Viruses

21 pages, 1286 KB

Open AccessReview

Deciphering HPAI Influenza A Virus (H5N1): Molecular Basis of Pathogenicity, Zoonotic Potential, and Advances in Vaccination Strategies

by Imran Mohammad, Mohammed Ibrahim Hajelbashir, Mahmoud H. El-Bidawy, Abdulwahab Abuderman, Murtaja Satea, Abdullah M. R. Arafah, Md. Rizwan Ansari, Mahjabeen Rahmani, Mohiuddin Khan Warsi, Nawal Helmi and Mohammad Azhar Kamal

Viruses 2026, 18(4), 410; https://doi.org/10.3390/v18040410 - 26 Mar 2026

Abstract

The ongoing panzootic of the highly pathogenic avian influenza (HPAI) H5N1 virus, dominated by clade 2.3.4.4b, constitutes a significant global threat to wildlife, animal health, and public health. Once characterized by sporadic outbreaks, H5N1 has evolved into a sustained, year-round infection with an [...] Read more.

The ongoing panzootic of the highly pathogenic avian influenza (HPAI) H5N1 virus, dominated by clade 2.3.4.4b, constitutes a significant global threat to wildlife, animal health, and public health. Once characterized by sporadic outbreaks, H5N1 has evolved into a sustained, year-round infection with an expanded host range that now includes numerous mammalian species. Its high pathogenicity is primarily driven by the acquisition of a polybasic haemagglutinin cleavage site, enabling systemic viral spread, alongside emerging endothelial and neurotropic properties that contribute to severe disease and high mortality in mammals. Although zoonotic transmission remains limited, H5N1 continues to accumulate mutations associated with mammalian adaptation, particularly within the haemagglutinin and polymerase complex. Notably, recent outbreaks in U.S. dairy cattle highlight the emergence of novel mammalian reservoirs with increased human exposure risk. Concurrently, vaccination strategies are advancing beyond traditional adjuvanted inactivated vaccines toward next-generation platforms, including mRNA and virus-like particle vaccines, designed for rapid deployment and broader immune protection. However, ongoing viral evolution, constrained vaccine availability, and gaps in coordinated surveillance underscore the urgent need for an integrated One Health approach to reduce panzootic risk. Full article

(This article belongs to the Special Issue H5N1 Influenza Viruses)

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14 pages, 2976 KB

Open AccessArticle

HHV-6A Drives Epigenetic Reprogramming via an EZH2–SIRT1 Axis to Sustain Mutant p53 and Reshape Oncogenic Inflammatory Signaling

by Rossella Benedetti, Michele Di Crosta, Alessia Stirparo, George Alexandru Aron, Stefania Mardente, Roberta Santarelli, Roberta Gonnella, Maria Saveria Gilardini Montani and Mara Cirone

Viruses 2026, 18(4), 409; https://doi.org/10.3390/v18040409 - 26 Mar 2026

Abstract

We previously demonstrated that human herpesvirus 6A infects papillary thyroid cancer cells (BCPAP), inducing molecular changes compatible with a tumor-promoting phenotype, including increased expression of R273H mutant TP53 (mutp53), upregulation of c-Myc, and enhanced secretion of IL-6. To investigate whether and how epigenetic [...] Read more.

We previously demonstrated that human herpesvirus 6A infects papillary thyroid cancer cells (BCPAP), inducing molecular changes compatible with a tumor-promoting phenotype, including increased expression of R273H mutant TP53 (mutp53), upregulation of c-Myc, and enhanced secretion of IL-6. To investigate whether and how epigenetic mechanisms contribute to these virus-induced effects, we examined the histone methyltransferase EZH2, a key regulator of chromatin repression frequently altered in cancer. HHV-6A infection reduced EZH2 expression and global H3K27me3 levels. Pharmacological inhibition of EZH2 using DS-3201 reproduced some of the molecular effects of viral infection, including increased mutp53 stability. Both viral infection and EZH2 inhibition induced delayed upregulation of SIRT1, which mediated deacetylation-dependent stabilization of mutp53 while reducing c-Myc expression. Indeed, the inhibition of SIRT1 with EX-527 reversed mutp53 accumulation but restored c-Myc expression and increased extracellular IL-6 release. This drug also reduced cell survival, suggesting that SIRT1 supports cellular adaptation to oncogenic stress triggered by EZH2 loss. Overall, our findings identify an epigenetic axis in which the HHV-6A-mediated downregulation of EZH2 induces SIRT1, regulating mutp53 stability and c-Myc expression and reshaping inflammatory signaling to maintain cell viability. These results establish a mechanistic link between viral infection, epigenetic remodeling, and oncogenic dependency. They also suggest that targeting IL-6 signaling could represent a therapeutic vulnerability in HHV-6A-associated thyroid cancer, particularly in combination with SIRT1 inhibitors. Full article

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

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10 pages, 887 KB

Open AccessArticle

Characterization of the Alfalfa Pollen Virome

by Lev G. Nemchinov, Sam Grinstead, Olga A. Postnikova and Brian M. Irish

Viruses 2026, 18(4), 408; https://doi.org/10.3390/v18040408 - 25 Mar 2026

Abstract

Vertical transmission of plant pathogenic viruses is an important component of viral persistence, survival, and spread in agricultural production systems. This type of transmission is of considerable economic significance as it can cause major crop losses by serving as the initial focus of [...] Read more.

