaviruses. Previous studies demonstrated that the nsp1 of various coronaviruses induces host shutoff through a variety of mechanisms; however, there is little information on the function of bovine coronavirus (BCoV) nsp1. We aimed to characterize the host gene expression suppression function of BCoV nsp1. We first confirmed that the expression of BCoV nsp1 in MAC-T cells, a bovine mammary epithelial cell line, suppressed host and reporter gene expression. Subsequently, lysine and phenylalanine at amino acid positions 232 and 233, respectively, were identified as key residues required for this suppressive effect. Expression levels of housekeeping genes are comparable in cells expressing wild-type BCoV nsp1 and a mutant with alanine substitutions at positions 232 and 233 (BCoV nsp1-KF). Wild-type BCoV nsp1 localized to both the cytoplasm and nucleus; however, BCoV nsp1-KF exhibited prominent nuclear accumulation with dot-like structures. Using confocal microscopy and co-sedimentation analysis, we identified an association between wild-type BCoV nsp1, but not BCoV nsp1-KF, and ribosomes, suggesting that ribosome binding is required for BCoV nsp1-mediated suppression of host gene expression. This is the first study of the characterization of host gene expression suppression by BCoV nsp1. 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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15 pages, 2000 KiB

Open AccessArticle

Residue 365 in Hemagglutinin–Neuraminidase Is a Key Thermostable Determinant of Genotype VI.2.1.1.2.2 Newcastle Disease Virus

by Tao Di, Ran Zhao, Qiankai Shi, Fangfang Wang, Zongxi Han, Huixin Li, Yuhao Shao, Junfeng Sun and Shengwang Liu

Viruses 2025, 17(7), 977; https://doi.org/10.3390/v17070977 (registering DOI) - 13 Jul 2025

Viewed by 148

Abstract

Newcastle disease virus (NDV) genotype VI from pigeon origin is an important causative agent for serious disease in pigeons. Although the biological characteristics of genotype VI NDV have been extensively studied, the understanding of the thermostability of this genotype is still incomplete. In [...] Read more.

Newcastle disease virus (NDV) genotype VI from pigeon origin is an important causative agent for serious disease in pigeons. Although the biological characteristics of genotype VI NDV have been extensively studied, the understanding of the thermostability of this genotype is still incomplete. In this study, an NDV strain, designated P0506, was isolated from a diseased pigeon in China and classified as genotype VI. Phylogenetic analysis on the basis of the Fusion gene coding sequence indicated that P0506 belonged to sub-genotype VI.2.1.1.2.2 of class II. The thermostability may be a universal characteristic of genotype VI NDV. Thus, the thermostability of two strains, including P0506 identified in this study and P0713 identified previously, belonging to VI.2.1.1.2.2, and another previously isolated strain, P0813, in VI.2.1.1.2.1, was investigated. It was indicated that all three viruses presented resistance to heat treatment, but P0713 was more robust than P0813 and P0506. By constructing a series of HN protein mutants, amino acid residues at both residues 365 and 497 in HN protein were found to be involved in the heat resistance. Furthermore, the effects of residues 365 and 497 in HN protein on the thermostability of the virus were further evaluated by using recombinant viruses generated by the reverse genetic system. Our results showed that residue at position 365 in HN protein was the key thermostable determinant of sub-genotype VI.2.1.1.2.2 NDV. These findings will help us better understand the thermostable mechanism of NDV and serve as a foundation for the further development of novel thermostable vaccines. Full article

(This article belongs to the Special Issue Avian Respiratory Viruses, 4th Edition)

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13 pages, 1422 KiB

Open AccessBrief Report

Detection of Lineage IV Peste Des Petits Ruminants Virus by RT-qPCR Assay via Targeting the Hemagglutinin Gene

by Jiao Xu, Qinghua Wang, Jiarong Yu, Yingli Wang, Huicong Li, Lin Li, Jingyue Bao and Zhiliang Wang

Viruses 2025, 17(7), 976; https://doi.org/10.3390/v17070976 (registering DOI) - 12 Jul 2025

Viewed by 163

Abstract

Peste des petits ruminants virus (PPRV) has been classified into four lineages based on the nucleocapsid and fusion genes, with lineage IV strains being the most widely distributed. In Africa, recent epidemiological data revealed that PPRV lineage IV is increasingly displacing other lineages [...] Read more.

Peste des petits ruminants virus (PPRV) has been classified into four lineages based on the nucleocapsid and fusion genes, with lineage IV strains being the most widely distributed. In Africa, recent epidemiological data revealed that PPRV lineage IV is increasingly displacing other lineages in prevalence, suggesting a competitive advantage in viral transmission and adaptability. Moreover, a lineage IV strain was the only confirmed strain in Europe and Asia. In this study, a one-step Taqman quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) assay for lineage IV PPRV was established by targeting the hemagglutinin (H) gene. The results indicated that this method could detect approximately six copies of PPRV RNA, indicating high sensitivity. No cross-reactions with related viruses or other lineages of PPRV were observed. The results of a repeatability test indicated that the coefficient of variation values were low in both the inter-assay and intra-assay experimental groups. Detection of field samples indicated that all positive samples could be detected successfully using the developed method. This RT-qPCR assay provides a valuable tool to facilitate targeted surveillance and rapid differential diagnosis in regions with active circulation of PPRV lineage IV, enabling timely epidemiological investigations and strain-specific identification. Full article

(This article belongs to the Special Issue Early Diagnosis and Surveillance of Transboundary and Emerging Viral Diseases of Animals, 2nd Edition)

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36 pages, 4483 KiB

Open AccessReview

A Beautiful Bind: Phage Display and the Search for Cell-Selective Peptides

by Babak Bakhshinejad and Saeedeh Ghiasvand

Viruses 2025, 17(7), 975; https://doi.org/10.3390/v17070975 (registering DOI) - 12 Jul 2025

Viewed by 110

Abstract

Phage display has advanced the discovery of peptides that selectively bind to a wide variety of cell surface molecules, offering new modalities to modulate disease-related protein–protein interactions (PPIs). These cell-binding peptides occupy a unique pharmaceutical space between small molecules and large biologics, and [...] Read more.

