Viruses

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Open AccessArticle

Screening of Single-Domain Antibodies to Adeno-Associated Viruses with Cross-Serotype Specificity and a Wide pH Tolerance

by Hailing Guo, Shuo Wang, Lujin Feng, Weiwei Xu, Jiandong Zhang, Xiaoju Zhou and Ningning Ma

Viruses 2025, 17(10), 1289; https://doi.org/10.3390/v17101289 - 23 Sep 2025

Abstract

Adeno-associated virus (AAV) vectors are the preferred gene delivery tool in gene therapy owing to their safety, long-term gene expression, broad tissue tropism, and low immunogenicity. Affinity ligands that can bind multiple AAV serotypes endure harsh clean-in-place (CIP) conditions and are critical for [...] Read more.

Adeno-associated virus (AAV) vectors are the preferred gene delivery tool in gene therapy owing to their safety, long-term gene expression, broad tissue tropism, and low immunogenicity. Affinity ligands that can bind multiple AAV serotypes endure harsh clean-in-place (CIP) conditions and are critical for industrial-scale purification. However, current ligands lack broad serotype recognition and adequate alkaline stability, which limits their reusability in large-scale manufacturing. In this study, we employed a competitive biopanning strategy to isolate a single-domain antibody (VHH) that simultaneously binds AAV2, AAV8, and AAV9. The VHH retained structural integrity and binding activity after exposure to 0.1 M NaOH, demonstrating robust alkaline stability. Structural modeling revealed that the VHH primarily recognizes the DE loop region of the VP3 capsid protein across the three serotypes, explaining its cross-serotype reactivity. Affinity chromatography using the VHH yielded infectious AAV particles, confirming its potential for downstream processing. This strategy provides a versatile platform for developing high-performance AAV affinity ligands and may be extended to other viral vector systems. Full article

(This article belongs to the Section General Virology)

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Open AccessArticle

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

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

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

Abstract

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

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

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

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Open AccessBrief Report

Virucidal Potential of 3,3′,4,4′,5,5′-Hexahydroxy-trans-Stilbene Against Respiratory Syncytial Virus

by Zoltán Bánki, Leonie Wolf, Brigitte Müllauer, Daniel Geisler-Moroder, Wegene Borena, Walter Jäger and Thomas Szekeres

Viruses 2025, 17(10), 1287; https://doi.org/10.3390/v17101287 - 23 Sep 2025

Abstract

Respiratory syncytial virus (RSV) infections have a significant impact on global health. Despite of recent advancements, the current treatment options for managing severe RSV infections remain primarily limited to supportive care, emphasizing the high priority for the development of effective antiviral therapies. Antiviral [...] Read more.

Respiratory syncytial virus (RSV) infections have a significant impact on global health. Despite of recent advancements, the current treatment options for managing severe RSV infections remain primarily limited to supportive care, emphasizing the high priority for the development of effective antiviral therapies. Antiviral activity of 3,3′,4,4′,5,5′-hexahydroxy-trans-stilbene (HHS), a synthetic polyhydroxyphenol, has previously been demonstrated against SARS-CoV-2. In this study, we provide evidence for a direct virucidal effect of HHS against RSV infection in permissive HEp-2 cells in vitro. HHS, with an IC50 of 3.44 μM, efficiently inhibited HEp-2 cell infection with no sign of toxicity at least up to 25 μM. Interestingly, resveratrol, a polyhydroxyphenol analogue, was less efficient. Mode of action experiments revealed that HHS directly interacts with RSV particles, indicating that its virucidal activity is based on this interaction rather than affecting HEp-2 cells or post-infection processes. Together with previous data, our results suggest a broad antiviral activity of HHS against different respiratory viruses. Further studies are necessary to unveil the exact mechanism and evaluate the potential of HHS in the treatment of severe respiratory virus infections. Full article

(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 2nd Edition)

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Open AccessArticle

Characterization of Novel Luteoviruses in Canadian Highbush Blueberries Using High-Throughput Sequencing

by Sachithrani Kannangara, Adam Gilewski, Juan Rodriguez Lopez, Gertruida de Villiers, Meghan Ellis, Peter Ellis, Eric Gerbrandt and Jim Mattsson

Viruses 2025, 17(10), 1286; https://doi.org/10.3390/v17101286 (registering DOI) - 23 Sep 2025

Abstract

The Fraser Valley of British Columbia, Canada is among the top ten blueberry producing regions globally. Viral diseases are established in the region and significantly reduce average yields. While testing for two viruses is routine, characterization of all the viruses present in the [...] Read more.