Vertical transmission of plant pathogenic viruses is an important component of viral persistence, survival, and spread in agricultural production systems. This type of transmission is of considerable economic significance as it can cause major crop losses by serving as the initial focus of infection for future epidemics. Vertical transmission occurs when a virus is passed on to offspring either by direct invasion of the developing seed embryo from infected mother plants or through infected pollen grains after fertilization. We have recently demonstrated via high-throughput sequencing that mature seeds of the agriculturally important forage crop alfalfa (Medicago sativa L.) are associated with a broad range of viruses, some of which could potentially spread over long distances via seed. With the exception of the alfalfa mosaic virus, little is currently known about viral transmission through alfalfa pollen and its subsequent impact on the disease epidemiology of the crop. The objective of this study was to screen pollen from diverse alfalfa genotypes for pathogenic viruses and assess their risk of transmission. The pollen was collected from alfalfa genotypes selected for fungal disease resistance and agronomic performance in the USDA ARS pre-breeding program in Prosser, WA. Full article

(This article belongs to the Special Issue Plant Virus Surveillance and Metagenomics 2026)

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22 pages, 3076 KB

Open AccessArticle

Identification of Conserved B and T Cell Epitopes in Glycoprotein S of Mexican Porcine Epidemic Diarrhea Virus (PEDV) Strains via Immunoinformatics Analysis, Molecular Docking, and Immunofluorescence

by Jesús Zepeda-Cervantes, Alan Fernando López Hernández, Yair Hernández Gutiérrez, Gerardo Guerrero Velázquez, Diego Emiliano Gaytan Vera, Alan Juárez-Barragán, Ana Paola Pérez Hernández, Mirna G. García-Castillo, Armando Hernández García, Rosa Elena Sarmiento Silva, Alejandro Benítez Guzmán and Luis Vaca

Viruses 2026, 18(4), 407; https://doi.org/10.3390/v18040407 - 25 Mar 2026

Abstract

The porcine epidemic diarrhea virus (PEDV) causes a gastrointestinal disease generating mortality rates approaching 100% in piglets worldwide. The S glycoprotein of PEDV is the main target for the development of vaccines. Two vaccines approved by the Ministry of Agriculture and Rural Development [...] Read more.

The porcine epidemic diarrhea virus (PEDV) causes a gastrointestinal disease generating mortality rates approaching 100% in piglets worldwide. The S glycoprotein of PEDV is the main target for the development of vaccines. Two vaccines approved by the Ministry of Agriculture and Rural Development are used in Mexico: the first vaccine is based on an inactivated virus isolated more than a decade ago, whereas the second vaccine is based on mRNA technology. The most important tool for controlling PEDV outbreaks is vaccination; however, coronaviruses are characterized by the accumulation of multiple mutations, which compromise the immune response elicited by outdated vaccines. In this work, we classified the Mexican strains of PEDV reported so far in GenBank, according to their genotypes. Subsequently, we searched for B and T cell epitopes conserved in Mexican PEDV strains using bioinformatic tools. In addition, we explored whether these epitopes can induce allergies, autoimmunity, and/or toxic effects. Next, we determined the localization of B cell epitopes in the S glycoprotein using the protein crystal and protein modeling of several S glycoproteins. Finally, we carried out molecular docking analysis to assess whether these T cell epitopes could interact with the peptide-binding groove of the Swine Leukocyte Antigens (SLAs). Five conserved B cell epitopes were found to be exposed on the surface of the S glycoprotein, whereas several promiscuous CTL and HTL epitopes were bound, with low free energy, to the peptide-binding grooves of SLA-I and SLA-II, respectively. The best epitopes were used to generate a plasmid carrying the sequence to produce a recombinant protein. This plasmid was used for transfection experiments in PK-15 cell culture. The B cell epitopes reported here were recognized by the sera from pigs infected with PEDV but not by the sera from uninfected animals. These results justify future evaluations of the ability of these epitopes to stimulate cytokine production by T cells, antibody generation, and their neutralizing activity. Full article

(This article belongs to the Special Issue Porcine Epidemic Diarrhea Virus (PEDV): A Persistent Threat to the Global Swine Industry)

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17 pages, 4252 KB

Open AccessArticle

Visualization of Bluetongue Virus RNA Segment Networks in Infected Cells: Multipartite Genomic RNA Assortment Is Independent of Viral Proteins NS2 and VP6

by Dong-Sheng Luo, Po-Yu Sung and Polly Roy

Viruses 2026, 18(4), 406; https://doi.org/10.3390/v18040406 - 25 Mar 2026

Abstract

Bluetongue virus (BTV), with a genome of ten double-stranded RNA segments (S1–S10), is an emerging animal pathogen causing major economic losses in livestock worldwide. BTV replication involves RNA-RNA and RNA–protein interactions, with RNA-binding proteins, VP6 and NS2 playing key roles in genome assembly [...] Read more.