Phage display has advanced the discovery of peptides that selectively bind to a wide variety of cell surface molecules, offering new modalities to modulate disease-related protein–protein interactions (PPIs). These cell-binding peptides occupy a unique pharmaceutical space between small molecules and large biologics, and their growing popularity has opened up new avenues for targeting cell surface proteins that were previously considered undruggable. This work provides an overview of methods for identifying cell-selective peptides using phage display combinatorial libraries, covering in vitro, ex vivo, and in vivo biopanning approaches. It addresses key considerations in library design, including the peptide conformation (linear vs. cyclic) and length, and highlights examples of clinically approved peptides developed through phage display. It also discusses the on-phage chemical cyclization of peptides to overcome the limitations of genetically encoded disulfide bridges and emphasizes advances in combining next-generation sequencing (NGS) with phage display to improve peptide selection and analysis workflows. Furthermore, due to the often suboptimal binding affinity of peptides identified in phage display selections, this article discusses affinity maturation techniques, including random mutagenesis and rational design through structure–activity relationship (SAR) studies to optimize initial peptide candidates. By integrating these developments, this review outlines practical strategies and future directions for harnessing phage display in targeting challenging cell surface proteins. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 3.0)

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14 pages, 1041 KiB

Open AccessReview

Surface Gene Mutations of Hepatitis B Virus and Related Pathogenic Mechanisms: A Narrative Review

by Tingxi Yan, Yusheng Zhang, Huifang Zhou, Ning Jiang, Xiaotong Wang, Wei Yan and Jianhua Yin

Viruses 2025, 17(7), 974; https://doi.org/10.3390/v17070974 (registering DOI) - 12 Jul 2025

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Abstract

Liver cancer has high incidence and mortality rates worldwide, with hepatocellular carcinoma (HCC) being the main histological subtype, accounting for 90% of primary liver cancers. The high mutation rate of viruses combined with endoplasmic reticulum stress may lead to the occurrence of cancer. [...] Read more.

Liver cancer has high incidence and mortality rates worldwide, with hepatocellular carcinoma (HCC) being the main histological subtype, accounting for 90% of primary liver cancers. The high mutation rate of viruses combined with endoplasmic reticulum stress may lead to the occurrence of cancer. Hepatitis B virus (HBV) infection is one of the most important pathogenic factors of HCC. The carcinogenic mechanisms of HBV have been widely studied. Among these mechanisms, immune escape and vaccine escape caused by mutations in the HBV S gene have been reported in numerous studies of patients with chronic hepatitis B. In addition, pre-S1/S2 mutations and surface protein truncation mutations may activate multiple signaling pathways. This activation leads to the abnormal proliferation and differentiation of hepatocytes, thereby contributing to the development of HCC. This review aims to integrate the existing literature, summarize the common mutations in the HBV S gene region, and explore the related pathogenic mechanisms. Full article

(This article belongs to the Special Issue Hepatitis B Surface Antigen: A Pivotal Role in the Virus–Host Interactions)

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9 pages, 520 KiB

Open AccessArticle

The Unprotected: Measles Seroprevalence in Children During the First Two Years of Life

by Sophie Rettenbacher-Riefler, Ina Holle and Mareike Wollenweber

Viruses 2025, 17(7), 973; https://doi.org/10.3390/v17070973 - 11 Jul 2025

Viewed by 185

Abstract

Young children are particularly vulnerable to measles infections. Investigating the gap between the waning of maternal antibodies and onset of vaccination-induced immunity via seroprevalence studies can be hampered by recruiting enough young-aged participants. We present measles IgG-antibody results from 2148 patients aged 0 [...] Read more.

Young children are particularly vulnerable to measles infections. Investigating the gap between the waning of maternal antibodies and onset of vaccination-induced immunity via seroprevalence studies can be hampered by recruiting enough young-aged participants. We present measles IgG-antibody results from 2148 patients aged 0 to 2 years, who were hospitalized with acute aseptic meningitis or encephalitis in Lower Saxony or Bremen. Measles serology was performed for differential diagnostics clarification of neurotropic pathogens, during syndromic surveillance between 2006 and 2024. At birth, 79% of children presented with measles IgG-antibodies, but only 30% of three-month-old patients and 11% of five-month-olds. From 0 to 10 months, seropositivity declined monthly by 8%. Over 95% of children aged six to 11 months were unprotected. From 11 months onwards, measles seroprevalence increased, reaching 80–90% towards the end of the second year of life. Our results indicate an absence of maternal measles IgG antibodies after nine months of age and that vaccination starts around 11 months of age; however, not all children had received vaccination by their second birthday. These findings confirm the current recommendation to advance first measles vaccination to nine months in high-exposure settings and support efforts to increase vaccination rates in small children and young adults. Full article

(This article belongs to the Special Issue Measles, Mumps, and Rubella)

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25 pages, 3506 KiB

Open AccessArticle

Repurposing of Some Nucleoside Analogs Targeting Some Key Proteins of the Avian H5N1 Clade 2.3.4.4b to Combat the Circulating HPAI in Birds: An In Silico Approach

by Mohd Yasir Khan, Abid Ullah Shah, Nithyadevi Duraisamy, Mohammed Cherkaoui and Maged Gomaa Hemida

Viruses 2025, 17(7), 972; https://doi.org/10.3390/v17070972 - 10 Jul 2025

Viewed by 207

Abstract

(1) Background: The highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b is an emerging threat that poses a great risk to the poultry industry. A few human cases have been linked to the infection with this clade in many parts of the world, [...] Read more.

