Journal Description
Viruses
Viruses
is a peer-reviewed, open access journal of virology, published monthly online by MDPI. The Spanish Society for Virology (SEV), Canadian Society for Virology (CSV), Italian Society for Virology (SIV-ISV), Australasian Virology Society (AVS), Brazilian Society for Virology (BSV) and others are affiliated with Viruses and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Virology) / CiteScore - Q1 (Virology/Infectious Diseases)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 18.6 days after submission; acceptance to publication is undertaken in 2.5 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Companion journal: Zoonotic Diseases.
Impact Factor:
3.5 (2024);
5-Year Impact Factor:
3.7 (2024)
Latest Articles
Cross-Species Transmission Risks of a Quail-Origin H7N9 Influenza Virus from China Between Avian and Mammalian Hosts
Viruses 2025, 17(10), 1402; https://doi.org/10.3390/v17101402 - 21 Oct 2025
Abstract
The H7N9 influenza viruses, which are capable of causing severe respiratory syndrome in humans, were first discovered to infect humans in 2013 and continue to pose a persistent public health threat. Quail has been proposed as a potential intermediate host that may facilitate
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The H7N9 influenza viruses, which are capable of causing severe respiratory syndrome in humans, were first discovered to infect humans in 2013 and continue to pose a persistent public health threat. Quail has been proposed as a potential intermediate host that may facilitate the emergence of novel reassorted influenza A viruses with the capacity to infect humans across species barriers; however, information on the biological characterization of quail H7N9 remains limited. In this study, we isolated and identified an avian H7N9 influenza virus from quails, designated as A/quail/Hebei/CH06-07/2018 (H7N9) and abbreviated as CH06-07, in Hebei, China. Phylogenetic analyses revealed that both the HA gene and the NA gene of CH06-07 were clustered in the Eurasian lineage. Furthermore, CH06-07 exhibited binding affinity for both α2,3-linked and α2,6-linked sialic acid receptors and demonstrated high pathogenicity in both quails and mice. Notably, transmission studies revealed that CH06-07 not only exhibited efficient inter-quail transmission and inter-guinea pig transmission but also demonstrated effective cross-species transmission. Importantly, infected quails and guinea pigs generated significant quantities of viral aerosols (≥18,998 ± 1672 copies per liter of air at 3 days post-infection), and infectious viruses were successfully recovered from environmental aerosols. These findings highlight the necessity for continuous surveillance of the prevalence of quail-origin H7N9 influenza A viruses in poultry populations due to their potential threat to human health.
Full article
(This article belongs to the Section Animal Viruses)
Open AccessEditorial
Viruses Beyond Pathogens: Partners and Tools for Biotechnology
by
Patrick Materatski and Carla Varanda
Viruses 2025, 17(10), 1401; https://doi.org/10.3390/v17101401 - 21 Oct 2025
Abstract
For many years, viruses were regarded solely as agents of devastating diseases in humans, animals, and plants [...]
Full article
(This article belongs to the Special Issue The Application of Viruses to Biotechnology 3.0)
Open AccessArticle
Baseline Dysregulation in B, T, and NK Cells in COVID-19 Predicts Increased Late Mortality but Not Long-COVID Symptoms: Results from a Single-Center Observational Study
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Aleksandra Matyja-Bednarczyk, Radosław Dziedzic, Anna Drynda, Ada Gradzikiewicz, Monika Bociąga-Jasik, Krzysztof Wójcik, Sabina Lichołai, Karolina Górka, Natalia Celejewska-Wójcik, Tomasz Stachura, Kamil Polok, Lech Zaręba, Teresa Iwaniec, Krzysztof Sładek and Stanisława Bazan-Socha
Viruses 2025, 17(10), 1400; https://doi.org/10.3390/v17101400 (registering DOI) - 21 Oct 2025
Abstract
The SARS-CoV-2 pandemic presents a broad clinical spectrum from asymptomatic cases to severe respiratory failure with high mortality. Severe COVID-19 is characterized by immune dysregulation, including lymphopenia and alterations in the counts of T, B, and NK cells in peripheral blood. Due to
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The SARS-CoV-2 pandemic presents a broad clinical spectrum from asymptomatic cases to severe respiratory failure with high mortality. Severe COVID-19 is characterized by immune dysregulation, including lymphopenia and alterations in the counts of T, B, and NK cells in peripheral blood. Due to the limited data on long-term outcomes related to immune dysregulation, we aimed to analyze immunologic features at baseline in severe and mild COVID-19 cases and assess follow-up characteristics associated with later mortality and long-COVID signs. We included adult patients consecutively hospitalized with COVID-19 between June and November 2020 at the University Hospital in Kraków, corresponding to the first and second waves of COVID-19 in Poland. We enrolled only those who had been thoroughly assessed in terms of clinic and laboratory data, including immunological workups, and survived the acute phase of the disease. In 2025, between February and April (median time of follow-up: 54 months), we conducted a telephone questionnaire on long-COVID symptoms among survivors who had given their consent. Statistical analyses were performed to compare groups with severe and mild disease in terms of dysregulation in lymphocyte subpopulations and the follow-up outcomes. The study included 103 COVID-19 patients, comprising 53 severe (based on the need for at least high-flow nasal oxygen therapy) and 50 mild cases, with no differences in age, sex, and body mass index. Severe COVID-19 patients compared to mild cases had lower CD3+ T cells (count and percentage), CD4+ T cells (count and percentage), CD8+ T cells (count), and NK cells (count), but higher CD19+ B cells (percentage) at baseline (p < 0.05, all). At the time of follow-up, we evaluated 80 patients (77.7% of the baseline participants), with 23 (22.3%) patients lost to follow-up. Among patients analyzed in the follow-up, 23 (28.8%) had died, and 29 of the 57 survivors (50.9%) reported persistent long-COVID symptoms. Patients who died had significantly lower baseline counts of CD3+ T cells (377 vs. 655 cells/µL), CD4+ T cells (224 vs. 372 cells/µL), CD8+ T cells (113 vs. 188 cells/µL), and NK cells (118 vs. 157 cells/µL) compared to survivors (p < 0.05, all). Notably, the percentage of CD19+ B cells was higher in deceased individuals (19.2% vs. 13.5%; p = 0.049). In contrast, we did not document differences in baseline immunological data among survivors with and without long-COVID signs. Our study suggests that dysregulation in lymphocyte subpopulations during the COVID-19 acute phase may be associated with increased late mortality, but not with the persistence of long-COVID symptoms.
