Viruses

18 pages, 1794 KB

Open AccessReview

Deciphering the Role of Macrophages in RSV Infection and Disease

by Sara Van Looy, Axelle Fransen, Lotte Jacobs, Sofie Schaerlaekens, Martina Ceconi, Francisco I. Serrano-Cano, Noor Ul Hudda, Laurence Van Moll, Marie De Smedt, Paul Cos and Peter L. Delputte

Viruses 2025, 17(10), 1351; https://doi.org/10.3390/v17101351 - 8 Oct 2025

Abstract

Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in infants, the elderly, and immunocompromised persons. Innate immune responses to RSV, which are crucial for containment of the infection yet may also be linked to severe disease, are well-studied in [...] Read more.

Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in infants, the elderly, and immunocompromised persons. Innate immune responses to RSV, which are crucial for containment of the infection yet may also be linked to severe disease, are well-studied in the main RSV target cells, respiratory epithelial cells, but the role of pulmonary macrophages (MΦs), key innate immune regulators, remains incompletely defined. This review addresses the interaction of RSV with MΦ, discussing the susceptibility of these cells to productive infection, and MΦ responses to RSV, including cytokine and chemokine release and inflammasome activation. Furthermore, factors contributing to variability in MΦ infectivity and responses, such as MΦ polarization, age, differences in RSV isolates, co-infections, and prior innate priming, are presented. Finally, the review highlights discrepancies observed across experimental models, MΦ origins, and RSV isolates used, complicating the interpretation of MΦ-RSV interactions, thereby underscoring the need for standardized methodologies. Full article

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

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Graphical abstract

23 pages, 3900 KB

Open AccessArticle

Stockholm Paradigm in the Study of Influenza H1N1 Viruses: A New Approach to the Study of Zoonotic Risk Coupling Multiple Correspondence Analysis and Multi-Locus Phylogenies

by Sofia Galvão Feronato, Rafael Antunes Baggio, Hellen Geremias Gatica Santos and Guilherme Ferreira Silveira

Viruses 2025, 17(10), 1350; https://doi.org/10.3390/v17101350 - 8 Oct 2025

Abstract

The Stockholm Paradigm, a multilevel framework for studying coevolutionary interactions, it is a promising method for obtaining a globally relevant understanding of the emergence of present and past host–parasite and insect–plant interactions. This research aimed to expand the application of the Paradigm to [...] Read more.

The Stockholm Paradigm, a multilevel framework for studying coevolutionary interactions, it is a promising method for obtaining a globally relevant understanding of the emergence of present and past host–parasite and insect–plant interactions. This research aimed to expand the application of the Paradigm to virus–host interactions, considering that viruses are being subjected to the same evolutionary forces as any other living organism. By applying different data science techniques, we described and discussed capacity and opportunity traits for Influenza A H1N1 strains, and how they might influence the pathogen’s host repertoire evolution, and thus ranked different strains according to their emergence risk in the human population. We hope to contribute to the application of different methods for understanding disease emergence, and consequently to the development of new public health strategies for preventing (re)emerging diseases. Full article

(This article belongs to the Section General Virology)

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14 pages, 2396 KB

Open AccessArticle

Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020–2021

by Taylor E. Weary, Lawrence H. Zhou, Lauren MacDonald, Daniel Ibañez IV, Chance Jaramillo, Christopher D. Dunn, Timothy F. Wright, Kathryn A. Hanley, Tony L. Goldberg and Teri J. Orr

Viruses 2025, 17(10), 1349; https://doi.org/10.3390/v17101349 - 8 Oct 2025

Abstract

Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 [...] Read more.

Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans. Full article

(This article belongs to the Section Animal Viruses)

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13 pages, 1564 KB

Open AccessArticle

Pan-Resistant HIV-1 Drug Resistance Among Highly Treated Patients with Virological Failure on Dolutegravir-Based Antiretroviral Therapy in Zimbabwe

by Tendai Washaya, Benjamin Chimukangara, Justin Mayini, Sandra Bote, Nyasha Chin’ombe, Shungu Munyati and Justen Manasa

Viruses 2025, 17(10), 1348; https://doi.org/10.3390/v17101348 - 8 Oct 2025

Abstract

The HIV-1 epidemic continues to challenge global public health, especially in sub-Saharan Africa. The rise in drug-resistant viruses, particularly pan-resistant strains, threatens treatment effectiveness, hindering progress toward UNAIDS viral suppression goals. This is critical in low-to-middle income countries (LMICs) like Zimbabwe, where treatment [...] Read more.