Bluetongue virus (BTV), with a genome of ten double-stranded RNA segments (S1–S10), is an emerging animal pathogen causing major economic losses in livestock worldwide. BTV replication involves RNA-RNA and RNA–protein interactions, with RNA-binding proteins, VP6 and NS2 playing key roles in genome assembly and RNA packaging. To explore the dynamics of RNA segment interactions and the roles of VP6 and NS2 in RNA complex formation, we used RNA fluorescence in situ hybridization chain reaction (HCR), along with site-specific mutagenesis and reverse genetics. We found that RNA segments interact sequentially, from the smallest (S10) to the largest (S1), forming a single complex that includes the entire genome. This process is independent of VP6 or NS2, although NS2 enhances the assembly of larger segments. Additionally, we show that VP6 binds to +ssRNAs before their incorporation into viral assembly factories (inclusion bodies/VIBs). These findings reveal that RNA-RNA interactions, rather than primary replicase proteins, govern the sorting and recruitment of genome segments. Our data offer new insights into BTV RNA packaging, showing that genome segments destined for packaging and dsRNA synthesis are segregated through complex formation, distinct from +ssRNAs used in protein synthesis, including those encoding the replicase complex. Full article

(This article belongs to the Special Issue Bluetongue, Epizootic Haemorrhagic Disease, and Other Emerging Orbiviruses, 2nd Edition)

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9 pages, 4462 KB

Open AccessCase Report

Parvovirus B19 DNA Detected in Ovarian Teratomatous Tissue in Anti-NMDAR Encephalitis: A Case Report

by Trifon Valkov, Dobroslav Kyurkchiev, Ekaterina Kurteva, Kalina Tumangelova-Yuzeir, Jeliazko Arabadjiev, Vesela Ivanova, Dimitrinka Kisova, Radka Argirova, George Dimitrov and Yordanka Yamakova

Viruses 2026, 18(4), 405; https://doi.org/10.3390/v18040405 - 25 Mar 2026

Abstract

Background: Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is an autoimmune disorder frequently associated with ovarian teratomas in young women. Although infectious triggers have been proposed to contribute to immune activation, direct evidence linking viral presence within tumor tissue to disease pathogenesis remains limited. Case Presentation: [...] Read more.

Background: Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is an autoimmune disorder frequently associated with ovarian teratomas in young women. Although infectious triggers have been proposed to contribute to immune activation, direct evidence linking viral presence within tumor tissue to disease pathogenesis remains limited. Case Presentation: An 18-year-old woman presented with acute neuropsychiatric symptoms, fever, gastrointestinal prodrome, and rapidly progressive behavioral disturbance progressing to encephalopathy. Cerebrospinal fluid and blood test results, together with clinical features, supported the diagnosis of anti-NMDAR encephalitis. Imaging identified an ovarian mass, and surgical resection was performed. Histopathology confirmed a mature teratoma containing neuroglial elements. Molecular analysis detected parvovirus B19 DNA within the resected teratomatous tissue. No systemic viremia or active central nervous system viral infection was identified. The patient received immunotherapy combined with tumor removal, with subsequent clinical improvement. Discussion: Ovarian teratomas remain a critical etiologic factor in anti-NMDAR encephalitis and mandate prompt surgical management. Detection of B19 viral DNA within teratomatous neuroglial tissue raises the hypothesis that viral persistence could enhance local immune activation and autoantibody generation. However, in this case polymerase chain reaction positivity does not indicate active infection, and the biological significance of this finding remains uncertain. Conclusions: This case documents rare detection of B19V DNA within an ovarian teratomatous tissue in anti-NMDAR encephalitis. The observation is hypothesis-generating rather than causal; established management priorities remain immunotherapy and tumor resection, and viral nucleic acid detection should be interpreted within the broader clinical context. Full article

(This article belongs to the Special Issue The Interplay Between Viral Infections and Autoimmune Diseases)

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22 pages, 1792 KB

Open AccessArticle

Sequential Phage Delivery Can Outperform Cocktails by Delaying Cross-Resistance Evolution

by Elizabeth C. Stuart and Justin R. Meyer

Viruses 2026, 18(4), 404; https://doi.org/10.3390/v18040404 - 25 Mar 2026

Abstract

Antimicrobial resistance has renewed interest in bacteriophage therapy, yet bacterial evolution frequently undermines treatment efficacy. Combination phage therapy is commonly implemented as simultaneous phage cocktails, but whether this is optimal remains in question. Here, we experimentally compared simultaneous versus sequential administration of two [...] Read more.