Full article
(This article belongs to the Special Issue COVID-19 Complications and Co-infections)
Open AccessArticle
JC Virus Agnogene Regulates Histone-Modifying Enzymes via PML-NBs: Transcriptomics in VLP-Expressing Cells
by
Yukiko Shishido-Hara and Takeshi Yaoi
Viruses 2025, 17(10), 1399; https://doi.org/10.3390/v17101399 (registering DOI) - 21 Oct 2025
Abstract
JC virus (JCV) replicates within the nuclei of glial cells in the human brain and causes progressive multifocal leukoencephalopathy. JCV possesses a small, circular, double-stranded DNA genome, divided into early and late protein-coding regions. The non-coding control region (NCCR) functions bidirectionally for both
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JC virus (JCV) replicates within the nuclei of glial cells in the human brain and causes progressive multifocal leukoencephalopathy. JCV possesses a small, circular, double-stranded DNA genome, divided into early and late protein-coding regions. The non-coding control region (NCCR) functions bidirectionally for both early and late genes, and the agnogene is located downstream of TCR and upstream of three capsid proteins in the late region. Previously, in cell culture systems, we demonstrated that these capsid proteins accumulate in intranuclear domains known as promyelocytic leukemia nuclear bodies (PML-NBs), where they assemble into virus-like particles (VLPs). To investigate the agnogene’s function, VLPs were formed in its presence or absence, and differential gene expression was analyzed using microarray technology. The results revealed altered expression of histone-modifying enzymes, including methyltransferases (EHMT1, PRMT7) and demethylases (KDM2B, KDM5C, KDM6B), as well as various kinases and phosphatases. Notably, CTDP1, which dephosphorylates the C-terminal domain of an RNA polymerase II subunit, was also differentially expressed. The changes were predominant in the presence of the agnogene. These findings indicate that the agnogene and/or its protein product likely influence epigenetic regulation associated with PML-NBs, which may influence cell cycle control. Consistently, in human brain tissue, JCV-infected glial cells displayed maintenance of a diploid chromosomal complement, likely through G2 arrest. The precise mechanism of this, however, remains to be elucidated.
Full article
(This article belongs to the Special Issue JC Polyomavirus)
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Open AccessReview
Immune Evasion by the NSs Protein of Rift Valley Fever Virus: A Viral Houdini Act
by
Kaylee Petraccione, James G. Omichinski and Kylene Kehn-Hall
Viruses 2025, 17(10), 1398; https://doi.org/10.3390/v17101398 (registering DOI) - 21 Oct 2025
Abstract
Rift Valley fever virus (RVFV) is a negative-sense arbovirus that causes several severe diseases, including hemorrhagic fever in ruminants and humans. There are currently no FDA-approved vaccines or therapeutics for RVFV. The viral nonstructural protein NSs acts like a molecular Harry Houdini, the
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Rift Valley fever virus (RVFV) is a negative-sense arbovirus that causes several severe diseases, including hemorrhagic fever in ruminants and humans. There are currently no FDA-approved vaccines or therapeutics for RVFV. The viral nonstructural protein NSs acts like a molecular Harry Houdini, the world-famous escape artist, to help the virus evade the host’s innate immune response and serves as the main virulence factor of RVFV. In this review, we discuss the molecular mechanisms by which NSs interacts with multiple factors to modulate host processes, evade the host immune response, and facilitate viral replication. The impact of NSs mutations that cause viral attenuation is also discussed. Understanding the molecular mechanisms by which NSs evades the host innate immune response is crucial for developing novel therapeutics and vaccines targeting RVFV.