The Fraser Valley of British Columbia, Canada is among the top ten blueberry producing regions globally. Viral diseases are established in the region and significantly reduce average yields. While testing for two viruses is routine, characterization of all the viruses present in the region is incomplete. We used high-throughput sequencing to obtain an unbiased overview of RNA viruses present in 97 plants collected across the region. In addition to known viruses, we identified four luteoviruses previously unidentified in the region. Two of them matched the blueberry virus L (BlVL) and blueberry virus M (BlVM). recently found in the USA, while the third constitutes a new major variant of BlVM (BlVM-2), and the fourth a new luteovirus, which we named blueberry virus N (BlVN). The genome sequences were ~5 kbp long and contained four open-reading frames similar to other luteoviruses. PCR screening revealed that these luteoviruses are widespread in the region, and that plants typically harbour more than one of these luteoviruses. While luteoviruses are typically vectored by aphids, they were also present in nursery stock, indicating that spread also occurs via vegetative propagation. Full article

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

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18 pages, 5986 KB

Open AccessArticle

Broadly Sarbecovirus-Neutralizing Antibodies Induced by Ancestral SARS-CoV-2 Infection

by Yiwei Zhang, Zhen Zhang, Feiyang Yu, Xianying Chen, Shangyu Yang, Jingyi Lin, Genmao Liu, Xinyang Liu, Ming Guo, Yu Chen, Ke Lan and Haiyan Zhao

Viruses 2025, 17(10), 1285; https://doi.org/10.3390/v17101285 - 23 Sep 2025

Abstract

The COVID-19 pandemic, driven by SARS-CoV-2, continues to challenge global health due to emerging variants and the potential risk posed by related sarbecoviruses. Neutralizing antibodies targeting the spike (S) glycoprotein, particularly the receptor-binding domain (RBD), play a crucial role in viral neutralization and [...] Read more.

The COVID-19 pandemic, driven by SARS-CoV-2, continues to challenge global health due to emerging variants and the potential risk posed by related sarbecoviruses. Neutralizing antibodies targeting the spike (S) glycoprotein, particularly the receptor-binding domain (RBD), play a crucial role in viral neutralization and vaccine design. Although broadly neutralizing anti-RBD antibodies have been identified, the nature of cross-reactive humoral responses induced by natural infection with ancestral SARS-CoV-2 strains remains incompletely understood. Here, we isolated 105 S-specific monoclonal antibodies (mAbs) from individuals recovered from prototype SARS-CoV-2 infection. Of these, 30 mAbs cross-recognized SARS-CoV-1, including 25 RBD-directed mAbs, of which 12 displayed cross-neutralizing activity against both viruses. Among them, mAb 12C2 potently neutralized SARS-CoV-1 and multiple SARS-CoV-2 variants, likely through mechanisms that include inhibition of membrane fusion and potential destabilization of the S trimer. Cryo-electron microscopy revealed that 12C2 engages the outer face of the RBD, overlapping with the epitope recognized by the broadly neutralizing antibody S309 derived from SARS-CoV-1 convalescent. Collectively, these findings demonstrate that ancestral SARS-CoV-2 infection can elicit robust cross-neutralizing antibody responses and provide valuable insights for the design of broadly protective antibodies and vaccines. Full article

(This article belongs to the Special Issue Humoral Immune Response to Viruses)

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19 pages, 3052 KB

Open AccessArticle

Genome-Wide Variation Profile of the Genus Tobamovirus

by Amany E. Gomaa and Hernan Garcia-Ruiz

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

Abstract

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

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

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

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10 pages, 683 KB

Open AccessBrief Report

Cervical Secretions from Women After Depot Medroxyprogesterone Acetate (Depo-Provera) Administration Promote HIV Infectivity Ex Vivo

by Carley Tasker, Natalie E. Roche, Yungtai Lo and Theresa L. Chang

Viruses 2025, 17(9), 1283; https://doi.org/10.3390/v17091283 - 22 Sep 2025

Abstract

Depot medroxyprogesterone acetate (Depo-Provera) has been associated with an increased risk of HIV acquisition. We have previously shown that Depo-Provera administration increases immune markers for HIV preference on peripheral and cervical CD4⁺ T cells but decreases the levels of most immune mediators [...] Read more.