(1) Background: The highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b is an emerging threat that poses a great risk to the poultry industry. A few human cases have been linked to the infection with this clade in many parts of the world, including the USA. Unfortunately, there are no specific vaccines or antiviral drugs that could help prevent and treat the infection caused by this virus in birds. Our major objective is to identify/repurpose some (novel/known) antiviral compounds that may inhibit viral replication by targeting some key viral proteins. (2) Methods: We used state-of-the-art machine learning tools such as molecular docking and MD-simulation methods from Biovia Discovery Studio (v24.1.0.321712). The key target proteins such as hemagglutinin (HA), neuraminidase (NA), Matrix-2 protein (M2), and the cap-binding domain of PB2 (PB2/CBD) homology models were validated through structural assessment via DOPE scores, Ramachandran plots, and Verify-3D metrics, ensuring reliable structural representations, confirming their reliability for subsequent in silico approaches. These approaches include molecular docking followed by molecular dynamics simulation for 50 nanoseconds (ns), highlighting the structural stability and compactness of the docked complexes. (3) Results: Molecular docking revealed strong binding affinities for both sofosbuvir and GS441524, particularly with the NA and PB2/CBD protein targets. Among them, GS441524 exhibited superior interaction scores and a greater number of hydrogen bonds with key functional residues of NA and PB2/CBD. The MM-GBSA binding free energy calculations further supported these findings, as GS441524 displayed more favorable binding energies compared to several known standard inhibitors, including F0045S for HA, Zanamivir for NA, Rimantadine and Amantadine for M2, and PB2-39 for PB2/CBD. Additionally, 50 ns molecular dynamics simulations highlighted the structural stability and compactness of the GS441524-PB2/CBD complex, further supporting its potential as a promising antiviral candidate. Furthermore, hydrogen bond monitor analysis over the 50 ns simulation confirmed persistent and specific interactions between the ligand and proteins, suggesting that GS441524 may effectively inhibit the NA, and PB2/CBD might potentially disrupt PB2-mediated RNA synthesis. (4) Conclusions: Our findings are consistent with previous evidence supporting the antiviral activity of certain nucleoside analog inhibitors, including GS441524, against various coronaviruses. These results further support the potential repurposing of GS441524 as a promising therapeutic candidate against H5N1 avian influenza clade 2.3.4.4b. However, further functional studies are required to validate these in silico predictions and support the inhibitory action of GS441524 against the targeted proteins of H5N1, specifically clade 2.3.4.4b. Full article

(This article belongs to the Special Issue Interplay Between Influenza Virus and Host Factors)

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42 pages, 6467 KiB

Open AccessReview

Marine Bacteriophages as Next-Generation Therapeutics: Insights into Antimicrobial Potential and Application

by Riza Jane S. Banicod, Aqib Javaid, Nazia Tabassum, Du-Min Jo, Md. Imtaiyaz Hassan, Young-Mog Kim and Fazlurrahman Khan

Viruses 2025, 17(7), 971; https://doi.org/10.3390/v17070971 - 10 Jul 2025

Viewed by 358

Abstract

Microbial infections are an escalating global health threat, driven by the alarming rise of antimicrobial resistance (AMR), which has made many conventional antibiotics increasingly ineffective and threatens to reverse decades of medical progress. The rapid emergence and spread of multidrug-resistant bacteria have severely [...] Read more.

Microbial infections are an escalating global health threat, driven by the alarming rise of antimicrobial resistance (AMR), which has made many conventional antibiotics increasingly ineffective and threatens to reverse decades of medical progress. The rapid emergence and spread of multidrug-resistant bacteria have severely limited treatment options, resulting in increased morbidity, mortality, and healthcare burden worldwide. In response to these challenges, phage therapy is regaining interest as a promising alternative. Bacteriophages, the most abundant biological entities, have remarkable specificity toward their bacterial hosts, enabling them to selectively eliminate pathogenic strains. Phage therapy presents several advantages over conventional antibiotics, which include minimal disruption to the microbiome and a slower rate of resistance development. Among the various sources of phages, the marine environment remains one of the least explored. Given their adaptation to saline conditions, high pressure, and variable nutrient levels, marine bacteriophages mostly exhibit enhanced environmental stability, broader host ranges, and distinct infection mechanisms, thus making them highly promising for therapeutic purposes. This review explores the growing therapeutic potential of marine bacteriophages by examining their ecological diversity, biological characteristics, infection dynamics, and practical applications in microbial disease control. It also deals with emerging strategies such as phage–antibiotic synergy, genetic engineering, and the use of phage-derived enzymes, alongside several challenges that must be addressed to enable clinical translation and regulatory approval. Advancing our understanding and application of marine phages presents a promising path in the global fight against AMR and the development of next-generation antimicrobial therapies. Full article

(This article belongs to the Section Bacterial Viruses)

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10 pages, 203 KiB

Open AccessArticle

Molecular Detection of Various Non-Seasonal, Zoonotic Influenza Viruses Using BioFire FilmArray and GenXpert Diagnostic Platforms

by Charlene Ranadheera, Taeyo Chestley, Orlando Perez, Breanna Meek, Laura Hart, Morgan Johnson, Yohannes Berhane and Nathalie Bastien

Viruses 2025, 17(7), 970; https://doi.org/10.3390/v17070970 - 10 Jul 2025

Viewed by 238

Abstract

Since 2020, the Gs/Gd H5N1 influenza virus (clade 2.3.4.4b) has established itself within wild bird populations across Asia, Europe, and the Americas, causing outbreaks in wild mammals, commercial poultry, and dairy farms. The impacts on the bird populations and the agricultural industry has [...] Read more.