The HIV-1 epidemic continues to challenge global public health, especially in sub-Saharan Africa. The rise in drug-resistant viruses, particularly pan-resistant strains, threatens treatment effectiveness, hindering progress toward UNAIDS viral suppression goals. This is critical in low-to-middle income countries (LMICs) like Zimbabwe, where treatment options and access to drug resistance testing are limited. This cross-sectional study analyzed 102 genotypes from patients with HIV-1 RNA ≥ 1000 copies/mL after at least 6 months on a dolutegravir (DTG)-based ART. HIV-1 genotyping and drug resistance interpretation were performed using the Stanford HIV Drug Resistance Database. Overall, 62% of genotypes harbored at least one drug resistance mutation, with 27% showing integrase strand transfer inhibitor (INSTI)-associated mutations. High-level resistance to DTG and cabotegravir was found in 14% and 23% of integrase sequences, respectively, primarily driven by G118R and E138K/T mutations. Pan-resistance was observed in 18% of complete genotypes, with one case of four class resistance. These results highlight the emergence of INSTI resistance in LMICs. The study underscores the urgent need for enhanced HIV drug resistance testing, continuous surveillance, and strategic optimization of ART regimens in resource-constrained settings to ensure effective HIV management. Full article

(This article belongs to the Special Issue Current ART, Virologic Failure and Implications for HIV Drug Resistance, 2nd Edition)

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17 pages, 2320 KB

Open AccessArticle

Virucidal and Antibacterial Chitosan–NanoCu Film-Coating-Based Technology: Complete Analysis of Its Performance on Various Surfaces

by Victoria Belen Ayala-Peña, María Julia Martin, Jessica Otarola, Florencia Favatela, Jimena Soledad Gonzalez, Ana Lucía Conesa, Cybele Carina García, Claudia Soledad Sepúlveda, Vera Alejandra Alvarez and Verónica Leticia Lassalle

Viruses 2025, 17(10), 1347; https://doi.org/10.3390/v17101347 - 7 Oct 2025

Abstract

The transmission of viruses and bacteria via surfaces remains a persistent challenge for healthcare systems, leading to high public health costs and significant environmental impact due to the widespread use and disposal of single-use products. This study aims to evaluate the feasibility of [...] Read more.

The transmission of viruses and bacteria via surfaces remains a persistent challenge for healthcare systems, leading to high public health costs and significant environmental impact due to the widespread use and disposal of single-use products. This study aims to evaluate the feasibility of using surface-covering films, based on biopolymers and inorganic nanoparticles, with strong antiviral and antibacterial properties, as a strategy to prevent infection transmission while offering a sustainable alternative to disposable materials. To this end, we developed a sprayable chitosan-based solution embedded with copper oxide nanoparticles (CH.CA@Cu). The solution demonstrated antibacterial activity against both Gram-positive and Gram-negative bacteria as well as virucidal activity, predominantly within one minute of exposure, against a wide range of viruses. After spraying various materials, the resulting film surfaces exhibited excellent adherence and uniform coverage, maintaining their integrity after contact. A field trial conducted in high-traffic environments confirmed the coating’s effectiveness. This long-lasting antiviral action supports their implementation, since the coated surface can continuously deactivate viruses regardless of infective doses of exposure, thereby reducing viral transmission. These findings will expand biopolymers’ current applicability while guiding us toward the adoption of green and eco-friendly technologies, thus reducing waste production. Full article

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

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21 pages, 2768 KB

Open AccessArticle

Sindbis Virus–Host Interactions in Human Neuroblastoma Cells: Implications for Viral Pathogenesis and Replication

by Kornélia Bodó, Zoltán Kopasz, Viktória Nyári, Krisztina Leiner, Péter Engelmann, Brigitta Zana, Roland Hetényi, Dániel Hanna, Krisztián Bányai, Mónika Madai, Gréta Varga and Anett Kuczmog

Viruses 2025, 17(10), 1346; https://doi.org/10.3390/v17101346 - 7 Oct 2025

Abstract

Sindbis virus (SINV) is a mosquito-borne alphavirus capable of causing neurological and immunological symptoms in humans, yet its effects on neural/immune systems remain insufficiently characterized. This study aimed to examine SINV replication, UV-C light inactivation, apoptosis induction, and immune gene modulation in human [...] Read more.