Depot medroxyprogesterone acetate (Depo-Provera) has been associated with an increased risk of HIV acquisition. We have previously shown that Depo-Provera administration increases immune markers for HIV preference on peripheral and cervical CD4⁺ T cells but decreases the levels of most immune mediators at vaginal and cervical mucosa. In this study, we determined the effect of cervicovaginal secretions from women before (visit 1), one month (visit 2) and three months (visit 3) after Depo-Provera treatment on HIV infectivity ex vivo. The effect of supernatants from vaginal, endocervical, and rectal swabs and from cervical cytobrush on HIV infectivity were assessed by a single-cycle infection assay using CCR5-using HIV-luciferase reporter viruses. We found that endocervical secretions from women after Depo-Provera treatment promoted HIV infectivity. When analyzing the association between endocervical mediator changes in response to Depo-Provera, available in our previous study, and the changes in HIV infectivity pre- and post-treatment, we found that changes in IL-17 and VEGF were positively associated with changes in HIV infectivity at visit 2 compared with visit 1, whereas changes in RANTES and IL-4 were negatively associated with HIV infectivity. The negative association between RANTES and HIV infectivity was also observed at visit 3 compared with visit 1. Additionally, changes in IL-1α at visit 3 were positively associated with changes in HIV infectivity compared with visit 1. These findings suggest that Depo-Provera may increase the HIV risk by shifting the mucosal milieu that promotes HIV infectivity. Full article

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

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17 pages, 2829 KB

Open AccessArticle

The ORF1ab of Feline Coronavirus Plays a Critical Role in Regulating the Innate Immune Response

by Haorong Gu, Chuqiao Xia, Hongtao Kang and Honglin Jia

Viruses 2025, 17(9), 1282; https://doi.org/10.3390/v17091282 - 22 Sep 2025

Abstract

Feline coronaviruses (FCoVs) are divided into two groups: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). FIPV is responsible for the severe disease known as feline infectious peritonitis, while FECV typically causes mild symptoms, such as diarrhea, and often does not [...] Read more.

Feline coronaviruses (FCoVs) are divided into two groups: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). FIPV is responsible for the severe disease known as feline infectious peritonitis, while FECV typically causes mild symptoms, such as diarrhea, and often does not lead to any disease at all. Currently, it is not possible to distinguish between FIPV and FECV at the molecular level. Therefore, there is an urgent need to understand the molecular features of FIPV. Here, we generated a recombinant virus by replacing the ORF1ab region and the coding sequence for the spike (S) protein of an FECV with the corresponding sequences from FIPVs. The recombinant virus (recFECV-S_DF-2-1ab_FIPV) exhibited similar growth kinetics to its parental strain. Our analysis revealed that the replacement of the ORF1ab in the FECV caused significant alterations in protein expression within the host cells. Furthermore, the presence of the ORF1ab from the FIPV strain resulted in enhanced suppression of the innate immune response compared to the parental strain, as determined through proteomic and transcriptomic studies. Additionally, we demonstrated that the papain-like protease 2 (PL2^pro) of the non-structural protein 3 (NSP3) from both FIPV and FECV functions in immune suppression, and the protease activity is required for this function. Full article

(This article belongs to the Section Animal Viruses)

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1 pages, 163 KB

Open AccessCorrection

Correction: Galuzo et al. CLEC5A Activation in Inflammatory Monocytes: A Mechanism for Enhanced Adaptive Immunity Following COVID-19 mRNA Vaccination in a Preclinical Study. Viruses 2025, 17, 1233

by Renan Galuzo, Thiago Lazari Machado, Ryann de Souza Nascimento, Jorvan Ramos de Medeiros, Luciana Neves Tubarão, Jane Silva, Vanessa Pimenta Rocha, Tamiris Azamor, Felipe Soares Coelho, Andrea Marques Vieira da Silva, Lorenna Carvalho da Rosa, Juliana Fernandes Amorim da Silva, Renata Tourinho Santos, Rodrigo Müller, Carolina Baeta Salvador Várady, Ana Paula Dinis Ano Bom, Patricia Cristina da Costa Neves and Juliana Gil Melgaço