Since 2020, the Gs/Gd H5N1 influenza virus (clade 2.3.4.4b) has established itself within wild bird populations across Asia, Europe, and the Americas, causing outbreaks in wild mammals, commercial poultry, and dairy farms. The impacts on the bird populations and the agricultural industry has been significant, requiring a One Health approach to enhanced surveillance in both humans and animals. To support pandemic preparedness efforts, we evaluated the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel for their ability to detect the presence of non-seasonal, zoonotic influenza A viruses, including circulating H5N1 viruses from clade 2.3.4.4b. Both assays effectively detected the presence of influenza virus in clinically-contrived nasal swab and saliva specimens at low concentrations. The results generated using the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel, in conjunction with clinical and epidemiological findings provide valuable diagnostic findings that can strengthen pandemic preparedness and surveillance initiatives. Full article

(This article belongs to the Section Animal Viruses)

17 pages, 13102 KiB

Open AccessArticle

Pharmacological Agent GW4869 Inhibits Tick-Borne Langat Virus Replication to Affect Extracellular Vesicles Secretion

by Md Bayzid, Biswajit Bhowmick, Waqas Ahmed, Girish Neelakanta and Hameeda Sultana

Viruses 2025, 17(7), 969; https://doi.org/10.3390/v17070969 - 10 Jul 2025

Viewed by 232

Abstract

GW4869, a cell-permeable, selective inhibitor of neutral sphingomyelinase is a pharmacological agent that blocks the production and release of extracellular vesicles (EVs). Our previous studies have shown that GW4869 inhibits flaviviral loads in tick, mosquito and mammalian cells, including murine cortical neurons. Yet [...] Read more.

GW4869, a cell-permeable, selective inhibitor of neutral sphingomyelinase is a pharmacological agent that blocks the production and release of extracellular vesicles (EVs). Our previous studies have shown that GW4869 inhibits flaviviral loads in tick, mosquito and mammalian cells, including murine cortical neurons. Yet the mechanism(s) of GW4869 inhibitor upon viral infections were not addressed. In the current study, we focused on how GW4869 interferes with Langat Virus (LGTV, a tick-borne flavivirus) replication in ISE6 tick cells. First, we found that GW4869 is neither cytotoxic at tested doses of 50, 100, and 150 µM in tick cells, nor does it directly bind to the free LGTV present in cell culture supernatants. When tick cells were treated with GW4869, followed by infection with viral stock at dilutions of 10⁻², 10⁻³, 10⁻⁴ (the infectious dose determination by viral dilution assay), it affected LGTV replication in tick cells. A reduction in viral burden was noted in GW4869-treated tick cells, which constituted more than half the amount of decrease when compared to the mock control. Next, GW4869 treatment not only resulted in decreased LGTV transcript levels in tick cells and EVs derived from these infected cells, but also revealed diminished EVs concentrations. Enhanced IsSMase transcripts in the LGTV-infected group was noted upon GW4869 treatment, thus suggesting a host response to perhaps inhibit virus replication. In addition, GW4869 treatment reduced LGTV loads in density gradient EVs fractions, which correlated with decreased EVs concentration in those fractions. These data not only indicate that GW4869 affects LGTV replication, but that it also interferes with EV secretion and release from tick cells. Lastly, we found that GW4869 inhibits LGTV replication in tick cells but does not directly affect the infectivity of LGTV viral particles. Overall, our study suggests that GW4869 is a potential therapeutic inhibitor in controlling tick-borne diseases. Full article

(This article belongs to the Special Issue Tick-Borne Viruses: Transmission and Surveillance, 2nd Edition)

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12 pages, 241 KiB

Open AccessArticle

Role of Common Fractalkine Receptor Variants with Chronic Hepatitis B Patients in Tunisia

by Imene Ben Dhifallah, Kaouther Ayouni, Zeineb Belaiba, Bacem AlaDdine Razgui, Sahar Trabelsi, Henda Touzi, Amel Sadraoui, Walid Hammemi, Hela Hannachi, Amira Kebir, Slimane Ben Miled and Henda Triki

Viruses 2025, 17(7), 968; https://doi.org/10.3390/v17070968 - 10 Jul 2025

Viewed by 235

Abstract

Chronic hepatitis B virus (CHB) infection remains a leading cause of hepatic inflammation and damage. Several studies have suggested the significant role of CX3C chemokine receptor 1 (CX3CR1) in inflammatory damages. The polymorphisms V249I and T280M affect receptor expression and function. In the [...] Read more.