Antimicrobial resistance has renewed interest in bacteriophage therapy, yet bacterial evolution frequently undermines treatment efficacy. Combination phage therapy is commonly implemented as simultaneous phage cocktails, but whether this is optimal remains in question. Here, we experimentally compared simultaneous versus sequential administration of two phages, an evolved λ called ‘λtrn’ and T2, on Escherichia coli K-12 under controlled laboratory conditions. Across replicated experiments, treatment outcome depended strongly on delivery strategy, dosing order, and timing. Contrary to expectations, sequential delivery consistently achieved greater and more sustained bacterial suppression than simultaneous cocktails, although only when T2 initiated the sequence. Phenotypic assays revealed that treatment differences were driven by the accessibility and timing of cross-resistance evolution. λ-first treatments rapidly selected for cross-resistant bacteria prior to exposure to the second phage, rendering subsequent treatment ineffective. In contrast, T2-first sequential treatments delayed or limited cross-resistance and frequently produced single-phage resistance or collateral sensitivity. Cocktail treatments showed intermediate dynamics, with cross-resistance evolving more slowly but consistently. Whole genome sequencing identified distinct genetic routes to cross-resistance, including regulatory mutations in envZ affecting expression of the phage receptor OmpF, as well as envelope-modifying, mucoidy-associated mutations. Engineering envZ mutations into unevolved backgrounds confirmed the mutation’s sufficiency to confer low-cost cross-resistance. Together, these results demonstrated that phage therapy efficacy depended not only on phage composition but on how selection pressures were ordered in time, highlighting evolutionary steering as a powerful principle for multi-phage therapy design. Full article

(This article belongs to the Special Issue Phage Cocktails: Promising Approaches Against Infections)

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14 pages, 405 KB

Open AccessReview

A Role of the Lower Genital Tract Microbiome in Promoting Cervical Intraepithelial Neoplasia: A Premalignant Precursor of Cervical Cancer—A Literature Review

by Weronika Knap-Wielgus, Agata Knap, Bronisława Pietrzak, Barbara Suchońska and Mirosław Wielgoś

Viruses 2026, 18(4), 403; https://doi.org/10.3390/v18040403 - 24 Mar 2026

Abstract

The cervicovaginal microbiome (CVMB) is pivotal in maintaining the homeostasis of the lower female genital tract and has emerged as a significant modulator of cervical carcinogenesis. Although persistent infection with high-risk human papillomavirus (HR-HPV) is a prerequisite for the development of cervical intraepithelial [...] Read more.

The cervicovaginal microbiome (CVMB) is pivotal in maintaining the homeostasis of the lower female genital tract and has emerged as a significant modulator of cervical carcinogenesis. Although persistent infection with high-risk human papillomavirus (HR-HPV) is a prerequisite for the development of cervical intraepithelial neoplasia (CIN) and subsequent cervical carcinoma, it remains insufficient alone to drive oncogenesis. Accumulating evidence suggests that alterations in the CVMB composition profoundly impact HPV persistence, local immune responses, and disease progression. A vaginal microbiota dominated by Lactobacillus species, most notably Lactobacillus crispatus, correlates with low microbial diversity, robust immune regulation, and facilitated HPV clearance. Conversely, microbial dysbiosis—characterized by Lactobacillus depletion and a concomitant proliferation of anaerobic taxa, typical of Community State Type (CST) IV and Lactobacillus iners-dominated profiles—is strongly associated with chronic inflammation, oxidative stress, epithelial barrier compromise, and an elevated risk of CIN progression. This review synthesizes current evidence regarding the multifaceted interactions among the cervicovaginal microbiome, HPV pathogenesis, immune dysregulation, and oxidative stress in the etiology of CIN. Elucidating these intricate host–microbiome dynamics may precipitate the discovery of novel microbiome-derived biomarkers, ultimately informing innovative prophylactic and therapeutic interventions for cervical cancer. Full article

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

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17 pages, 2603 KB

Open AccessArticle

Common Acquisition of Broadly Neutralizing Antibodies in an HTLV-1c+ First Nations Cohort from Central Australia

by Samantha L. Grimley, Sarah C. Monard, Ashley Hirons, Ashley H. Y. Yap, Sarah Collins, David Yurick, Georges Khoury, Paula C. Ellenberg, Marc Pellegrini, Lloyd J. Einsiedel and Damian F. J. Purcell

Viruses 2026, 18(4), 402; https://doi.org/10.3390/v18040402 - 24 Mar 2026

Abstract

Human T-cell leukemia virus type-1 (HTLV-1) is endemic to numerous regions worldwide, including Central Australia. The Australo-Melanesian subtype-C is endemic within Australia and Oceania, whereas subtype-A is the most widely distributed subtype globally. The lack of an approved vaccine highlights HTLV-1 as a [...] Read more.