Viruses 2025, 17(9), 1281; https://doi.org/10.3390/v17091281 - 22 Sep 2025

Abstract

In the original publication [...] Full article

17 pages, 2566 KB

Open AccessArticle

Ruvidar^®—An Effective Anti-Herpes Simplex Virus Agent

by Kevin M. Coombs, Roger DuMoulin-White and Arkady Mandel

Viruses 2025, 17(9), 1280; https://doi.org/10.3390/v17091280 - 20 Sep 2025

Abstract

Infectious agents account for millions of deaths every year. The Herpes Simplex Viruses (HSVs) are large double-stranded DNA viruses that infect more than 90% of the human population and can establish life-long latency in human hosts. Currently, effective FDA approved anti-herpetic drugs include [...] Read more.

Infectious agents account for millions of deaths every year. The Herpes Simplex Viruses (HSVs) are large double-stranded DNA viruses that infect more than 90% of the human population and can establish life-long latency in human hosts. Currently, effective FDA approved anti-herpetic drugs include acyclovir and later-generation derivatives (valacyclovir and famciclovir), which inhibit viral DNA synthesis. In previous work, we demonstrated that the small molecule Ruvidar^® could inhibit numerous pathogenic human viruses when added to solutions of viruses both with and without light activation. In these experiments, we evaluated the ability of Ruvidar^® to restrict HSV-1 replication in Vero cells, both by itself and in combination with acyclovir and metformin in the absence of light activation to mimic deep tissue. Ruvidar^® successfully inhibited HSV-1 replication at significantly lower concentrations and more effectively than either acyclovir or metformin alone. We also discovered additive and synergistic anti-HSV-1 effects when combinational therapy was tested. Ruvidar^® also restricted HSV-1 replication in human U251 glioblastoma astrocytoma cells, remained highly effective against acyclovir-resistant HSV-1 mutants, and protected infected cells from virus-induced cytopathology. Full article

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

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17 pages, 1606 KB

Open AccessArticle

Structural Insights into the Nuclear Import of Haliotid Herpesvirus 1 Large Tegument Protein Homologue

by Babu Kanti Nath, Crystall M. D. Swarbrick, Renate H. M. Schwab, Daryl Ariawan, Ole Tietz, Jade K. Forwood and Subir Sarker

Viruses 2025, 17(9), 1279; https://doi.org/10.3390/v17091279 - 20 Sep 2025

Abstract

Abalone are highly susceptible to haliotid herpesvirus 1 (HaHV1), the causative agent of abalone viral ganglioneuritis (AVG), a re-emerging disease responsible for significant mortality events in both wild and farmed populations. Currently, there are no effective antiviral treatments or preventive measures available against [...] Read more.

Abalone are highly susceptible to haliotid herpesvirus 1 (HaHV1), the causative agent of abalone viral ganglioneuritis (AVG), a re-emerging disease responsible for significant mortality events in both wild and farmed populations. Currently, there are no effective antiviral treatments or preventive measures available against HaHV1, which is partly due to the limited understanding of the immune responses and viral pathogenesis in this non-model marine invertebrate. This highlights the urgent need for novel intervention strategies, including investigations into the molecular mechanisms underlying HaHV1 infection. In other herpesviruses, the large tegument protein UL36 plays a crucial role in transporting the viral capsid to the host cell’s nuclear pore complex (NPC), mediated by N-terminal nuclear localization signals (NLSs). However, the nuclear import mechanism of UL36 homologue (UL36h) in HaHV1 remains largely uncharacterized. In this study, we identified and functionally characterized the NLS motif within HaHV1 UL36h and elucidated its interactions with the importin alpha (IMPα) nuclear import receptor. Through a combination of high-resolution crystallography and quantitative binding assays, we determined the key residues responsible for binding to IMPα and demonstrated isoform-specific variations in binding affinity. Our biochemical and structural analyses confirmed key interactions within the NLS that are essential for IMPα interactions. These findings advance our molecular understanding of HaHV1 host interactions and pave the way for the development of targeted antiviral strategies against abalone herpesvirus infection. Full article

(This article belongs to the Special Issue Veterinary Virology: Unraveling Host–Pathogen Interactions for Animal Health)