Chronic hepatitis B virus (CHB) infection remains a leading cause of hepatic inflammation and damage. Several studies have suggested the significant role of CX3C chemokine receptor 1 (CX3CR1) in inflammatory damages. The polymorphisms V249I and T280M affect receptor expression and function. In the current study, we investigated the association of V249I and T280M variants of the CX3CR1 fractalkine receptor with susceptibility to CHB disease. In total, 280 patients with chronic hepatitis B and 260 controls from different cities of Tunisia recruited in the Pasteur Institute of Tunisia between January 2017 and December 2022 were genotyped for the V249I and T280M CX3CR1 gene. The allele and genotype frequencies of these variants did not show significant associations with susceptibility to CHB infection (p > 0.05). Analysis of allele and genotype frequencies showed that there was no differences in age and sex distribution between patients and the control group, but when CHB patients were stratified according to age, a clear significant difference was obtained for the T280M polymorphism (p < 10⁻³, OR = 88.91; p < 10⁻³, OR = 37.42, for genotype and allelic distribution, respectively) with the MM genotype being more frequent in patients aged ≥ 50 years. The most frequently combined genotypes in the Tunisian population were VVTT, VITT and VITM both in patients (48.9%, 22.5% and 22.1%, respectively) and in controls (52%, 23.8%, 13.5%, respectively) compared to the extremely rare IITT, IITM or IIMM genotypes. In conclusion, this study suggests a noteworthy genotype–age association, particularly involving the T280M variant Full article

(This article belongs to the Special Issue Viral Hepatitis and Liver Diseases)

14 pages, 1382 KiB

Open AccessArticle

Molecular Identification and Characterization of a Novel Gammaherpesvirus in Wild Rabbits

by Fábio A. Abade dos Santos, Ana Duarte, Inês C. Varandas, Silvia S. Barros, Ana M. Henriques, Teresa Fagulha and Margarida D. Duarte

Viruses 2025, 17(7), 967; https://doi.org/10.3390/v17070967 - 10 Jul 2025

Viewed by 227

Abstract

To date, five herpesviruses have been identified in Leporidae (LeHV-1, LeHV-2, LeHV-3, LeHV-4, and LeHV-5). Two of these have been shown to infect the European rabbit (Oryctolagus cuniculus), causing either asymptomatic infection (LeHV-2, a gammaherpesvirus) or virulent disease (LeHV-4, an alphaherpesvirus). Unfortunately, apart [...] Read more.

To date, five herpesviruses have been identified in Leporidae (LeHV-1, LeHV-2, LeHV-3, LeHV-4, and LeHV-5). Two of these have been shown to infect the European rabbit (Oryctolagus cuniculus), causing either asymptomatic infection (LeHV-2, a gammaherpesvirus) or virulent disease (LeHV-4, an alphaherpesvirus). Unfortunately, apart from LeHV-4, for which complete genome sequences are available, molecular data on leporid herpesviruses are extremely limited, with no sequences available in public databases for LeHV-1 and LeHV-3, and only a few short sequences for LeHV-2 and LeHV-5. In this study, we investigated the presence of herpesviruses in biological samples from wild rabbits (n = 34) found dead in the field during 2024. A pan-herpesvirus nested PCR directed to the herpesviral DNA polymerase gene was used for screening. Positive samples (n = 14, 41.17%) were further investigated by sequencing analysis of a longer region of the DNA polymerase gene, as well as the glycoprotein B gene and the terminase gene. Blastn analysis of the amplicons revealed the highest similarity to gammaherpesvirus. Phylogenetic analyses based on glycoprotein B, DNA polymerase, and concatenated amino acid sequences consistently placed the newly identified LeHV-6 in close proximity to LeHV-5. Both viruses form a well-supported clade within the Gammaherpesvirinae, clustering with rodent-associated herpesviruses, such as Murine herpesvirus, MuHV-4, and A. sylvaticus rhadinovirus 1. Considering the species susceptibility and the nucleotide similarities with the five previously described leporid herpesviruses, we conclude that a new rabbit gammaherpesvirus has been identified, which we propose to name LeHV-6. Full article

(This article belongs to the Special Issue Animal Virus Discovery and Genetic Diversity: 2nd Edition)

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20 pages, 1215 KiB

Open AccessArticle

Epidemiological Profiles of Human Rabies Cases in Tunisia Between 2000 and 2022

by Amal Ayachi, Rym Benabdallah, Aida Bouratbine, Karim Aoun, Jihen Bensalem, Nourhen Basdouri, Samia Benmaiz, Farah Bassalah, Chaima Nouioui, Mohamed Soltani, Khaled Ghouili, Zied Bouslema, Habib Kharmechi and Mariem Handous

Viruses 2025, 17(7), 966; https://doi.org/10.3390/v17070966 - 10 Jul 2025

Viewed by 351

Abstract

In Tunisia, rabies is endemic and represents a significant public health issue. The objectives of our study were to describe the epidemiological and clinical profiles of human rabies cases and report the risk factors associated with their occurrence. We conducted a retrospective, descriptive, [...] Read more.

In Tunisia, rabies is endemic and represents a significant public health issue. The objectives of our study were to describe the epidemiological and clinical profiles of human rabies cases and report the risk factors associated with their occurrence. We conducted a retrospective, descriptive, and analytical study of human rabies cases confirmed at the Rabies Laboratory of the Pasteur Institute in Tunis from January 2000 to November 2022. Temporal–spatial, sociodemographic, and clinical variables and factors related to the exposure context, post-exposure, and response were collected for each patient. A total of 58 human rabies cases were identified. The governorates of Kairouan and Nabeul were the most affected, with a predominance of rural areas (77%, 34/44). The highest number of cases was recorded between May and November (74%, 43/58). The cases predominantly involved males, with the most affected age group being individuals aged from 31 to 59 years (30%, 17/57). Rabies transmission was primarily due to dogs (86%, 43/50) and a single bite (55%, 32/58). After an average incubation period of 60.3 days, hydrophobia and behavioral disturbances were the most common symptoms. This study demonstrates that the risk of human rabies remains present in Tunisia, highlighting the need to improve awareness and post-exposure prophylaxis practices. Full article