Human T-cell leukemia virus type-1 (HTLV-1) is endemic to numerous regions worldwide, including Central Australia. The Australo-Melanesian subtype-C is endemic within Australia and Oceania, whereas subtype-A is the most widely distributed subtype globally. The lack of an approved vaccine highlights HTLV-1 as a neglected public health issue. To inform the development of HTLV-1 Envelope (Env)-based vaccines, we assessed anti-Env antibodies in an HTLV-1c+ cohort of First Nations individuals in Central Australia. Of the 62 plasma samples from patients with confirmed HTLV-1 serological diagnosis, 76% were positive for Env binding in ELISA, but 90% neutralized HTLV-1c pseudovirus (PSV) infection. Neutralization breadth with the capability of blocking both subtype-A and subtype-C PSV infection was identified in 100% of samples tested. Proviral load was positively associated with anti-Env response, with binding epitopes mapping to the proline-rich region of gp46-SU. Env-directed IgG showed the capacity to engage Fcγ receptors key to inducing antibody-dependent cellular cytotoxicity/phagocytosis responses. Serological response was not associated with comorbidities linked to HTLV-1c in this population (bronchiectasis, chronic kidney disease, diabetes). These findings demonstrate that potent humoral immunity arises and is sustained during HTLV-1 infection, suggesting that an Env-based vaccine displaying authentically native epitopes will be capable of recapitulating these neutralizing responses. Full article

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

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2 pages, 131 KB

Open AccessCorrection

Correction: Hsu et al. Vaccinia Virus: Mechanisms Supporting Immune Evasion and Successful Long-Term Protective Immunity. Viruses 2024, 16, 870

by Joy Hsu, Suyon Kim and Niroshana Anandasabapathy

Viruses 2026, 18(4), 401; https://doi.org/10.3390/v18040401 - 24 Mar 2026

Abstract

The email address of the corresponding author has been updated [...] Full article

(This article belongs to the Special Issue Innate and Adaptive Immunity to Cutaneous Virus Infection)

11 pages, 942 KB

Open AccessArticle

Epidemiological Investigation and Partial NS5 Sequence Analysis of Duck Tembusu Virus in Several Regions of China in 2024

by Wenxin Li, Yang Li, Qingling Ren, Yang Wang, Chengjie Cai, Ying Wang, Xiaohui Yu, Yixin Wang and Hualei Liu

Viruses 2026, 18(4), 400; https://doi.org/10.3390/v18040400 - 24 Mar 2026

Abstract

In order to investigate the prevalence of duck Tembusu virus (DTMUV) in several regions of China, this study conducted an epidemiological survey on 2674 avian throat swab samples (including chickens, ducks, geese, and pigeons) collected from seven provincial-level administrative regions in China in [...] Read more.

In order to investigate the prevalence of duck Tembusu virus (DTMUV) in several regions of China, this study conducted an epidemiological survey on 2674 avian throat swab samples (including chickens, ducks, geese, and pigeons) collected from seven provincial-level administrative regions in China in 2024. Following RT-qPCR testing, 198 positive samples were identified, demonstrating an overall positivity rate of 7.40% (198/2674) across the seven provinces included in the study. Subsequent virus isolation using BHK-21 cells led to successful isolation in 17 cases. Additionally, genetic evolution analysis of the partial NS5 gene was carried out on these 17 isolates through RT-PCR amplification and sequencing. The data analysis indicated that Guangdong Province had the highest positive detection rate, reaching 22.40% (86/384), followed by Henan at 12.24% (47/384). Among infected hosts, geese were primarily affected by DTMUV, with a positivity rate of 40.76% (97/238). The prevailing subgroup of DTMUV in circulation in China is subgroup 3.2. Farmer’s markets, wholesale markets, slaughterhouses, and poultry farms all showed evidence of DTMUV presence, indicating widespread contamination across diverse locations. This study examines the distribution, genetics, and phylogenetic features of DTMUV in China, which will enhance our comprehension of the epidemiological landscape of DTMUV in China. Full article

(This article belongs to the Special Issue Avian Viruses and Antiviral Immunity)

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14 pages, 664 KB

Open AccessReview

A Viral Protein Antagonist for Both AID and APOBEC3

by Jaquelin P. Dudley

Viruses 2026, 18(4), 399; https://doi.org/10.3390/v18040399 - 24 Mar 2026

Abstract

The APOBEC family of cytidine deaminases is part of the innate immune response to infections by multiple RNA- and DNA-containing viruses. Since the activity of these enzymes, typically APOBEC3, often involves mutations that inhibit or block viral replication, viruses have evolved antagonists that [...] Read more.

The APOBEC family of cytidine deaminases is part of the innate immune response to infections by multiple RNA- and DNA-containing viruses. Since the activity of these enzymes, typically APOBEC3, often involves mutations that inhibit or block viral replication, viruses have evolved antagonists that limit APOBEC function. The retrovirus mouse mammary tumor virus (MMTV) encodes an APOBEC antagonist, Rem. Surprisingly, Rem appears to inhibit APOBEC3 through proteasomal degradation of a different APOBEC enzyme, AID. Full article

(This article belongs to the Special Issue Host-Mediated Viral Mutations: APOBECs, ADARs, and Beyond)

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16 pages, 3518 KB

Open AccessArticle

Phage Stability Across Conditions: Ensuring Accurate Use of Viral Surrogates in Antiviral Testing

by Sabine Poelzl and Clemens Kittinger

Viruses 2026, 18(3), 398; https://doi.org/10.3390/v18030398 - 23 Mar 2026

Abstract

Bacteriophages can serve as practical surrogates for human viruses in laboratory tests. They share key structural characteristics but are non-pathogenic and can be handled under lower biosafety conditions. This facilitates experiments on persistence, disinfection and materials-testing while reducing time, costs and logistical requirements. [...] Read more.