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15 pages, 1561 KB

Open AccessArticle

RNA Polymerase III Regulates HIV Replication and Latency

by Landon Thompson, Imran Jamal, Juthika Das, Casey Dang, Zhenzi Hong, Doran Katz, Alberto Bosque and Vir B. Singh

Viruses 2025, 17(9), 1278; https://doi.org/10.3390/v17091278 - 20 Sep 2025

Abstract

The elimination of HIV latent reservoirs is an extremely challenging task due to the interplay of multiple mechanisms regulating latency. Thus, we need to identify novel strategies to target heterogeneous reservoirs uniformly. Recent reports have provided intriguing evidence for the novel antiviral function [...] Read more.

The elimination of HIV latent reservoirs is an extremely challenging task due to the interplay of multiple mechanisms regulating latency. Thus, we need to identify novel strategies to target heterogeneous reservoirs uniformly. Recent reports have provided intriguing evidence for the novel antiviral function of RNA Polymerase III (RNAP III), which remains to be further explored. In this study, we evaluated the role of RNA Pol III in regulating HIV latency and replication. We first demonstrated that the pharmacological inhibition of RNAP III can lead to a strong reactivation of latency in cell lines representing both T and monocytic cellular reservoirs. Next, we investigated the involvement of RNA Pol III in regulating HIV-1 replication using HIV-1 pseudotyped (DuoFluo) virus and HIV-1-Bal in THP-1 and Sup-T1 cells. We show that the pharmacological inhibition of RNAP III significantly induced HIV transcription. These findings were further confirmed in physiologically relevant primary CD4 T cells, and a consistent increase in HIV transcription was observed up to 72 h. Collectively, our study suggests that inhibition of RNAP III can increase the rate of HIV transcription, while the total HIV DNA remains unchanged. Overall, our study identifies a previously unknown role of RNA Pol III in restricting HIV transcription and advocates that targeting RNAP III-driven mechanisms could be a novel strategy to reactivate HIV latent reservoirs. Full article

(This article belongs to the Special Issue Cellular Mechanisms Regulating HIV Replication, 2nd Edition)

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29 pages, 7171 KB

Open AccessArticle

Antibody-Dependent Enhancement of Porcine Reproductive and Respiratory Syndrome Virus Infection Antagonizes the Secretion of Type I Interferons in Porcine Alveolar Macrophages by Interfering with the Retinoic Acid-Inducible Gene I/Melanoma Differentiation-Associated Gene 5 Pathway via Fc Gamma Receptor I

by Liujun Zhang, Aiyang Wang, Weizhen Chen, Xing Feng, Bo Wang, Shaojun He and Hongjie Fan

Viruses 2025, 17(9), 1277; https://doi.org/10.3390/v17091277 - 20 Sep 2025

Abstract

Type I interferons (IFNs), mainly IFN-α and IFN-β, play an essential role in defending against viral invasion by inducing the host’s innate antiviral response. Porcine reproductive and respiratory syndrome virus (PRRSV) is known to impair the IFN responses of infected hosts through the [...] Read more.

Type I interferons (IFNs), mainly IFN-α and IFN-β, play an essential role in defending against viral invasion by inducing the host’s innate antiviral response. Porcine reproductive and respiratory syndrome virus (PRRSV) is known to impair the IFN responses of infected hosts through the antibody-dependent enhancement (ADE) infection pathway, but the precise mechanisms employed are poorly understood. In this study, we showed that PRRSV alone induced a strong secretion of IFN-α and IFN-β in infected porcine alveolar macrophages (PAMs) by activating the retinoic acid-inducible gene I (RIG-I)/melanoma differentiation-associated gene 5 (MDA5) signaling pathway. By contrast, ADE infection of PRRSV significantly down-regulated the production levels of IFN-α and IFN-β in PAMs by negatively regulating the RIG-I/MDA5 signaling pathway and considerably enhancing the replication level of PRRSV in PAMs. Next, small interfering RNA (siRNA) experiments revealed that Fc gamma receptor I (FcγRI) was responsible for the ADE infection of PRRSV in PAMs. In addition, we observed that FcγRI mediated the potent inhibition of IFN-α and IFN-β production through blocking the activation of the RIG-I/MDA5 signaling pathway in PAMs. Further, we found that FcγRI effectively inhibited PRRSV-induced synthesis of IFN-α and IFN-β by negatively regulating PRRSV-induced activation of the RIG-I/MDA5 signaling pathway in PAMs and significantly increased the viral production of PRRSV in PAMs. In conclusion, these results suggest that ADE infection of PRRSV may antagonize the secretion of type I IFNs (IFN-α/β) by interfering with the RIG-I/MDA5 pathway via FcγRI in PAMs, thereby facilitating the proliferation level of PRRSV in PAMs. Full article