Sindbis virus (SINV) is a mosquito-borne alphavirus capable of causing neurological and immunological symptoms in humans, yet its effects on neural/immune systems remain insufficiently characterized. This study aimed to examine SINV replication, UV-C light inactivation, apoptosis induction, and immune gene modulation in human SH-SY5Y neuroblastoma cells. Following viral adaptation and infectious dose determination, SINV replication and inactivation were assessed using RT-qPCR and dsRNA immunofluorescence. Apoptotic markers (caspase-3, Bax, Bcl-2) were analyzed by immunofluorescence and immune genes expression kinetics (TLR3/7, RIGI, MDA5, IL-1β, IL-6, TNFα, IL-10, IFNβ and β-catenin) were measured at defined time points post-infection by RT-qPCR. SH-SY5Y cells supported productive SINV infection, with viral RNA detectable as early as 3 hpi and marked cytopathic effects by 24 hpi. A custom-built UV-C chamber achieved complete viral inactivation following 3 × 30 s exposures. We observed SINV time-course replication and UV-C inactivation with conspicuous morphological alterations in SH-SY5Y cells. Furthermore, SINV triggered caspase-dependent apoptosis and robust transcriptional upregulation of innate immune genes, peaking between 12–16 hpi and declining by 30 hpi. These findings elucidate the temporal dynamics of SINV replication, cell death mechanisms, and immune activation in a neuronal context, contributing to a better understanding of SINV neuropathogenesis. Full article

(This article belongs to the Special Issue Mosquito-Borne Encephalitis Viruses)

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3 pages, 133 KB

Open AccessEditorial

Impact of Co-Infections on COVID-19: Special Issue Editorial

by Telugu Akula Narasaraju, Sunil More and Yee-Joo Tan

Viruses 2025, 17(10), 1345; https://doi.org/10.3390/v17101345 - 7 Oct 2025

Abstract

Since its emergence in December 2019, the COVID-19 pandemic has culminated in over 7 [...] Full article

(This article belongs to the Special Issue Impact of Co-infections in COVID-19: Predisposing Mechanisms and Interplay between Invasive Viral, Bacterial and Fungal Pathogens)

15 pages, 1663 KB

Open AccessArticle

Elucidating Alterations in Viral and Human Gene Expression Due to Human Papillomavirus Integration by Using Multimodal RNA Sequencing

by Kana Tamai, Sonoko Kinjo, Ayumi Taguchi, Kazunori Nagasaka, Daisuke Yoshimoto, Anh Quynh Duong, Yoko Yamamoto, Hitoshi Iuchi, Mayuyo Mori, Kenbun Sone, Michiaki Hamada, Kei Kawana, Kazuho Ikeo, Yasushi Hirota and Yutaka Osuga

Viruses 2025, 17(10), 1344; https://doi.org/10.3390/v17101344 (registering DOI) - 6 Oct 2025

Abstract

Human papillomavirus (HPV) infection is a primary driver of cervical cancer. Integration of HPV into the human genome causes persistent expression of viral oncogenes E6 and E7, which promote carcinogenesis and disrupt host genomic function. However, the impact of integration on host gene [...] Read more.

Human papillomavirus (HPV) infection is a primary driver of cervical cancer. Integration of HPV into the human genome causes persistent expression of viral oncogenes E6 and E7, which promote carcinogenesis and disrupt host genomic function. However, the impact of integration on host gene expression remains incompletely understood. We used multimodal RNA sequencing, combining total RNA-seq and Cap Analysis of Gene Expression (CAGE), to clarify virus–host interactions after HPV integration. HPV-derived transcripts were detected in 17 of 20 clinical samples. In most specimens, transcriptional start sites (TSSs) showed predominant early promoter usage, and transcript patterns differed with detectable E4 RNA region. Notably, the high RNA expressions of E4 region and viral-human chimeric RNAs were mutually exclusive. Chimeric RNAs were identified in 13 of 17 samples, revealing 16 viral integration sites (ISs). CAGE data revealed two patterns of TSS upregulation centered on the ISs: a two-sided pattern (43.8%) and a one-sided pattern (31.3%). Total RNA-seq showed upregulation of 12 putative cancer-related genes near ISs, including MAGI1-AS1, HAS3, CASC8, BIRC2, and MMP12. These findings indicate that HPV integration drives transcriptional activation near ISs, enhancing expression of adjacent oncogenes. Our study deepens understanding of HPV-induced carcinogenesis and informs precision medicine strategies for cervical cancer. Full article

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

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19 pages, 2770 KB

Open AccessArticle

Strain-Specific Variability in Viral Kinetics, Cytokine Response, and Cellular Damage in Air–Liquid Cultures of Human Nasal Organoids After Infection with SARS-CoV-2

by Gina M. Aloisio, Trevor J. McBride, Letisha Aideyan, Emily M. Schultz, Ashley M. Murray, Anubama Rajan, Erin G. Nicholson, David Henke, Laura Ferlic-Stark, Amal Kambal, Hannah L. Johnson, Elina A. Mosa, Fabio Stossi, Sarah E. Blutt, Pedro A. Piedra and Vasanthi Avadhanula

Viruses 2025, 17(10), 1343; https://doi.org/10.3390/v17101343 - 6 Oct 2025

Abstract

SARS-CoV-2 variants have demonstrated distinct epidemiological patterns and clinical presentations throughout the COVID-19 pandemic. Understanding variant-specific differences at the respiratory epithelium is crucial for understanding their pathogenesis. Here, we utilized human nasal organoid air–liquid interface (HNO-ALI) cell cultures to compare the viral replication [...] Read more.