Full article
(This article belongs to the Special Issue Bunyaviruses 2025)
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Open AccessArticle
Metatranscriptomic Analysis of Oropharyngeal Samples Reveals Common Respiratory Viruses and a Potential Interspecies Transmitted Picobirnavirus in the Wayuu Population, La Guajira, Colombia
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Beatriz Elena De arco-Rodríguez, Jhindy Tatiana Pérez-Lozada, Katherine Laiton-Donato, Dioselina Peláez-Carvajal, Gloria Mercedes Puerto-Castro and Diego Alejandro Álvarez-Díaz
Viruses 2025, 17(10), 1397; https://doi.org/10.3390/v17101397 (registering DOI) - 21 Oct 2025
Abstract
Acute respiratory infections and other infectious diseases causing acute febrile syndrome are major public health concerns in Colombia, particularly among vulnerable populations such as the Wayuu Indigenous community in Manaure, La Guajira. To investigate their viral etiology, 55 nasopharyngeal swabs and 58 serum
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Acute respiratory infections and other infectious diseases causing acute febrile syndrome are major public health concerns in Colombia, particularly among vulnerable populations such as the Wayuu Indigenous community in Manaure, La Guajira. To investigate their viral etiology, 55 nasopharyngeal swabs and 58 serum samples were collected from febrile Wayuu individuals in Manaure. RT-qPCR screening identified Coronavirus, Enteroviruses, Adenovirus, and Influenza A/B in respiratory samples, while no arboviruses were detected in serum. Sixteen representative samples underwent metatranscriptomic next-generation sequencing (mtNGS) using the Chan-Zuckerberg ID (CZ-ID) platform. This analysis confirmed RT-qPCR findings and additionally revealed six viral contigs related to Orthopicobirnavirus hominis. Sequencing coverage enabled the reconstruction of a consensus RdRp segment, which was phylogenetically compared with sequences from diverse hosts. The virus clustered within genogroup 1, alongside Colombian isolates linked to severe acute respiratory infection. The absence of strict host-specific clustering suggests possible interspecies transmission. These findings underscore the complementary roles of targeted and unbiased approaches: RT-qPCR detected common respiratory viruses, whereas mtNGS uncovered a virus previously unreported in this community. Overall, mtNGS emerges as a powerful tool to support viral surveillance and provide baseline evidence in indigenous populations, emphasizing the need to decentralize advanced molecular diagnostics and strengthen public health capacity in Colombia.
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(This article belongs to the Special Issue Virus Biosensing)
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Open AccessCorrection
Correction: Shehata et al. The Hidden Threat: Rodent-Borne Viruses and Their Impact on Public Health. Viruses 2025, 17, 809
by
Awad A. Shehata, Rokshana Parvin, Shadia Tasnim, Phelipe Magalhães Duarte, Alfonso J. Rodriguez-Morales and Shereen Basiouni
Viruses 2025, 17(10), 1396; https://doi.org/10.3390/v17101396 (registering DOI) - 21 Oct 2025
Abstract
In the original publication [...]
Full article
(This article belongs to the Special Issue Rodent-Borne Viruses 2026)
Open AccessSystematic Review
Vertical Transmission of Hepatitis B and C—Then and Now—A Comprehensive Literature Systematic Review
by
Ruxandra Dobritoiu, Daniela Pacurar, Raluca Maria Vlad and Doina Anca Plesca
Viruses 2025, 17(10), 1395; https://doi.org/10.3390/v17101395 - 20 Oct 2025
Abstract
Background: According to a WHO global hepatitis report, the global prevalence of hepatitis B in 2022 was 254 million and for hepatitis C it was 50 million. The estimated number of people newly infected by viral hepatitis declined from 3 million in 2019
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Background: According to a WHO global hepatitis report, the global prevalence of hepatitis B in 2022 was 254 million and for hepatitis C it was 50 million. The estimated number of people newly infected by viral hepatitis declined from 3 million in 2019 to 2.2 million in 2022. Of these, 1.2 million are hepatitis B infections and nearly 1.0 million are hepatitis C infections. Regarding vertical transmission, it is estimated that 4 to 5 million children are infected worldwide every year from HBV-positive mothers. The United States declared that hepatitis C is the commonest chronic blood-borne infection, with an increase in HCV birth infections from 1.8 to 4.7 per 1000 births. Objectives: This systematic review focuses on highlighting the most suitable screening methods and maternal interventions to prevent HBV/HCV mother-to-child transmission, as well as the appropriate prophylactic strategies for newborns. Materials and methods: We searched a medical database (PubMed) to find papers regarding mother-to-child transmission of hepatitis B and C. Inclusion criteria were human-based studies, studies with large cohorts of subjects, studies conducted in different parts of the globe and position papers from various international associations. Exclusion criteria were non-human-based studies and non-English publications. To present and synthesize results we made use of thematic analysis and narrative synthesis. Results: We included 103 publications. For hepatitis B, the combination of maternal antiviral therapy during pregnancy and timely administration of HBV vaccine alongside HBIG to the newborn has proven to be highly effective in lowering transmission rates. Hepatitis C vertical transmission lacks an effective vaccine or immuno-prophylaxis, turning prevention strategies into a continuous battle. Conclusions: Vertical transmission of hepatitis B and C continues to be a major contributor to the global burden of chronic viral hepatitis. Strengthening prenatal care programs, improving access to diagnostic and therapeutic resources and enhancing public health policies are essential to curb vertical transmission of both hepatitis B and C.