(This article belongs to the Section Animal Viruses)

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28 pages, 3125 KB

Open AccessReview

Molecular Insights into HPV-Driven Head and Neck Cancers: From Viral Oncoproteins to Precision Therapeutics

by Mustafa Ozdogan, Gizem Tutkun, Muharrem Okan Cakir and Gholam Hossein Ashrafi

Viruses 2025, 17(9), 1276; https://doi.org/10.3390/v17091276 - 20 Sep 2025

Abstract

Human papillomavirus (HPV) plays a major role in the development of head and neck cancers (HNCs), particularly oropharyngeal squamous cell carcinoma. This review highlights the key molecular mechanisms of HPV-driven carcinogenesis, focusing on the oncogenic E6 and E7 proteins and their disruption of [...] Read more.

Human papillomavirus (HPV) plays a major role in the development of head and neck cancers (HNCs), particularly oropharyngeal squamous cell carcinoma. This review highlights the key molecular mechanisms of HPV-driven carcinogenesis, focusing on the oncogenic E6 and E7 proteins and their disruption of tumor suppressor pathways and epigenetic regulation. We discuss the rising prevalence of HPV-related HNCs, their distinct clinical features, and diagnostic approaches such as p16 immunohistochemistry and HPV DNA/RNA detection. HPV-positive tumors show better prognosis and response to treatment, prompting interest in therapy de-escalation. Emerging strategies including immune checkpoint inhibitors, therapeutic vaccines, CRISPR-based gene editing, and ctDNA monitoring are advancing precision oncology in this field. We also examine the preventive potential of HPV vaccination and ongoing research into its role across various HNC subtypes. A deeper understanding of HPV’s molecular impact may guide more effective, targeted, and less toxic interventions. Full article

(This article belongs to the Special Issue Oncogenic Infections and Cancer: Clinical Insights and Emerging Therapeutics)

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26 pages, 1719 KB

Open AccessArticle

Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses

by Marcelle L. Johnson, Dieke Boezen, Alexey A. Grum-Grzhimaylo, René A. A. van der Vlugt, J. Arjan G. M. de Visser and Mark P. Zwart

Viruses 2025, 17(9), 1275; https://doi.org/10.3390/v17091275 - 20 Sep 2025

Abstract

Background: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single [...] Read more.

Background: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form. Methods: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose–response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data. Results: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses. Conclusions: Our analyses suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus–host systems demands pluralistic explanatory frameworks. Full article

(This article belongs to the Section General Virology)

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16 pages, 2156 KB

Open AccessArticle

Comparative Acquisition, Transmission, and Retention of Distinct Grapevine Red Blotch Virus Isolates in Relation to the Genotype and Sex of Spissistilus festinus, the Treehopper Vector

by Victoria J. Hoyle, Anna O. Wunsch, Heather McLane, Scottie Browning, Madison T. Flasco, Elizabeth J. Cieniewicz and Marc Fuchs

Viruses 2025, 17(9), 1274; https://doi.org/10.3390/v17091274 - 20 Sep 2025

Abstract

Grapevine red blotch virus (GRBV), the causal agent of red blotch disease of grapevines, is transmitted by Spissistilus festinus, the threecornered alfalfa hopper. Isolates of GRBV belong to two phylogenetic clades (I and II) and S. festinus is a dimorphic insect, with [...] Read more.