SARS-CoV-2 variants have demonstrated distinct epidemiological patterns and clinical presentations throughout the COVID-19 pandemic. Understanding variant-specific differences at the respiratory epithelium is crucial for understanding their pathogenesis. Here, we utilized human nasal organoid air–liquid interface (HNO-ALI) cell cultures to compare the viral replication kinetics, innate immune response, and epithelial damage of six different strains of SARS-CoV-2 (B.1.2, WA, Alpha, Beta, Delta, and Omicron). All variants replicated efficiently in HNO-ALIs, but with distinct replication kinetic patterns. The Delta variant exhibited delayed replication kinetics, achieving a steady state at 6 days post-infection compared to 3 days for other variants. Cytokine analysis revealed robust pro-inflammatory and chemoattractant responses (IL-6, IL-8, IP-10, CXCL9, and CXCL11) in WA1, Alpha, Beta, and Omicron infections, while Delta significantly dampened the innate immune response, with no significant induction of IL-6, IP-10, CXCL9, or CXCL11. Immunofluorescence and H&E analysis showed that all variants caused significant ciliary damage, though WA1 and Delta demonstrated less destruction at early time points (3 days post-infection). Together, these data show that, in our HNO-ALI model, the Delta variant employs a distinct “stealth” strategy characterized by delayed replication kinetics and epithelial cell innate immune evasion when compared to other variants of SARS-CoV-2, potentially explaining a mechanism that the Delta variant can use for its enhanced transmissibility and virulence observed clinically. Our findings demonstrate that variant-specific differences at the respiratory epithelium could explain some of the distinct clinical presentations and highlight the utility of the HNO-ALI system for the rapid assessment of emerging variants. Full article

(This article belongs to the Special Issue Viral Infection in Airway Epithelial Cells)

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13 pages, 707 KB

Open AccessArticle

Pulmonary Embolism in Hospitalized COVID-19 Patients in Romania: Prevalence, Risk Factors, Outcomes

by Diana-Maria Mateescu, Adrian-Cosmin Ilie, Ioana Cotet, Cristina Guse, Camelia-Oana Muresan, Ana-Maria Pah, Marius Badalica-Petrescu, Stela Iurciuc, Maria-Laura Craciun, Adina Avram and Alexandra Enache

Viruses 2025, 17(10), 1342; https://doi.org/10.3390/v17101342 - 5 Oct 2025

Abstract

(1) Background: Pulmonary embolism (PE) is a severe complication of coronavirus disease 2019 (COVID-19), particularly in hospitalized patients. Data from Eastern Europe, including Romania, are limited, despite potential regional differences in demographics, comorbidities, and thromboprophylaxis practices. (2) Methods: This retrospective cohort study included [...] Read more.

(1) Background: Pulmonary embolism (PE) is a severe complication of coronavirus disease 2019 (COVID-19), particularly in hospitalized patients. Data from Eastern Europe, including Romania, are limited, despite potential regional differences in demographics, comorbidities, and thromboprophylaxis practices. (2) Methods: This retrospective cohort study included 395 adults hospitalized with RT-PCR-confirmed COVID-19 at the “Victor Babeș” Clinical Hospital of Infectious Diseases and Pneumophthisiology, Timișoara, Romania, from September 2022 to December 2024. Demographic, clinical, laboratory, and imaging data were extracted from medical records. PE was confirmed by computed tomography pulmonary angiography (CTPA). Group comparisons used chi-square and t-tests, with multivariable logistic regression to identify independent PE predictors. (3) Results: PE was diagnosed in 47 patients (11.9%). Compared to those without PE, patients with PE had higher D-dimer (5305.00 ± 1251.00 vs. 537.00 ± 203.00 ng/mL, p < 0.001), fibrinogen (6.33 ± 0.74 vs. 3.51 ± 0.60 g/L, p < 0.001), and PT/INR (1.68 ± 0.21 vs. 1.05 ± 0.09, p < 0.001). Prior venous thromboembolism (VTE; 19.1% vs. 8.3%, p = 0.03) and prolonged immobilization (61.7% vs. 23.0%, p < 0.001) were significant risk factors. Intensive care unit (ICU) transfer occurred in 59.6% of PE cases, with a 25.5% in-hospital mortality rate. All PE patients received anticoagulation; 10.6% underwent thrombolysis. (4) Conclusions: In this Romanian cohort, one of the first large-scale studies in Eastern Europe, PE was prevalent among hospitalized COVID-19 patients, associated with elevated coagulation markers, identifiable risk factors, and high mortality. Early recognition and optimized thromboprophylaxis are critical to improve outcomes. Full article