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(This article belongs to the Section Human Virology and Viral Diseases)
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Open AccessArticle
Investigating Apple Rubbery Wood Virus 2: HTS-Based Detection in Hungary and Involvement of sRNA-Based Regulation Processes During Its Infection
by
Almash Jahan and Éva Várallyay
Viruses 2025, 17(10), 1394; https://doi.org/10.3390/v17101394 - 20 Oct 2025
Abstract
Pomme fruits are propagated vegetatively, thereby facilitating frequent viral transmission. The causative agent of apple rubbery wood disease, apple rubbery wood virus 2 (ARWV2), can infect apple and pear. The branches of ARWV2-infected, symptomatic trees are flexible due to the decreased lignification of
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Pomme fruits are propagated vegetatively, thereby facilitating frequent viral transmission. The causative agent of apple rubbery wood disease, apple rubbery wood virus 2 (ARWV2), can infect apple and pear. The branches of ARWV2-infected, symptomatic trees are flexible due to the decreased lignification of the xylem. In this research, we reanalysed our small RNA (sRNA) HTS datasets to survey the presence of ARWV2 in Hungary. Validation of HTS using RT-PCR revealed infection in several cultivars. The following RT-PCR-based survey revealed the infection of 17 trees, including not only apple, but also pears, one quince, and a rootstock, without showing any rubbery wood symptoms. Analysis of the sRNA datasets allowed us to profile the sRNA pattern of ARWV2-infected and non-infected trees, and characterise the differential expression pattern of vsiRNAs, sRNAs, and miRNAs targeting the lignin biosynthetic pathway. The results confirmed that the gene-expression changes in the genes that regulate lignification cannot be directly correlated with the presence of the virus, which can explain its frequent latent presence. The variable titre and sequence of the virus, and mixed-infection status of the trees, make its reliable diagnostics challenging, which could be achieved as a result of further research.
Full article
(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)
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Open AccessArticle
Reinfection Dynamics of Disease-Free Cassava Plants in Three Agroecological Regions of Côte d’Ivoire
by
John Steven S. Seka, Justin S. Pita, Modeste K. Kouassi, William J. -L. Amoakon, Bekanvié S. M. Kouakou, Mariam Combala, Daniel H. Otron, Brice Sidoine Essis, Konan Evrard B. Dibi, Angela O. Eni, Nazaire K. Kouassi and Fidèle Tiendrébéogo
Viruses 2025, 17(10), 1393; https://doi.org/10.3390/v17101393 - 20 Oct 2025
Abstract
Cassava mosaic disease (CMD) is caused by begomoviruses and can result in yield losses of up to 90% in susceptible varieties. Using disease-free planting material from in vitro cultures is one of the most effective ways of controlling this disease. A CMD epidemiological
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Cassava mosaic disease (CMD) is caused by begomoviruses and can result in yield losses of up to 90% in susceptible varieties. Using disease-free planting material from in vitro cultures is one of the most effective ways of controlling this disease. A CMD epidemiological assessment was conducted in fields established with disease-free plantlets in Bouaké, Dabou, and Man, selected for their contrasting agroecological and CMD prevalence conditions. Virus and whitefly species characterisation was performed using PCR and sequencing. CMD incidence and severity were lowest at the Man site and highest at the Dabou site. Although whitefly abundance was relatively low at the Man and Bouaké sites compared to the Dabou site, they were a significant factor in the spread of the disease. While all resistant varieties remained asymptomatic, susceptible and tolerant varieties became infected, and some tolerant varieties were able to recover from the disease. Molecular analyses revealed the presence of two viral species: Begomovirus manihotis (ACMV) and Begomovirus manihotiscameroonense (EACMCMV). No viral infection was detected 4 weeks after planting (WAP). Cases of single infection and double infection were observed at 12 and 20 WAP. Also, no double infections were found at the Man site, in contrast to the Bouaké site (12 WAP: 2.36%) and Dabou site (12 WAP: 2.59%; 20 WAP: 5.76%). EACMCMV was found in a single infection in Bouaké (12 WAP: 1.39%) and Man (20 WAP: 0.66%). The whitefly species Bemisia tabaci and Bemisia afer were most commonly found feeding on all cassava varieties. A high diversity of whitefly species was observed in Bouaké and Dabou compared to Man. Furthermore, the Bemisia tabaci species identified in this study was found to be able to transmit ACMV and EACMCMV viruses. These highlights would contribute to improving CMD management and control strategies.