Grapevine red blotch virus (GRBV), the causal agent of red blotch disease of grapevines, is transmitted by Spissistilus festinus, the threecornered alfalfa hopper. Isolates of GRBV belong to two phylogenetic clades (I and II) and S. festinus is a dimorphic insect, with two genotypes found in the western (California, CA) and the southeastern (SE) regions of the United States. The transmission of GRBV by S. festinus is circulative and nonpropagative, yet some parameters of transmission remain to be characterized. Here, we compared the acquisition, transmission, and retention of GRBV isolates from phylogenetic clades I and II by S. festinus males and females of the two genotypes. Results indicated that the SE genotype acquired GRBV more efficiently (72.5%, 29/40) than the CA genotype (22.5%, 18/80), with differences in acquisition observed between males (32.5%, 26/80) and females (52.5%, 21/40) of the two S. festinus genotypes and between GRBV isolates of phylogenetic clades I (29%, 23/80) and II (60%, 24/40). Following acquisition, both S. festinus genotypes and sexes retained GRBV isolates of phylogenetic clades I and II for at least 60 days without access to an infected plant. For transmission, the GRBV isolate of phylogenetic clade II was more efficiently transmitted by the SE genotype (54%, 13/24) than the CA genotype (17%, 4/24) and SE females (75%, 12/16) were significantly more efficient transmitters of GRBV than CA females (19%, 3/16). Together, our findings revealed that S. festinus genotype, sex, and virus isolate influence GRBV acquisition and transmission but not retention. This research addressed important knowledge gaps in S. festinus-mediated transmission of GRBV that are essential for advancing red blotch disease epidemiology and developing appropriate disease management responses. Full article

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

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17 pages, 2323 KB

Open AccessArticle

Discovery of Landscape Phage Probes Against Cellular Communication Network Factor 1 (CCN1/Cyr61)

by James W. Gillespie and Valery A. Petrenko

Viruses 2025, 17(9), 1273; https://doi.org/10.3390/v17091273 - 19 Sep 2025

Abstract

Detection of cancer biomarkers at the earliest stages of disease progression is commonly assumed to extend the overall quality of life for cancer patients as the result of earlier clinical management of the disease. Therefore, there is an urgent need for the development [...] Read more.

Detection of cancer biomarkers at the earliest stages of disease progression is commonly assumed to extend the overall quality of life for cancer patients as the result of earlier clinical management of the disease. Therefore, there is an urgent need for the development of standardized, sensitive, robust, and commonly available screening and diagnostic tools for detecting the earliest signals of neoplastic pathology progression. Recently, a new paradigm of cancer control, known as multi-cancer detection (MCD), evolved, which measures the composition of cancer-related molecular analytes in the patient’s fluids using minimally invasive techniques. In this respect, the “Holy Grail” of cancer researchers and bioengineers for decades has been composing a repertoire or molecular sensing probes that would allow for the diagnosis, prognosis, and monitoring of cancer diseases via their interaction with cell-secreted and cell-associated cancer antigens and biomarkers. Therefore, the current trend in screening and detection of cancer-related pathologies is the development of portable biosensors for mobile laboratories and individual use. Phage display, since its conception by George Smith 40 years ago, has emerged as a premier tool for molecular evolution in molecular biology with widespread applications including identification and screening of cancer biomarkers, such as Circulating Cellular Communication Network Factor 1 (CCN1), an extracellular matrix-associated signaling protein responsible for a variety of cellular functions and has been shown to be overexpressed as part of the response to various pathologies including cancer. We hypothesize that CCN1 protein can be used as a soluble marker for the early detection of breast cancer in a multi-cancer detection (MCD) platform. However, validated probes have not been identified to date. Here, we screened the multi-billion clone landscape phage display library for phages interacting specifically with immobilized CCN1 protein. Through our study, we discovered a panel of 26 different phage-fused peptides interacting selectively with CCN1 protein that can serve for development of a novel phage-based diagnostic platform to monitor changes in CCN1 serum concentration by liquid biopsy. Full article

(This article belongs to the Special Issue Phage Display in Cancer Diagnosis and Screening)

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22 pages, 3096 KB

Open AccessArticle

Deep Learning-Based Automatic Segmentation and Analysis of Mitochondrial Damage by Zika Virus and SARS-CoV-2

by Brianda Alexia Agundis-Tinajero, Miguel Ángel Coronado-Ipiña, Ignacio Lara-Hernández, Rodrigo Aparicio-Antonio, Anita Aguirre-Barbosa, Gisela Barrera-Badillo, Nidia Aréchiga-Ceballos, Irma López-Martínez, Claudia G Castillo, Vanessa Labrada-Martagón, Mauricio Comas-García and Aldo Rodrigo Mejía-Rodríguez

Viruses 2025, 17(9), 1272; https://doi.org/10.3390/v17091272 - 19 Sep 2025

Abstract

Viruses can induce various mitochondrial morphological changes, which are associated with the type of immune response. Therefore, characterization and analysis of mitochondrial ultrastructural changes could provide insights into the kind of immune response elicited, especially when compared to uninfected cells. However, this analysis [...] Read more.