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

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16 pages, 3401 KB

Open AccessArticle

Bovine Viral Diarrhea in Kazakhstan

by Elvira Bashenova, Raikhan Nissanova, Vladimir Kirpichenko, Perizat Akshalova, Angelina Malysheva, Fariza Ikramkulova, Alena Cherusheva, Yergali Abduraimov, Aralbek Rsaliyev, Kunsulu Zakarya, Aisha Zharmukhametova, Saltanat Kuatbekova, Artyom Kuligin, Zhandos Abay, Zhibek Zhetpisbay, Seidigapbar Mamadaliyev, Ainur Nurpeisova and Markhabat Kassenov

Viruses 2025, 17(10), 1341; https://doi.org/10.3390/v17101341 - 5 Oct 2025

Abstract

Bovine Viral Diarrhea Virus (BVDV) is a globally important cattle pathogen causing substantial economic losses. In Kazakhstan, BVDV’s epidemiological status remains poorly characterized due to the absence of systematic surveillance. We carried out a cross-sectional study of cattle herds across Kazakhstan, using ELISA [...] Read more.

Bovine Viral Diarrhea Virus (BVDV) is a globally important cattle pathogen causing substantial economic losses. In Kazakhstan, BVDV’s epidemiological status remains poorly characterized due to the absence of systematic surveillance. We carried out a cross-sectional study of cattle herds across Kazakhstan, using ELISA to detect anti-BVDV antibodies and RT-PCR to identify active infections. Positive samples underwent sequencing for phylogenetic analysis of circulating strains. Additionally, a standard reference serum panel was developed to measure virus neutralization titers (ND₅₀) and to evaluate cross-neutralization with Border Disease virus (BDV). Antibodies against BVDV were prevalent, with seropositivity ranging from 28.89% to 96.13% across surveyed regions. Active BVDV infection was confirmed by RT-PCR in 17 animals. Phylogenetic analysis with 2 samples from Mangystau region classified the virus as BVDV2 genotype. The reference serum panel exhibited high neutralizing titers ND₅₀ up to 1:286 against the local BVDV-1 isolate. Notably, these sera also neutralized BDV, albeit at lower titers ND₅₀ 1:45. These findings provide crucial baseline epidemiological data and enhanced diagnostic tools for BVDV in Kazakhstan. They highlight the need for improved surveillance and will inform strategic control measures against this economically significant cattle disease. Full article

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

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14 pages, 2344 KB

Open AccessArticle

Development of a Highly Specific Monoclonal Antibody-Based Sandwich ELISA for Rapid Detection of Porcine Circovirus Type 3

by Zhen Li, Jiaying Zhao, Ang Tian, Hao Wu, Huanchun Chen and Yunfeng Song

Viruses 2025, 17(10), 1340; https://doi.org/10.3390/v17101340 - 5 Oct 2025

Abstract

Porcine circovirus type 3 (PCV3), initially identified in the United States in 2016, is associated with multisystemic inflammation, myocarditis, reproductive failure in sows, and growth retardation in piglets, posing a significant economic threat to the swine industry. In this study, prokaryotic-expressed recombinant PCV3 [...] Read more.

Porcine circovirus type 3 (PCV3), initially identified in the United States in 2016, is associated with multisystemic inflammation, myocarditis, reproductive failure in sows, and growth retardation in piglets, posing a significant economic threat to the swine industry. In this study, prokaryotic-expressed recombinant PCV3 Cap protein was used to immunize mice and rabbits. A monoclonal antibody (mAb 4G1) was generated through hybridoma technology, targeting a novel linear epitope (³⁷DYYDKK⁴²) within the first β-sheet of the Cap structure. This epitope exhibits high conservation (99.35%, 1239/1247) based on sequence alignment analysis, and residues 39 and 42 are critical residues affecting mAb binding. Subsequently, using rabbit polyclonal antibody (pAb) as the capture antibody and mAb 4G1 as the detection antibody, a double antibody sandwich ELISA (DAS-ELISA) method was developed. The assay demonstrates a cut-off value of 0.271, a detection limit for positive pig serum is 1:800, and shows no cross-reactivity with other swine pathogens. Intra- and inter-assay coefficients of variation were <10%, with a linear detection range for Cap protein down to 3.4 ng/mL. The coincidence rate between the DAS-ELISA and qPCR was 93.33% (70/75) for PCV3 detection in serum, with a kappa value of 0.837. This study establishes a simple, sensitive, and operationally efficient DAS-ELISA and provides a reference for monitoring PCV3 infection in swine herds. Full article