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(This article belongs to the Special Issue Economically Important Viruses in African Crops)
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Open AccessArticle
A Novel Municipal-Level Approach to Uncover the Hidden Burden of Hepatitis C: A Replicable Model for National Elimination Strategies
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Pietro Torre, Silvana Mirella Aliberti, Tommaso Sarcina, Mariano Festa, Chiara D’Amore, Giuseppe D’Adamo, Michele Gambardella, Antonella Santonicola, Gaetano Manzi, Mario Masarone, Mario Capunzo and Marcello Persico
Viruses 2025, 17(10), 1392; https://doi.org/10.3390/v17101392 - 19 Oct 2025
Abstract
Background: Hepatitis C Virus (HCV) remains a global health challenge as WHO elimination targets are not achievable in most countries, mainly due to the high number of undiagnosed individuals. In Italy, where national elimination efforts are ongoing, regional disparities further hinder progress. This
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Background: Hepatitis C Virus (HCV) remains a global health challenge as WHO elimination targets are not achievable in most countries, mainly due to the high number of undiagnosed individuals. In Italy, where national elimination efforts are ongoing, regional disparities further hinder progress. This study aimed to characterize the hidden burden of chronic HCV infection across t he territory of the Province of Salerno, Southern Italy, to suggest a novel municipal-level screening approach, with implications for national strategies. Methods: We analyzed records of residents diagnosed with chronic HCV infection and linked to care between 2015 and 2022. Data included age, sex, municipality of residence, HCV genotype, and fibrosis stage. Observed prevalence was compared with expected prevalence derived from national/regional benchmarks. Municipalities were categorized as urban or rural based on the resident population. Results: A total of 3528 cases were identified across 139 municipalities. Patients had a mean age of 63 years, and 54% were male. Half were diagnosed at an advanced stage (F3–F4), with genotype 1b being predominant. The hidden burden increased with age and showed a higher prevalence in rural areas compared to urban ones, with values of about 7 vs. 3 per 1000 inhabitants respectively. Logistic regression analysis identified age, male sex, urban residence, and genotype 1b as factors associated with advanced fibrosis or cirrhosis. Conclusions: This is the first Italian study to apply a standardized municipal-level classification to quantify the hidden burden of HCV. The model identifies underdiagnosed areas, highlights urban–rural disparities (a higher degree of underdiagnosis in rural areas versus a higher frequency of late diagnosis in urban ones), and provides a replicable tool for precision public health. Its adoption could enhance national HCV elimination efforts by supporting targeted screening, optimized resource allocation, and equitable access to care.
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(This article belongs to the Section Human Virology and Viral Diseases)
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Open AccessArticle
A Highly Sensitive BRET-Based Reporter for Live-Cell Detection of HIV-1 Protease Activity and Inhibitor Screening
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Matteo Centazzo, Atalie Verra-Victoria Djossou, Silvia Pavan and Gualtiero Alvisi
Viruses 2025, 17(10), 1391; https://doi.org/10.3390/v17101391 (registering DOI) - 19 Oct 2025
Abstract
Given their role in viral polyprotein processing, viral proteases (PRs) are excellent targets for antiviral therapy. Most assays developed for screening PR inhibitors are in vitro assays, and therefore have several limitations, including the inability to account for cell permeability, toxicity and the
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Given their role in viral polyprotein processing, viral proteases (PRs) are excellent targets for antiviral therapy. Most assays developed for screening PR inhibitors are in vitro assays, and therefore have several limitations, including the inability to account for cell permeability, toxicity and the need for compounds activation within cells. The development of cellular reporters overcoming these limitations is therefore highly desirable. In this study, we developed two different Bioluminescence Resonance Energy Transfer (BRET)-based reporters for Human Immunodeficiency virus-1 (HIV-1) PR, allowing the simultaneous monitoring of cell viability and HIV-1 PR activity. The reporters employ two different BRET pairs as donor and acceptor moieties: Renilla luciferase (RLuc) with Yellow Fluorescent Protein (YFP), and Nano luciferase (NLuc) with mNeonGreen (mNG), both linked by the HIV-1 p2/p7 cleavage site. While both reporters specifically detected HIV-1 protease activity, mNG-p2/p7-NLuc exhibited higher sensitivity, increased energy transfer and better spectral separation between donor and acceptor emissions, resulting in a significantly higher BRET ratio. mNG-p2/p7-NLuc was used to quantify the effect of a panel of protease inhibitors in living cells, assessing simultaneously cell viability and HIV-1 PR activity. Additionally, it was employed to measure the potency of well-known HIV-1 PR inhibitors. Together, these findings demonstrate the utility of the mNG-p2/p7-NLuc reporter as a cell-based tool for the evaluation of HIV-1 PR activity and inhibitor efficacy. Its dual-readout capability provides a valuable platform for antiviral drug screening in physiologically relevant conditions.
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(This article belongs to the Special Issue HIV Protease)
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Open AccessArticle
Assessment of Biological Properties of Recombinant Lumpy Skin Disease Viruses with Deletions of Immunomodulatory Genes
by
Aisha Issabek, Arailym Bopi, Nurlan Kozhabergenov, Bermet Khudaibergenova, Kulyaisan Sultankulova and Olga Chervyakova
Viruses 2025, 17(10), 1390; https://doi.org/10.3390/v17101390 - 19 Oct 2025
Abstract
Rational design of capripoxvirus-based vaccine vectors can be achieved by knockout of immunomodulatory genes. In this study, the effect of knockout of the immunomodulatory genes LSDV005, LSDV008 and LSDV066 on the replication of Lumpy skin disease virus in cell cultures and the immune
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Rational design of capripoxvirus-based vaccine vectors can be achieved by knockout of immunomodulatory genes. In this study, the effect of knockout of the immunomodulatory genes LSDV005, LSDV008 and LSDV066 on the replication of Lumpy skin disease virus in cell cultures and the immune response to an integrated foreign antigen were assessed. The knockout of genes was performed by homologous recombination under conditions of temporary dominant selection. It was found that single knockout of the LSDV005 gene and the LSDV008 gene did not affect the replicative activity of recombinant viruses in vitro (Atyrau-5 and Atyrau-B). Both single knockout of the LSDV066 gene and in combination with knockout of LSDV005 or LSDV008 led to a decrease in the replicative activity of recombinant LSDVs. The recombinant Atyrau-5J(IL18) with LSDV005 gene knockout induced production of antibodies to the integrated antigen in mice. Prime-boost vaccination with all studied recombinants increased the level of interferon-γ. In addition, during immunization with the recombinant Atyrau-5J(IL18) secretion of interleukin-2 was significantly increased. The study of the functions of immunomodulatory genes and their effect on the expression of inserted sequences of foreign antigens is promising for the creation of highly effective polyvalent vector vaccines for animals.