(This article belongs to the Section General Virology)

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18 pages, 2023 KiB

Open AccessArticle

Avian Metapneumovirus in Thailand: Molecular Detection, Genetic Diversity, and Its Potential Threat to Poultry

by Sudarat Wanarat, Manakorn Sukmak, Nantana Soda, Pimpakarn Suwan, Natchaya Satayaphongpan, Worata Klinsawat, Wilairat Chumsing, Chatnapa Janmeethat, Taweesak Songserm, Nuananong Sinwat, Sittinee Kulprasertsri, Pun Panomwan and Kriangkrai Witoonsatian

Viruses 2025, 17(7), 965; https://doi.org/10.3390/v17070965 - 9 Jul 2025

Viewed by 326

Abstract

Avian metapneumovirus subtype B (aMPV/B) is an economically significant pathogen in poultry, causing respiratory and reproductive disorders. In this study, 167 clinical samples were collected from commercial poultry farms across Thailand to investigate the prevalence, genetic diversity, and evolutionary dynamics of aMPV/B. Nested [...] Read more.

Avian metapneumovirus subtype B (aMPV/B) is an economically significant pathogen in poultry, causing respiratory and reproductive disorders. In this study, 167 clinical samples were collected from commercial poultry farms across Thailand to investigate the prevalence, genetic diversity, and evolutionary dynamics of aMPV/B. Nested RT-PCR targeting the G gene revealed a positivity rate of 34.13% (57/167). Phylogenetic and Median-joining network analyses of sequenced amplicons identified two distinct Thai lineages: one genetically similar to vaccine strains and another of unknown origin. Divergence time analysis using a Bayesian framework estimated the time to the most recent common ancestor (tMRCA) of these lineages around 2006, with further sub-lineage diversification occurring around 2009 and 2016. These findings suggest that the circulating Thai aMPV/B strains likely stem from limited introduction events followed by local evolution. Lineage-specific amino acid substitutions within the G gene were identified, which may affect antigenic properties and immune recognition. This study highlights the molecular heterogeneity and ongoing diversification of aMPV/B in Thailand and underscores the need for sustained genomic surveillance and regionally tailored vaccination strategies. Full article

(This article belongs to the Special Issue Avian Respiratory Viruses, 4th Edition)

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22 pages, 4670 KiB

Open AccessArticle

3,3′-Diindolylmethane Improves the Viral Pneumonia Outcomes After Influenza and SARS-CoV-2 Infection in Animal Models

by Vsevolod Kiselev, Irina Leneva, Anna Ivanina, Artem Poromov, Irina Falynskova, Nadezhda Kartashova, Ekaterina Glubokova, Galina Trunova, Sergey Sudakov, Vadim Drukh, Vitaly Zverev and Oleg Kiselev

Viruses 2025, 17(7), 964; https://doi.org/10.3390/v17070964 - 9 Jul 2025

Viewed by 290

Abstract

Influenza and SARS-CoV-2 are often associated with viral pneumonia, resulting from direct exposure of the virus to lung tissue. 3,3′-Diindolylmethane (DIM) is a naturally occurring substance with multi-target activity, including anti-inflammatory and epigenetic modulation. In this study, we evaluated the therapeutic efficacy in [...] Read more.

Influenza and SARS-CoV-2 are often associated with viral pneumonia, resulting from direct exposure of the virus to lung tissue. 3,3′-Diindolylmethane (DIM) is a naturally occurring substance with multi-target activity, including anti-inflammatory and epigenetic modulation. In this study, we evaluated the therapeutic efficacy in vivo of a DIM formulation with fish oil (Cesarox Epi) against influenza A (H1N1) infection in mice and against SARS-CoV-2 infection in Syrian hamsters. In a model of lethal influenza pneumonia induced by A/California/04/2009 (H1N1)pdm09 virus, we showed that 5 days’ treatment with DIM Epi at 10, 20, and 60 mg/kg/day delayed the time to death, prevented body weight loss, and resulted in significant improvements in survival. DIM Epi tested in hamsters infected with SARS-CoV2 Dubrovka (Wuhan-like) strain at doses 50 and 100 mg/kg/day reduced clinical signs, weight loss, temperature elevation, and lung pathology. In both models of infections, treatment with DIM Epi did not significantly decrease viral titer in the animals’ lungs. DIM Epi and Oseltamivir were more effective against influenza infection when given in combination than given singly, while co-administration of DIM Epi with Molnupiravir did not yield an additive benefit against SARS-CoV-2 infection. These findings support DIM Epi as a promising host-directed adjunct therapy for viral pneumonia with potential to enhance outcomes in respiratory infections. Full article

(This article belongs to the Section Coronaviruses)

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29 pages, 14985 KiB

Open AccessArticle

Spatiotemporal Characterization of Changes in the Respiratory Tract and the Nervous System, Including the Eyes in SARS-CoV-2-Infected K18-hACE2 Mice

by Malgorzata Rosiak, Tom Schreiner, Georg Beythien, Eva Leitzen, Anastasiya Ulianytska, Lisa Allnoch, Kathrin Becker, Lukas M. Michaely, Sandra Lockow, Sabrina Clever, Christian Meyer zu Natrup, Asisa Volz, Wolfgang Baumgärtner, Malgorzata Ciurkiewicz, Kirsten Hülskötter and Katharina M. Gregor