(This article belongs to the Section Animal Viruses)

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11 pages, 262 KB

Open AccessReview

Advances in Prevention, Screening, and Early Detection of HPV-Associated Head and Neck Cancers

by Evangelos Zazas, Panagiota Economopoulou, Ioannis Kotsantis, Anastasios Kyriazoglou, Menelaos G. Samaras, Periklis Foukas and Amanda Psyrri

Viruses 2025, 17(10), 1339; https://doi.org/10.3390/v17101339 - 5 Oct 2025

Abstract

HPV-related head and neck cancers are increasing globally and although they constitute a major public health problem, there are currently no validated screening or early detection methods in widespread clinical use. This review discusses advances in clinical and molecular aspects of prevention, screening, [...] Read more.

HPV-related head and neck cancers are increasing globally and although they constitute a major public health problem, there are currently no validated screening or early detection methods in widespread clinical use. This review discusses advances in clinical and molecular aspects of prevention, screening, and early detection of HPV-related head and neck cancers (HNCs), such as potential use of HPV blood or saliva seropositivity, RNA biomarkers, liquid biopsy, circulating tumor DNA, and proteomics. In addition to HPV vaccination, public education about vaccination, smoking, and safe sexual practices is warranted. Continued research is warranted to define optimal use and integration of approaches for prevention, screening, and early detection methods of HNCs. Full article

(This article belongs to the Special Issue HPV-Associated Cancers 2025)

16 pages, 3706 KB

Open AccessArticle

Molecular Epidemiology of Human Metapneumovirus Infections in Children from San Luis Potosí-Mexico

by Nadia Martínez-Marrero, Juan Carlos Muñoz-Escalante, Jan Michell Yerena-Rivera, Luis Rubén Jaime-Rocha, José J. Leija-Martínez, Ana María González-Ortiz and Daniel E. Noyola

Viruses 2025, 17(10), 1338; https://doi.org/10.3390/v17101338 - 2 Oct 2025

Abstract

Lower respiratory infections are a leading cause of death in children under five years. Human metapneumovirus (HMPV) is an underestimated causal agent of these infections. In this study, the molecular epidemiology of HMPV associated with respiratory infections in Mexican children between August 2023 [...] Read more.

Lower respiratory infections are a leading cause of death in children under five years. Human metapneumovirus (HMPV) is an underestimated causal agent of these infections. In this study, the molecular epidemiology of HMPV associated with respiratory infections in Mexican children between August 2023 and August 2024 was determined. Sequences were also analyzed for predicted N- and O-linked glycosylation sites. Overall, 34 sequences from infants with respiratory infections were obtained; 32 were assigned to the A2b2 genotype, one to A2b1, and one to B2. All but one of the A2b2 sequences carried the 111-nucleotide duplication of the G gene; the remaining sequence carried the 180-nucleotide duplication. The samples assigned to the A2b1 and B2 genotypes did not have a duplication. The HMPV-A phylogeny did not show a clustering of Mexican sequences as a single monophyletic group. Four N-linked glycosylation sites were predicted in the HMPV-A sequences and three in the B sequence. The number of O-linked glycosylation sites predicted in HMPV-A ranged from 61 to 77 and were 61 in the HMPV-B sequence. This first description of HMPV genotypes and the diverse array of G protein N- and O-linked glycosylation patterns found in a Mexican pediatric population in the post-pandemic period contributes to the understanding of the global spread of HMPV. Full article

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

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21 pages, 3978 KB

Open AccessArticle

Role of the Chaperone Protein 14-3-3η in Regulation of the Infection Dynamics of the Influenza A (H1N1) Virus

by Debarima Chatterjee, Partha Pratim Mondal, Anneshwa Bhattacharya and Alok Kumar Chakrabarti

Viruses 2025, 17(10), 1337; https://doi.org/10.3390/v17101337 - 30 Sep 2025

Abstract

The 14-3-3 protein family, which includes the isoforms η, γ, ε, θ, β, and ζ, is essential for controlling a number of pathways linked to DNA and RNA viruses, including HIV, influenza A virus (IAV), measles virus, HRSV, and double-stranded DNA viruses. TRIM32, [...] Read more.