Full article
(This article belongs to the Special Issue Veterinary Virology: Unraveling Host–Pathogen Interactions for Animal Health)
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Open AccessArticle
Molecular Epidemiology of Hepatitis E Virus in Hungary (2018–2025): Emergence of Rare Subtypes and First Detection of HEV-4 in Central Europe
by
Ágnes Dencs, Andrea Hettmann, Levente Zsichla, Viktor Müller, Anett Dömötör, Ágnes Barna-Lázár, Erzsébet Barcsay and Mária Takács
Viruses 2025, 17(10), 1389; https://doi.org/10.3390/v17101389 - 18 Oct 2025
Abstract
Hepatitis E virus (HEV) is an emerging cause of viral hepatitis in Europe, with increasing recognition in immunocompromised patients. While genotype 3 (HEV-3) is most prevalent in the region, molecular epidemiology data from Hungary have been limited. HEV strains from 118 RNA-positive patients
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Hepatitis E virus (HEV) is an emerging cause of viral hepatitis in Europe, with increasing recognition in immunocompromised patients. While genotype 3 (HEV-3) is most prevalent in the region, molecular epidemiology data from Hungary have been limited. HEV strains from 118 RNA-positive patients diagnosed between 2018 and 2025 were genotyped. Next-generation sequencing yielded near-complete HEV genomes for 76 samples. HEV-3 was dominant (98.3%). Subtype 3a was the most common (34.7%), followed by 3c, 3f, and 3e. Rare subtypes (3g, 3h, 3i, 3m, 3ra) and HEV-4b were detected for the first time in Hungary. Among immunocompromised patients, 41.6% developed chronic infection. Ribavirin resistance-associated mutations G1634R and V1479I were frequently detected. In silico analysis of potential multiple infections indicated the presence of at least two HEV strains of distinct origin in six patients. Our surveillance revealed extensive genetic diversity of HEV in Hungary. The detection of rare HEV-3 subtypes and the first documented occurrence of HEV-4b in the country highlight likely viral introductions linked to the increasing international trade. Ongoing surveillance is essential in protecting high-risk groups and limiting HEV transmission in a globalized food system.
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(This article belongs to the Section Human Virology and Viral Diseases)
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Open AccessCommunication
Serological Evidence of Exposure to Eurasian-Lineage HPAI H5N1 Clade 2.3.4.4b in Wild Mammals in Ohio, USA, 2024–2025
by
Mohammad Jawad Jahid, Madison C. Owsiany, Lauren M. Smith, Bryant M. Foreman, Zijing Cao, Deborah L. Carter, David E. Stallknecht, Brendan Shirkey, Rebecca L. Poulson and Jacqueline M. Nolting
Viruses 2025, 17(10), 1388; https://doi.org/10.3390/v17101388 - 18 Oct 2025
Abstract
The Goose/Guandong lineage of highly pathogenic avian influenza virus [A/Goose/Guangdong/1/1996(H5N1)] is the progenitor of the currently circulating Eurasian-lineage highly pathogenic avian influenza H5N1 clade 2.3.4.4b and has been the most consequential highly pathogenic avian influenza lineage globally. Despite increased reports of infections, the
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The Goose/Guandong lineage of highly pathogenic avian influenza virus [A/Goose/Guangdong/1/1996(H5N1)] is the progenitor of the currently circulating Eurasian-lineage highly pathogenic avian influenza H5N1 clade 2.3.4.4b and has been the most consequential highly pathogenic avian influenza lineage globally. Despite increased reports of infections, the extent of exposure and role of wild mammals in the ecology and transmission dynamics of the virus remains poorly understood. We surveyed wild mammals in Ohio, United States to investigate the potential spillover of highly pathogenic H5N1 avian influenza clade 2.3.4.4b. While no active infections—defined as positive results indicative of viral replication and potential propagation—were detected by swab-based molecular tests, serological assays revealed antibodies against multiple avian influenza virus antigens in raccoons and opossums. Specifically, antibodies to avian influenza virus nucleoprotein were detected in 54.9% (n = 61) of samples using enzyme-linked immunosorbent assay; antibodies to Eurasian-lineage highly pathogenic avian influenza H5 clade 2.3.4.4b and North American low pathogenic avian influenza H5 were detected in 43.2% (n = 48) and 22.5% (n = 25) of samples, respectively, using virus neutralization assays; and antibodies to avian influenza virus neuraminidase were detected in 44.1% (n = 49) of samples using enzyme-linked lectin assay. All seropositive animals were sampled at Ohio marshes with previously confirmed highly pathogenic avian influenza H5N1 detections in waterfowl. These findings suggest prior exposure of wild mammals to these viruses without mortality events. Wild mammals may play an intermediary role in the mammalian adaptation of avian influenza A viruses. Therefore, ongoing surveillance of wild mammals is crucial for assessing the risk to public health.