Bacteriophages can serve as practical surrogates for human viruses in laboratory tests. They share key structural characteristics but are non-pathogenic and can be handled under lower biosafety conditions. This facilitates experiments on persistence, disinfection and materials-testing while reducing time, costs and logistical requirements. However, phage survival strongly depends on many factors including environmental conditions, such as temperature and relative humidity (RH). This study investigates the survival of bacteriophages Phi6, Qbeta and MS2 under different incubation conditions including storage on a surface, in liquid and in the fridge. Standardized ISO protocols for antimicrobial surface testing and extensions were applied. All phages demonstrated good survival in liquid, although stability was temperature-dependent. At refrigerator temperatures, phages remained stable for several months with only minor reduction in the initial titer. At 50 °C, the two non-enveloped phages survived for up to one week, whereas the enveloped phage Phi6 was inactivated within one day. On glass surfaces, Phi6 exhibited reduced stability and was detectable only up to one week at 25 °C and >90% RH. Qbeta and MS2 survived from several days at 50 °C to two to seven days at 37 °C, depending on RH, and remained detectable at 25 °C regardless of humidity. These differences highlight the importance of carefully selecting incubation conditions, as these directly affect phage stability. In particular, unsuitable conditions for antimicrobial testing may cause phage inactivation and thus lead to false-positive results. Therefore, it is essential to define the conditions under which each phage produces reliable results. Full article

(This article belongs to the Section Bacterial Viruses)

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13 pages, 1945 KB

Open AccessArticle

Distribution of Ugandan Passiflora Virus (Potyvirus passiflorafricanse) in Major Passion Fruit Growing Areas in Rwanda

by Esperance Munganyinka, Bancy W. Waweru, Marie Claire Kanyange, Josiane Umubyeyi, Ghislain Niyonteze, Lydie Kankundiye and Melanie Mukashimwe

Viruses 2026, 18(3), 397; https://doi.org/10.3390/v18030397 - 23 Mar 2026

Abstract

Passion fruit (Passiflora edulis Sims) is an important economic fruit crop in Rwanda grown for both domestic consumption and export markets. However, viral diseases pose a significant threat to passion fruit production. Among these, passion fruit woodiness disease (PWD) is the most [...] Read more.

Passion fruit (Passiflora edulis Sims) is an important economic fruit crop in Rwanda grown for both domestic consumption and export markets. However, viral diseases pose a significant threat to passion fruit production. Among these, passion fruit woodiness disease (PWD) is the most destructive, causing yield losses of up to 100%. A survey was carried out to assess the distribution of Ugandan passiflora virus (UPV; Potyvirus passiflorafricanse) in major passion fruit growing areas. UPV is one of the major viruses known to cause PWD. The incidence of viral symptoms observed in the field did not differ significantly among districts, ranging from 81% in Rusizi to 100% in Rwamagana. However, mean symptom severity scores varied significantly between districts, with the highest severity recorded in Kayonza (3.1) and the lowest in Rulindo (1.9). Serological analysis detected potyviruses in 44% of the total samples (n = 216), including 43% of symptomatic (n = 144) and 47% of asymptomatic (n = 72) leaf samples collected from passion fruit fields. Further analysis using Reverse-Transcription Polymerase Chain Reaction (RT-PCR) detected UPV in 56% of symptomatic (n = 126) and 53% of asymptomatic (n = 60) samples, corresponding to 55% of the total samples tested (n = 186). The virus was present in all surveyed districts, with UPV infection prevalence of 89% in Rusizi, 75% in Rwamagana, 74% in Karongi, 59% in Nyamagabe, 44% in Nyaruguru, 38% in Kayonza, and 30% in both Gakenke and Rulindo. Fifteen partial coat-protein gene sequences for the Rwandan isolates were obtained. The newly described Rwandan isolates shared 97–99% nucleotide (nt) identity with one another, 89–94% with previously reported Rwandan isolates, 81–97% with Ugandan isolates, and 80–82% with Kenyan UPV isolates, suggesting that the Rwandan virus population is relatively homogenous. Genetic distances among the 15 new UPV isolates and previously reported Rwandan, Ugandan, and Kenyan isolates were very short (0.01–0.03), indicating high sequence similarity. All Rwandan isolates clustered into a single major clade, together with some Ugandan and Kenyan isolates. This close genetic relationship suggests a common ancestry and the regional spread of a single dominant UPV lineage. These findings highlight the need to reinforce seed and planting-material certification systems, as well as the need to enhance farmer capacity through targeted training on viral disease identification and management practices. This is vital to limiting the spread of viral diseases that threaten income security among smallholder passion fruit farmers. Full article