Viruses 2025, 17(7), 963; https://doi.org/10.3390/v17070963 - 9 Jul 2025

Viewed by 315

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is known to affect multiple organ systems, including the respiratory tract and nervous and ocular systems. This retrospective study aimed to characterize the spatiotemporal distribution of viral antigen [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is known to affect multiple organ systems, including the respiratory tract and nervous and ocular systems. This retrospective study aimed to characterize the spatiotemporal distribution of viral antigen and associated pathological changes in the nose, lungs, brain, and eyes of K18-hACE2 mice intranasally infected with SARS-CoV-2. Using histology and immunohistochemistry, tissues were examined at 3, 6, and 7/8 days post-infection (dpi). In addition, lung and brain tissues were analyzed by means of RT-qPCR to determine viral RNA titers. Viral antigen was most pronounced in the nose, brain, and lung at 3, 6, and 7/8 dpi, respectively, whereas viral antigen was detected at 6 and 7/8 dpi in the retina. Quantitative PCR confirmed increasing viral RNA levels in both lung and brain, peaking at 7/8 dpi. Nasal and lung inflammation mirrored viral antigen distribution and localization. In the brain, the predominantly basal viral spread correlated with lymphohistiocytic meningoencephalitis, neuronal vacuolation, and altered neurofilament immunoreactivity. Retinal ganglion cells showed viral antigen expression without associated lesions. Microglial activation was evident in both the optic chiasm and the brain. These findings highlight the K18-hACE2 model’s utility for studying extrapulmonary SARS-CoV-2 pathogenesis. Understanding the temporal and spatial dynamics of viral spread enhances insights into SARS-CoV-2 neurotropism and its clinical manifestations. Full article

(This article belongs to the Section Coronaviruses)

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16 pages, 871 KiB

Open AccessArticle

Primary HSV-2 Infection in an Immunocompromised Patient Reveals High Diversity of Drug-Resistance Mutations in the Viral DNA Polymerase

by Hanna Helena Schalkwijk, Sarah Gillemot, Emilie Frobert, Florence Morfin, Sophie Ducastelle, Anne Conrad, Pierre Fiten, Ghislain Opdenakker, Robert Snoeck and Graciela Andrei

Viruses 2025, 17(7), 962; https://doi.org/10.3390/v17070962 - 9 Jul 2025

Viewed by 272

Abstract

Herpes simplex virus 2 (HSV-2) remains a significant cause of morbidity and mortality in immunocompromised individuals, despite the availability of effective antivirals. Infections caused by drug-resistant isolates are an emerging concern among these patients. Understanding evolutionary aspects of HSV-2 resistance is crucial for [...] Read more.

Herpes simplex virus 2 (HSV-2) remains a significant cause of morbidity and mortality in immunocompromised individuals, despite the availability of effective antivirals. Infections caused by drug-resistant isolates are an emerging concern among these patients. Understanding evolutionary aspects of HSV-2 resistance is crucial for designing improved therapeutic strategies. Here, we characterized 11 HSV-2 isolates recovered from various body sites of a single immunocompromised patient suffering from a primary HSV-2 infection unresponsive to acyclovir and foscarnet. The isolates were analyzed phenotypically and genotypically (Sanger sequencing of viral thymidine kinase and DNA polymerase genes). Viral clone isolations, deep sequencing, viral growth kinetics, and dual infection competition assays were performed retrospectively to assess viral heterogeneity and fitness. Sanger sequencing identified mixed populations of DNA polymerase mutant variants. Viral clones were plaque-purified and genotyped, revealing 17 DNA polymerase mutations (K533E, A606V, C625R, R628C, A724V, S725G, S729N, I731F, Q732R, M789T/K, Y823C, V842M, R847C, F923L, T934A, and R964H) associated with acyclovir and foscarnet resistance. Deep-sequencing of the DNA polymerase detected drug-resistant variants ranging between 1 and 95%, although the first two isolates had a wild-type DNA polymerase. Some mutants showed reduced fitness, evidenced by (i) the frequency of variants identified by deep-sequencing not correlating with the proportion of mutants found by plaque-purification, (ii) loss of the variants upon passaging in cell culture, or (iii) reduced frequencies in competition assays. This study reveals the rapid evolution of heterogeneous drug-resistant HSV-2 populations under antiviral therapy, highlighting the need for alternative treatment options and resistance surveillance, especially in severe infections. Full article

(This article belongs to the Special Issue Mechanisms of Herpesvirus Resistance)

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16 pages, 1242 KiB

Open AccessArticle

Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy

by Jenna M. Hasson, Mary Grace Katusiime, Adam A. Capoferri, Michael J. Bale, Brian T. Luke, Wei Shao, Mark F. Cotton, Gert van Zyl, Sean C. Patro and Mary F. Kearney

Viruses 2025, 17(7), 961; https://doi.org/10.3390/v17070961 - 9 Jul 2025

Viewed by 286

Abstract

HIV-1 proviral landscapes were investigated using near-full-length HIV single-genome sequencing on blood samples from five children with vertically acquired infection and on ART for ~7–9 years. Proviral structures were compared to published datasets in children prior to ART, children on short-term ART, and [...] Read more.