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(This article belongs to the Special Issue Influenza Viruses in Wildlife 2025)
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Open AccessArticle
SARS-CoV-2 Entry Can Be Mimicked in C. elegans Expressing Human ACE2: A New Tool for Pharmacological Studies
by
Margherita Romeo, Sara Baroni, Maria Monica Barzago, Samuela Gambini, Ada De Luigi, Daniela Iaconis, Andrea Rosario Beccari, Maddalena Fratelli and Luisa Diomede
Viruses 2025, 17(10), 1387; https://doi.org/10.3390/v17101387 - 18 Oct 2025
Abstract
Testing medical countermeasures for SARS-CoV-2 transmission using vertebrates can be hindered by legislation regulating animal experimentation, high costs, and ethical concerns. To overcome these challenges, we propose a new Caenorhabditis elegans strain that constitutively expresses the human angiotensin-converting enzyme 2 receptor (ACE2). This
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Testing medical countermeasures for SARS-CoV-2 transmission using vertebrates can be hindered by legislation regulating animal experimentation, high costs, and ethical concerns. To overcome these challenges, we propose a new Caenorhabditis elegans strain that constitutively expresses the human angiotensin-converting enzyme 2 receptor (ACE2). This resulted in significant impairment of reproduction and a defect in pharyngeal function compared to wild-type (WT) worms. SARS-CoV-2 infection was simulated by treating worms with the receptor-binding domain (RBD) of the spike protein, which caused dose-dependent and time-dependent pharyngeal impairment in ACE2 worms but not in WT worms. The toxicity of RBD was prevented by administering an anti-human ACE2 antibody, demonstrating that interactions with the ACE2 receptor are essential. The ACE2-expressing worm strain was further used for pharmacological research with Raloxifene. In vitro, 1–3 μM of Raloxifene reduced the entry of lentiviral particles carrying the Wuhan variant and B.1.1.7 UK and B.1.1.529 Omicron strains into HEK293-ACE2, in addition to particles expressing N501Y-mutated or P681H-mutated spike proteins. Raloxifene (0.1–1 μM) completely counteracted RBD toxicity in ACE2 worms, indicating that this strain offers a cost-effective in vivo screening platform for molecules with effects involving interactions with the ACE2 receptor.
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(This article belongs to the Section Coronaviruses)
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Open AccessReview
Metabolic Hostile Takeover: How Influenza Virus Reprograms Cellular Metabolism for Replication
by
Xianfeng Hui, Xiaowei Tian, Shihuan Ding, Ge Gao, Xin Zhao, Jiyan Cui, Yiru Hou, Tiesuo Zhao and Hui Wang
Viruses 2025, 17(10), 1386; https://doi.org/10.3390/v17101386 - 17 Oct 2025
Abstract
Influenza viruses are adept at hijacking host cellular machinery to facilitate their replication and propagation. A critical aspect of this hijacking involves the reprogramming of host cell metabolism. This review summarizes current findings on how influenza virus infection alters major metabolic pathways, including
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Influenza viruses are adept at hijacking host cellular machinery to facilitate their replication and propagation. A critical aspect of this hijacking involves the reprogramming of host cell metabolism. This review summarizes current findings on how influenza virus infection alters major metabolic pathways, including enhanced glycolysis, suppression of oxidative phosphorylation, diversion of TCA cycle intermediates for biosynthesis, and upregulation of lipid and amino acid metabolism. Key nutrients like glucose, glutamine, and serine are redirected to support viral RNA synthesis, protein production, and membrane formation. Moreover, these metabolic changes also modulate host immune responses, potentially aiding in immune evasion. We highlight the role of transcription factors such as SREBPs in lipid synthesis and the impact of one-carbon metabolism on epigenetic regulation. Finally, we discuss how targeting virus-induced metabolic shifts, using agents like 2-deoxyglucose or fatty acid synthesis inhibitors, offers promising avenues for antiviral intervention, while emphasizing the need for selective approaches to minimize harm to normal cells.