(This article belongs to the Special Issue Economically Important Viruses in African Crops)

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22 pages, 1119 KB

Open AccessArticle

High Seroprevalence of Bluetongue Virus Serotype 3 in Belgian Cattle and Sheep After the 2024 Epidemic

by Mickaël Cargnel, Xavier Simons, Ilse De Leeuw, Nick De Regge and Jean-Baptiste Hanon

Viruses 2026, 18(3), 396; https://doi.org/10.3390/v18030396 - 22 Mar 2026

Abstract

To monitor the epidemiological situation of bluetongue virus (BTV) in Belgium, a national surveillance programme was conducted during the 2024–2025 winter season. The objective was to estimate the apparent seroprevalence of BTV-3 following the 2023–2024 epidemic and to prove the absence of active [...] Read more.

To monitor the epidemiological situation of bluetongue virus (BTV) in Belgium, a national surveillance programme was conducted during the 2024–2025 winter season. The objective was to estimate the apparent seroprevalence of BTV-3 following the 2023–2024 epidemic and to prove the absence of active circulation of other BTV serotypes in mixed herds (cattle and sheep). A total of 2551 cattle and 1458 sheep were sampled across Belgium. Serological analyses were performed using ELISA, and molecular detection of BTV-3, BTV-8, and BTV-12 was conducted by RT-qPCR. The majority of cattle and sheep herds showed evidence of exposure to BTV-3, with a very high herd-level apparent seroprevalence (100%; 95% CI: 96.2–100% in cattle and 98.9%; 95% CI: 93.8–99.8% in sheep). Apparent within-herd seroprevalence was also high in cattle (94.6%; 95% CI: 91.8–96.5%) and sheep (85.5%; 95% CI: 80.4–89.5%). No evidence of active circulation of BTV-8 or BTV-12 was detected. A moderate significant positive correlation between Ct values and sampling date was observed both for bovine and ovine samples, consistent with a progressive decline in detectable BTV RNA during winter in the absence of vector activity. Full article

(This article belongs to the Special Issue Bluetongue, Epizootic Haemorrhagic Disease, and Other Emerging Orbiviruses, 2nd Edition)

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16 pages, 5272 KB

Open AccessArticle

Metagenomics Analysis of Viruses Associated with Cassava Brown Streak Disease in Kenya

by Florence M. Munguti, Katherine LaTourrette, Gonçalo Silva, Solomon Maina, Dora C. Kilalo, Isaac Macharia, Agnes W. Mwango’mbe, Evans N. Nyaboga and Hernan Garcia-Ruiz

Viruses 2026, 18(3), 395; https://doi.org/10.3390/v18030395 - 21 Mar 2026

Abstract

Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of [...] Read more.

Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of Africa, especially in Eastern, Central and Southern Africa. In Kenya, the disease continues to wreak havoc on cassava production leading to a significant reduction in crop yields and economic losses of up to USD 1 billion. Variation in virus populations make the control of CBSD challenging as virus genomic variation can affect the accuracy of diagnostic tests, lead to resistance breaking isolates and jeopardize strategies of breeding for resistance. CBSV and UCBSV populations obtained from cassava fields in Kenya were characterized. In total, 44 new complete sequences of CBSV and UCBSV were assembled and 40 sequences successfully submitted to GenBank. Single Nucleotide Polymorphism (SNP) analysis revealed that the cylindrical inclusion protein (CI) is the most stable region across the genome of CBSV and UCBSV. In contrast, protein 1 (PI) and the coat protein (CP) were the most hypervariable regions. Phylogenetic analysis showed three major geographical groupings for both UCBSV and CBSV isolates, suggesting a continued spread of the viruses through human-mediated movement of infected planting materials. The data obtained in this study can support the development of disease management strategies through improved molecular diagnostic tests and targets for breeding for resistance against CBSD. Full article

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

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13 pages, 246 KB

Open AccessArticle

Seroepidemiology and Reactivation Rates of Cytomegalovirus in HIV-Positive Patients in Istanbul: A Retrospective Analysis

by Derya Sevimli Saydan, Murat Hakan Kir, Muammer Osman Köksal, Kutay Sarsar, Arat Hulikyan, Atahan Cagatay, Mehmet Demirci, Pınar Soguksu, Eray Yurtseven, Serra Zeynep Akkoyunlu, Sevim Meşe, Ali Agacfidan and Hayriye Kirkoyun Uysal

Viruses 2026, 18(3), 394; https://doi.org/10.3390/v18030394 - 21 Mar 2026

Abstract

Cytomegalovirus (CMV) remains a major opportunistic pathogen in individuals with HIV. The aim of this study was to investigate the seroprevalence and reactivation rates of CMV among HIV-positive individuals. A total of 300 people with HIV presenting to the Istanbul Faculty of Medicine [...] Read more.