The 14-3-3 protein family, which includes the isoforms η, γ, ε, θ, β, and ζ, is essential for controlling a number of pathways linked to DNA and RNA viruses, including HIV, influenza A virus (IAV), measles virus, HRSV, and double-stranded DNA viruses. TRIM32, an E3 ubiquitin ligase, has been reported to target IAV’s PB1 polymerase for species-specific degradation via ubiquitination. Notably, 14-3-3η binds to phosphorylated TRIM32, preventing its autoubiquitylation and forming soluble but inactive cytoplasmic aggregates that regulate TRIM32 levels. However, the functional link between 14-3-3η, TRIM32, and PB1 during viral infection remains unclear. In this study, we establish a mechanistic connection between 14-3-3η–TRIM32 and TRIM32–PB1 interactions in IAV (H1N1) infection. We demonstrate that 14-3-3η directly interacts with PB1, influencing viral replication. Using transient knockdown models, we show that 14-3-3η deficiency alters influenza virus-induced cytotoxicity, cell death, immune responses, and reactive oxygen species (ROS) production. Additionally, we observe a significant reduction in the soluble TRIM32 levels in 14-3-3η-deficient cells, which leads to increased PB1 accumulation and thus suggests a critical regulatory role for 14-3-3η in PB1 stability. Our findings reveal a novel function of 14-3-3η in influenza virus infection, demonstrating its role in PB1 regulation via TRIM32 and its impact on innate immune activation. This study highlights 14-3-3η as a possible target for antiviral treatments against influenza and offers fresh insights into the host–virus relationship. Full article

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

16 pages, 2455 KB

Open AccessArticle

Prevalence and VP1 Gene Evaluation Analysis of Porcine Sapelovirus in Yunnan Province, China, from 2024 to 2025

by Zhanhong Li, Xuyu Tang, Zhenxing Zhang, Pei Zhu, Zhuoran Li, Peng Liu, Qi Yang, Li Meng, Xiutao Sun, Zhen Yang, Qiuyan Yang, Yifang Zhang and Jianling Song

Viruses 2025, 17(10), 1336; https://doi.org/10.3390/v17101336 - 30 Sep 2025

Abstract

Porcine Sapelovirus (PSV) is widely prevalent in pig herds throughout the world and induces diarrhea, encephalomyelitis, respiratory tract symptoms, and reproductive disorders. However, the epidemiological and genetic evolution characteristics of PSV remain unclear in Yunnan Province. In this study, 1622 fecal samples were [...] Read more.

Porcine Sapelovirus (PSV) is widely prevalent in pig herds throughout the world and induces diarrhea, encephalomyelitis, respiratory tract symptoms, and reproductive disorders. However, the epidemiological and genetic evolution characteristics of PSV remain unclear in Yunnan Province. In this study, 1622 fecal samples were collected from pig farms in Yunnan Province. PSV and its co-infection rates with other pathogens were detected; then, the PSV VP1 gene was amplified and sequenced; and the genetic evolution characteristics of the VP1 gene were analyzed. The overall infection rate of PSV in Yunnan Province was 36.50%, and the differences among regions were significant (p < 0.05). The positive rates among different seasons were significantly different (p < 0.01), ranging from 73.33% (autumn) to 19.00% (summer). The PSV positive rate in diarrhea samples (47.26%) was significantly higher (p < 0.001) than that of non-diarrhea samples (31.77%). The co-infection rates of PSV with porcine rotavirus (PoRV) and PSV with porcine epidemic diarrhea virus (PEDV) were 5.07% and 3.04%. A total of 36 VP1 sequences were obtained, and the average identity among the 36 sequences was 85.3%, which was higher than that with other reference strains. Phylogenetic analysis revealed that all 36 PSV strains belonged to the PSV-1 genotype. The VP1 gene was under strong negative selection pressure (average dN/dS = 0.0838); however, the 95th amino acid was under positive selection pressure. Our study revealed the epidemiological, co-infection, and genetic evolution characteristics of PSV in pig herds of Yunnan Province, providing more data for preventing and controlling diarrhea pathogens in pigs. Full article

(This article belongs to the Section Animal Viruses)

12 pages, 871 KB

Open AccessArticle

First Serological Evidence of Crimean-Congo Hemorrhagic Fever Virus Infections in Croatia: A Multispecies Surveillance Approach Emphasising the Role of Sentinel Hosts

by Gorana Miletic, Ivona Coric, Snjezana Kovac, Alenka Skrinjaric, Magda Kamber Taslaman, Margarita Bozikovic, Ljubo Barbic, Viktor Masovic, Jelena Prpic, Lorena Jemersic and Vladimir Stevanovic

Viruses 2025, 17(10), 1335; https://doi.org/10.3390/v17101335 - 30 Sep 2025

Abstract

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne zoonotic pathogen of growing public health concern in southeastern Europe. This study provides the first serological evidence of CCHFV circulation in Croatia, based on testing 1473 serum samples from farm and companion animals, including sheep, [...] Read more.