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(This article belongs to the Special Issue Interaction Between Influenza Virus and Host Cell)
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Open AccessTechnical Note
vvv2_align_SE, vvv2_align_PE/vvv2_display: Galaxy-Based Workflows and Tool Designed to Perform, Summarize and Visualize Variant Calling and Annotation in Viral Genome Assemblies
by
Alexandre Flageul, Edouard Hirchaud, Céline Courtillon, Flora Carnet, Paul Brown, Béatrice Grasland and Fabrice Touzain
Viruses 2025, 17(10), 1385; https://doi.org/10.3390/v17101385 (registering DOI) - 17 Oct 2025
Abstract
Background: Next-generation sequencing (NGS) analysis of viral samples generates results dispersed across multiple files—genome assembly, variant calling, and functional annotations—making integrated interpretation challenging. Variants often yield numerous low-frequency or non-significant variants, yet only a small fraction are biologically relevant. Virologists must manually
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Background: Next-generation sequencing (NGS) analysis of viral samples generates results dispersed across multiple files—genome assembly, variant calling, and functional annotations—making integrated interpretation challenging. Variants often yield numerous low-frequency or non-significant variants, yet only a small fraction are biologically relevant. Virologists must manually sift through extensive data to identify meaningful mutations, a time-consuming and error-prone process. To address these practical challenges, we developed vvv2_display, a dedicated summarization and visualization tool, integrated within comprehensive Galaxy workflows. Results: vvv2_display streamlines variant interpretation by consolidating key results into two concise and interoperable outputs. The first output is a PNG image showing alignment coverage depth and genomic annotations, with significant variants displayed along the genome as symbols whose height reflects frequency and shape indicates the affected protein. At a glance, this enables virologists to identify all deviations from a reference viral genome. Each significant variant is assigned a unique identifier that directly links to the second output: a tab-separated (TSV) text file listing only high-confidence variants, with frequencies, flanking nucleotides, and impacted genes and proteins. This cross-referenced design supports rapid, accurate, and intuitive data exploration. Availability: vvv2_display is open source, available on Github and installable via Mamba.
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(This article belongs to the Section Animal Viruses)
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Open AccessArticle
Dissecting the Unique Self-Assembly Landscape of the HIV-2 Capsid Protein
by
Matthew Cook, Pushpanjali Bhardwaj, Faith Lozano, Christian Freniere, Ryan J. Malonis and Yong Xiong
Viruses 2025, 17(10), 1384; https://doi.org/10.3390/v17101384 - 17 Oct 2025
Abstract
Human immunodeficiency virus type 2 (HIV-2) is a lentivirus closely related to HIV-1 but exhibits distinct molecular and clinical features that influence viral infectivity and efficacy of antiretroviral therapy. The HIV capsid is a critical structural component with multifaceted roles during infection and
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Human immunodeficiency virus type 2 (HIV-2) is a lentivirus closely related to HIV-1 but exhibits distinct molecular and clinical features that influence viral infectivity and efficacy of antiretroviral therapy. The HIV capsid is a critical structural component with multifaceted roles during infection and mediates some of the observed divergence between HIV-1 and HIV-2. Unlike HIV-1, study of the HIV-2 capsid is limited and standard protocols for the in vitro assembly of HIV-1 capsid protein (CA) lattice structures have not been successfully translated to the HIV-2 context. This work identifies effective approaches for the assembly of the HIV-2 CA lattice and leverages this to biochemically characterize HIV-2 CA assemblies and mutant phenotypes. Our findings elaborate on the sensitivity of HIV-2 CA to chemical conditions and reveal that it assembles into a more varied spectrum of particle morphologies compared to HIV-1. Utilizing these assemblies, we tested the hypothesis that HIV-1 and HIV-2 employ divergent mechanisms to stabilize CA oligomer forms and investigate the effects of non-conserved substitutions at the CA inter-protomer interfaces. This work advances our understanding of the key biochemical determinants of HIV-2 CA assembly that are distinct from HIV-1 and may contribute to their divergent virological properties.
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(This article belongs to the Special Issue Structural and Mechanistic Advances in Retroviral Biology)
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Predicting the Landscape Epidemiology of Foot-and-Mouth Disease in Endemic Regions: An Interpretable Machine Learning Approach
by
Moh A. Alkhamis, Hamad Abouelhassan, Abdulaziz Alateeqi, Abrar Husain, John M. Humphreys, Jonathan Arzt and Andres M. Perez
Viruses 2025, 17(10), 1383; https://doi.org/10.3390/v17101383 - 17 Oct 2025
Abstract
Foot-and-mouth disease (FMD) remains a devastating threat to livestock health and food security in the Middle East and North Africa (MENA), where complex interactions among host, environmental, and anthropogenic factors constitute an optimal endemic landscape for virus circulation. Here, we applied an interpretable
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Foot-and-mouth disease (FMD) remains a devastating threat to livestock health and food security in the Middle East and North Africa (MENA), where complex interactions among host, environmental, and anthropogenic factors constitute an optimal endemic landscape for virus circulation. Here, we applied an interpretable machine learning (ML) statistical framework to model the epidemiological landscape of FMD between 2005 and 2025. Furthermore, we compared the ecological niche of serotypes O and A in the MENA region. Our ML algorithms demonstrated high predictive performance (accuracies > 85%) in identifying the geographical extent of high-risk areas, including under-reported regions such as the Southern and Northeastern Arabian Peninsula. Sheep density emerged as the dominant predictor for all FMD outbreaks and serotype O, with significant non-linear relationships with wind, temperature, and human population density. In contrast, serotype A risk was primarily influenced by buffalo density and proximity to roads and cropland. Our in-depth interaction and Shapley value analyses provided fine-scale interpretability by interrogating the threshold effects of each feature in shaping the spatial risk of FMD. Further implementation of our analytical pipeline to guide risk-based surveillance programs and intervention efforts will help reduce the economic and public health impacts of this devastating animal pathogen.
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(This article belongs to the Special Issue Advances in Endemic and Emerging Viral Diseases in Livestock: 2nd Edition)
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