Cytomegalovirus (CMV) remains a major opportunistic pathogen in individuals with HIV. The aim of this study was to investigate the seroprevalence and reactivation rates of CMV among HIV-positive individuals. A total of 300 people with HIV presenting to the Istanbul Faculty of Medicine were enrolled. Serological assessments were performed using enzyme-linked immunosorbent assay (ELISA), while molecular analyses were conducted through PCR-based methods. Sociodemographic and clinical characteristics of the patients were also evaluated. Of the participants, 90% were male, with an age range of 18–76 years. Serological testing demonstrated CMV IgG positivity in 292 patients (97.3%) and CMV IgM positivity in 11 patients (4.07%). CMV DNA was detected in 91 patients (30.3%) by molecular assays, with viral loads ranging from <150 to 2,404,678 copies/mL. CMV DNA positivity was significantly more frequent in older patients (p < 0.05) and was associated with lower CD4+ T lymphocyte counts. CMV disease was identified in 50 patients (16.7%), with organ involvement (64%) representing the most common clinical manifestation. CMV seropositivity is remarkably high in HIV-positive individuals, and reactivation rates are increased, particularly in older patients and those with advanced immunosuppression. These findings underscore the clinical relevance of routine CMV surveillance in the management of HIV infection. Full article

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

14 pages, 708 KB

Open AccessArticle

Disentangling SARS-CoV-2 Sustained Viremia Cases: Evolution, Persistence and Reinfection

by Brunna M. Alves, Filipe R. R. Moreira, Marianne M. Garrido, Pedro S. de Carvalho, Élida M. de Oliveira, Caroline C. de Sá, James Arthos, Claudia Cicala, João P. B. Viola, Livia R. Goes, Juliana D. Siqueira and Marcelo A. Soares

Viruses 2026, 18(3), 393; https://doi.org/10.3390/v18030393 - 21 Mar 2026

Abstract

Based on the follow-up of patients who recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, several reports of people who re-tested positive have been described. This may result from viral reactivation, true reinfection, superinfection, or an initial infection by more than [...] Read more.

Based on the follow-up of patients who recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, several reports of people who re-tested positive have been described. This may result from viral reactivation, true reinfection, superinfection, or an initial infection by more than one virus (multiple infection). These scenarios can only be correctly distinguished through viral quasispecies analysis. Herein, 26 cancer patients under extended follow-up for SARS-CoV-2 infection were submitted to multiple longitudinal analyses through nucleic acid isolation, PCR amplification and high-throughput sequencing. SARS-CoV-2 classification and the definition of cases as persistent or repeated infections were based on phylogenetic reconstruction. Supported by their viral complete genomes and intrahost quasispecies over time, the different scenarios were identified. Nine confirmed and 12 plausible persistence cases were identified. Virus evolution dynamics in the intrahost population from patients with persistent infection was shown for the first time. Regarding reinfection, three confirmed and two plausible cases were identified, including one case of multiple infection. Altogether, this is the first study that analyzes the plethora of SARS-CoV-2 within-host minor variants and describes reinfections, multiple infections and viral evolution across time in cancer patients, contributing to the understanding of SARS-CoV-2’s within-host population dynamics in the natural history of COVID-19. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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16 pages, 322 KB

Open AccessReview

Bacteriophages as Antibacterial Agents Against Bovine Pathobionts Associated with Foodborne Human Morbidity

by Mary Garvey

Viruses 2026, 18(3), 392; https://doi.org/10.3390/v18030392 - 20 Mar 2026

Abstract

Rates of foodborne infectious disease are increasing globally. The One Health zoonoses report shows increasing cases of shigatoxigenic Escherichia coli, campylobacteriosis, salmonellosis and listeriosis in the last 5 years. The ESKAPE pathogens are the top priority due to their alarming rate of [...] Read more.

Rates of foodborne infectious disease are increasing globally. The One Health zoonoses report shows increasing cases of shigatoxigenic Escherichia coli, campylobacteriosis, salmonellosis and listeriosis in the last 5 years. The ESKAPE pathogens are the top priority due to their alarming rate of resistance to broad-spectrum beta-lactams, carbapenems, glycopeptides, fluoroquinolones, aminoglycosides and biocide solutions. Research assessing alternative biocontrol options highlight the advantages of bacteriophages in the control of resistant bacterial species. Phage formulations including ListShield^TM and SalmoFresh^TM have gained FDA approval for food production. As biocontrol agents, however, phages are limited by their specificity in a multispecies environment, the presence of environmental variables and bacterial resistance mechanisms. Genetic modification and the use of phage cocktails aim to overcome such limitations. Future research is warranted in a harmonised approach supported by a defined legal framework to establish best formulation and exposure protocols. This review discusses phages as biocontrol agents in the control of high-risk pathobionts associated with foodborne illness. Pathobionts associated with bovine livestock are discussed due to the morbidity and incidence of disease associated with such pathogens. Full article

(This article belongs to the Special Issue Dual Nature of Bacteriophages: Friends or Enemies in the Food Industry?—2nd Edition)

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