HIV-1 proviral landscapes were investigated using near-full-length HIV single-genome sequencing on blood samples from five children with vertically acquired infection and on ART for ~7–9 years. Proviral structures were compared to published datasets in children prior to ART, children on short-term ART, and adults on ART. We found a strong selection for large internal proviral deletions in children, especially deletions of the env gene. Only 2.5% of the proviruses were sequence-intact, lower than in the comparative datasets from adults. Of the proviruses that retained the env gene, >80% contained two or more defects, most commonly stop codons and/or gag start mutations. Significantly fewer defects in the major splice donor site (MSD) and packaging signal were found in the children on short or long-term ART compared to the adults, and tat was more frequently defective in children. These results suggest that different selection pressures may shape the proviral landscape in children compared to adults and reveal potentially different genetic regions to target for measuring the intact HIV reservoir and for achieving HIV remission in children. Full article

(This article belongs to the Special Issue Intra-patient Viral Evolution and Diversity)

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45 pages, 2714 KiB

Open AccessReview

mRNA Vaccine Development in the Fight Against Zoonotic Viral Diseases

by Brandon E. K. Tan, Seng Kong Tham and Chit Laa Poh

Viruses 2025, 17(7), 960; https://doi.org/10.3390/v17070960 - 8 Jul 2025

Viewed by 449

Abstract

Zoonotic diseases are transmitted from animals to humans, and they impose a significant global burden by impacting both animal and human health. It can lead to substantial economic losses and cause millions of human deaths. The emergence and re-emergence of zoonotic diseases are [...] Read more.

Zoonotic diseases are transmitted from animals to humans, and they impose a significant global burden by impacting both animal and human health. It can lead to substantial economic losses and cause millions of human deaths. The emergence and re-emergence of zoonotic diseases are heavily influenced by both anthropogenic and natural drivers such as climate change, rapid urbanization, and widespread travel. Over time, the unprecedented rise of new and re-emerging zoonotic diseases has prompted the need for rapid and effective vaccine development. Following the success of the COVID-19 mRNA vaccines, mRNA-based platforms hold great promise due to their rapid design, swift development and ability to elicit robust immune responses, thereby highlighting their potential in combating emerging and pre-pandemic zoonotic viruses. In recent years, several mRNA vaccines targeting emerging and re-emerging zoonotic viral diseases, such as rabies, Nipah, Zika, and influenza, have advanced to clinical trials, demonstrating promising immunogenicity. This review explores recent advances, challenges, and future directions in developing mRNA vaccines against emerging and re-emerging zoonotic viral diseases. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Zoonotic Viruses: Current Challenges in Vaccinology)

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14 pages, 3187 KiB

Open AccessCommentary

The Meandrous Route of Rilpivirine in the Search for the Miraculous Drug to Treat HIV Infections

by Erik De Clercq

Viruses 2025, 17(7), 959; https://doi.org/10.3390/v17070959 - 8 Jul 2025

Viewed by 393

Abstract

Rilpivirine (RPV, R278474) was highlighted in 2005, two years after the death of Dr. Paul Janssen, as the ideal non-nucleoside reverse transcriptase inhibitor (NNRTI) to treat HIV infections. For this purpose, it was subsequently combined with tenofovir disoproxil fumarate (TDF), tenofovir alafenamide (TAF), [...] Read more.

Rilpivirine (RPV, R278474) was highlighted in 2005, two years after the death of Dr. Paul Janssen, as the ideal non-nucleoside reverse transcriptase inhibitor (NNRTI) to treat HIV infections. For this purpose, it was subsequently combined with tenofovir disoproxil fumarate (TDF), tenofovir alafenamide (TAF), darunavir (boosted with ritonavir or cobicistat) or dolutegravir. Its wide-spread use is thanks to its combination with cabotegravir (CAB) in the form of a long-acting intramuscular injection once per month (QM), later twice per month (Q2M), for the treatment of adults, later extended to adolescents and pregnant women, with HIV infections. The long-acting CAB plus RPV should not be administered in patients treated with rifampicin or rifabutin, patients with virological failure or patients with resistance to CAB or RPV, or patients with hepatitis B virus (HBV) infection. Long-acting CAB+RPV may lead to pain at the site of injection which would diminish over time. Full article

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

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19 pages, 2082 KiB

Open AccessArticle

De Novo Expressed Vpr Stimulates HIV-1 Replication in T Cells

by Blessing Enya and Jacek Skowronski

Viruses 2025, 17(7), 958; https://doi.org/10.3390/v17070958 - 7 Jul 2025

Viewed by 281

Abstract

Vpr, a virion-associated accessory virulence factor of HIV-1, promotes virus replication in both T cells and macrophages. Although Vpr’s early activity—antagonism of preintegration silencing and host restriction factors—has been documented, the relative contribution of virion-associated versus de novo expressed Vpr to HIV-1 replication [...] Read more.

Vpr, a virion-associated accessory virulence factor of HIV-1, promotes virus replication in both T cells and macrophages. Although Vpr’s early activity—antagonism of preintegration silencing and host restriction factors—has been documented, the relative contribution of virion-associated versus de novo expressed Vpr to HIV-1 replication fitness remains unclear. Here, we developed a T cell-based system that genetically separates early and late Vpr functions by combining tetracycline-inducible Vpr expression in CEM.SS T cells with vpr-deficient HIV-1 constructs and Gag p6 mutations that block Vpr packaging. CEM.SS T cells have been shown to recapitulate the positive effect of Vpr on HIV-1 replication observed in activated primary T cells. Using pairwise replication fitness assays under spreading infection conditions, we demonstrate that de novo synthesized Vpr exerts the dominant effect on HIV-1 replication in T cells, while virion-associated Vpr plays a lesser role. Somewhat unexpectedly, our findings reveal that antagonism of preintegration HIV-1 silencing by virion-associated Vpr is unlikely to be the major driver of enhanced HIV-1 replication in proliferating T cells. Instead, this function may play a more prominent role in the infection of non-dividing T cells and/or other cell types. Full article

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

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Viruses, Volume 17, Issue 7 (July 2025) – 119 articles

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