Viruses can induce various mitochondrial morphological changes, which are associated with the type of immune response. Therefore, characterization and analysis of mitochondrial ultrastructural changes could provide insights into the kind of immune response elicited, especially when compared to uninfected cells. However, this analysis is highly time-consuming and susceptible to observer bias. This work presents the development of a deep learning-based approach for the automatic identification, segmentation, and analysis of mitochondria from thin-section transmission electron microscopy images of cells infected with two SARS-CoV-2 variants or the Zika virus, utilizing a convolutional neural network with a U-Net architecture. A comparison between manual and automatic segmentations, along with morphological metrics, was performed, yielding an accuracy greater than 85% with no statistically significant differences between the manual and automatic metrics. This approach significantly reduces processing time and enables a prediction of the immune response to viral infections by allowing the detection of both intact and damaged mitochondria. Therefore, the proposed deep learning-based tool may represent a significant advancement in the study and understanding of cellular responses to emerging pathogens. Additionally, its applicability could be extended to the analysis of other organelles, thereby opening up new opportunities for automated studies in cell biology. Full article

(This article belongs to the Section Animal Viruses)

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20 pages, 729 KB

Open AccessArticle

Linking Pollution and Viral Risk: Detection of Dioxins and Coronaviruses in Cats and Dogs

by Francesco Serra, Silvia Canzanella, Sergio Brandi, Gerardo Picazio, Anna Maria Pugliese, Luca Del Sorbo, Gianluca Miletti, Enza Ragosta, Emanuela Sannino, Filomena Fiorito, Mauro Esposito, Esterina De Carlo, Giovanna Fusco and Maria Grazia Amoroso

Viruses 2025, 17(9), 1271; https://doi.org/10.3390/v17091271 - 19 Sep 2025

Abstract

Viral and chemical analyses were performed on 80 dead cats and 51 dead dogs from the Campania Region (Southern Italy), with the aim of evaluating in vivo the potential correlation between coronavirus (CoV) infections and levels of environmental pollutants such as dioxins and [...] Read more.

Viral and chemical analyses were performed on 80 dead cats and 51 dead dogs from the Campania Region (Southern Italy), with the aim of evaluating in vivo the potential correlation between coronavirus (CoV) infections and levels of environmental pollutants such as dioxins and PCSs (PCDD/F, DL-PCB and NDL-PCB). The overall viral prevalence was 16.3% in cats and 23.5% in dogs. Both feline coronavirus (FCoV) and canine coronavirus (CCoV) were identified, with variable detection rates in all the other organs investigated, supporting studies that provide evidence of systemic viral spread. The highest prevalence of coronaviruses (CoVs) was observed in Naples (19.2% for FCoV; 30.7% for CCoV) and Caserta (11.1% for FCoV; 50.0% for CCoV), areas that include municipalities with the highest Municipality Index of Environmental Pressure (MIEP) scores. Chemical analyses showed that DL-PCBs were present at more elevated concentrations in CoV-infected dogs and cats than in non-infected animals, whereas ∑NDL-PCB and ∑PCDD/F were detected in greater amounts in non-infected subjects. Among PCDDs, the congener 2,3,7,8-TCDD displayed different distribution patterns between infected and non-infected animals. In cats, 70.0% of FCoV-positive individuals had 2,3,7,8-TCDD levels above the limit of quantification (LOQ), compared with 38.0% of FCoV-negative cats. In dogs, 78.0% of CCoV-infected animals exceeded the LOQ, compared with 20.0% of non-infected ones; this difference was statistically significant. The results of the study suggest that elevated levels of 2,3,7,8-TCDD may be associated with CCoV infection and replication in dogs, suggesting a possible relationship between environmental pollution and susceptibility to coronavirus infections. Full article

(This article belongs to the Section Animal Viruses)

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