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne zoonotic pathogen of growing public health concern in southeastern Europe. This study provides the first serological evidence of CCHFV circulation in Croatia, based on testing 1473 serum samples from farm and companion animals, including sheep, horses, cattle, goats, dogs, and cats. A total of 109 samples (7.4%) tested positive for CCHFV antibodies using a commercially available enzyme-linked immunosorbent assay (ELISA) kit. The highest seroprevalence was recorded in sheep (28.3%), followed by horses (4.3%) and a single cat (0.5%), with no antibodies detected in cattle, goats, or dogs. Almost all seropositive animals originated from coastal and subcoastal Croatia, where Hyalomma ticks are present. Only two seropositive cases were detected in continental areas. Sheep samples from several farms in Zadar County showed intra-farm seropositivity rates of up to 85.7%, suggesting localised virus circulation likely influenced by vector distribution and farm-level practices. No viral ribonucleic acid (RNA) was detected by quantitative reverse transcription polymerase chain reaction (qRT-PCR), consistent with the transient nature of viremia in most animal hosts. These findings confirm the silent circulation of CCHFV in Croatia and reinforce the need for targeted, regionally adapted surveillance strategies that integrate multiple hosts and support early warning systems aligned with the One Health concept. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Viral Zoonoses)

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26 pages, 3861 KB

Open AccessArticle

Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest

by Zafeiro Zisi, Isabel Ruiz Movilla, Nikolas Basler, Lila Close, Lucas Ghijselings, Robby Van der Hoeven, Maria Ioanna Papadaki, Ester Rabbinowitsch, Fiona Van Reeth, Jill Swinnen, Elise Vogel, Christine Vos, Inge Hanssen and Jelle Matthijnssens

Viruses 2025, 17(10), 1334; https://doi.org/10.3390/v17101334 - 30 Sep 2025

Abstract

Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In [...] Read more.

Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2–99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples’ virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development. Full article

(This article belongs to the Special Issue Advances in Plant Virus/Viroid Detection and Identification Methods)

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19 pages, 955 KB

Open AccessReview

HTLV-1 and ATLL: Epidemiology, Oncogenesis, and Opportunities for Community-Informed Research in the United States

by Adrian Altieri, Sean Patrick Reilly, Abu Mansalay, Alan Soo-Beng Khoo, Nettie Johnson, Zafar K. Khan, Amy Leader, Pooja Jain and Pierluigi Porcu

Viruses 2025, 17(10), 1333; https://doi.org/10.3390/v17101333 - 30 Sep 2025

Abstract

Human T-cell leukemia virus type 1 (HTLV-1), the first oncogenic human retrovirus, causes adult T-cell leukemia/lymphoma (ATLL), an aggressive neoplasm of mature CD4+ T-cells that is incurable in most patients and is associated with a median survival of less than 1 year. HTLV-1 [...] Read more.

Human T-cell leukemia virus type 1 (HTLV-1), the first oncogenic human retrovirus, causes adult T-cell leukemia/lymphoma (ATLL), an aggressive neoplasm of mature CD4+ T-cells that is incurable in most patients and is associated with a median survival of less than 1 year. HTLV-1 also causes inflammatory disorders, including HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and uveitis. The estimated lifetime risks of ATLL and HAM/TSP in HTLV-1 carriers are 3–5% and 0.25–1.8%, respectively. Although there is uncertainty about other health effects of HTLV-1, a recent meta-analysis showed an association between HTLV-1 and cardiovascular, cerebrovascular, and metabolic diseases and a 57% increased risk of early mortality in HTLV-1 carriers, independent of ATLL or HAM/TSP. Furthermore, emerging studies in endemic areas show that outcomes for common cancers, such as cervical cancer and lymphoma (non-ATLL), are inferior in HTLV-1 carriers compared to publicly reported data. Thus, the impact of HTLV-1 may be greater and more diverse than currently understood. This review provides an outline of the prevalence and impact of HTLV-1 and associated disorders in the US, focused on—but not limited to—ATLL, with an emphasis on the social determinants of health that can affect the success of screening and prevention strategies. We also discuss the mechanisms by which HTLV-1 drives the pathogenesis of ATLL and potential strategies for early diagnosis and intervention. Finally, we conclude by suggesting approaches to designing and implementing community-informed research initiatives in HTLV-1 and ATLL. Full article

(This article belongs to the Special Issue Human T-Cell Leukemia Virus (HTLV) Infection and Treatment: 2nd Edition)

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