Viruses

15 pages, 4368 KiB

Open AccessArticle

First Report of the Yezo Virus Isolates Detection in Russia

by Mikhail Kartashov, Kirill Svirin, Alina Zheleznova, Alexey Yanshin, Nikita Radchenko, Valentina Kurushina, Tatyana Tregubchak, Lada Maksimenko, Mariya Sivay, Vladimir Ternovoi, Alexander Agafonov and Anastasia Gladysheva

Viruses 2025, 17(8), 1125; https://doi.org/10.3390/v17081125 - 15 Aug 2025

Abstract

The recent discovery of the Yezo virus (YEZV) in Japan and China has raised particular concern due to its potential to cause human diseases ranging from mild febrile illnesses to severe neurological disorders. We report, for the first time, the detection of five [...] Read more.

The recent discovery of the Yezo virus (YEZV) in Japan and China has raised particular concern due to its potential to cause human diseases ranging from mild febrile illnesses to severe neurological disorders. We report, for the first time, the detection of five YEZV isolates in I.persulcatus ticks from three regions of Russia. The analysis was performed using 5318 ticks of two Ixodes genus collected in 2024 from 23 regions of Russia. The minimum infection rate of YEZV in Russia among I. persulcatus ticks was 0.12% (95% CI: 0.05–0.28). The westernmost and northernmost YEZV detection points have been recorded. YEZV isolates circulating in Russia are genetically diverse. Protein domains of Russian YEZV isolates’ genomes were characterized using HMMER, AlphaFold 3, and InterProScan. The YEZV nucleoprotein (N) of Russian isolates has a racket-shaped structure with “head” and “stalk” domains similar to those of Orthonairovirus haemorrhagiae. The Lys261–Arg261 substitution in the YEZV N Chita 2024-1 isolate occurs in the α11 structure in the region of interaction with viral RNA. Our results show that the distribution area of YEZV is much wider than previously known, provide new data on complete YEZV genomes, extend our structural insight into YEZV N, and suggest a potential target for antiviral drug development to treat YEZV infection. Full article

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

14 pages, 15804 KiB

Open AccessArticle

Herpes Simplex 2 Virus Depletes Cells of DEAD-Box Helicase 3 Protein by Packaging It into Virions

by Carmen Rita Piazza, Giulia Lottini, Paola Quaranta, Paola Perrera, Fabio Filippini, Michele Lai, Cristina Di Primio, Giulia Freer and Mauro Pistello

Viruses 2025, 17(8), 1124; https://doi.org/10.3390/v17081124 - 15 Aug 2025

Abstract

Human DEAD-box helicase 3 (DDX3) is a multifunctional RNA helicase implicated in mRNA unwinding and the regulation of gene expression. While DDX3 has been extensively studied in the context of RNA virus replication, its role in DNA virus replication remains less understood. In [...] Read more.

Human DEAD-box helicase 3 (DDX3) is a multifunctional RNA helicase implicated in mRNA unwinding and the regulation of gene expression. While DDX3 has been extensively studied in the context of RNA virus replication, its role in DNA virus replication remains less understood. In this study, we explore the involvement of DDX3 in the life cycle of Herpes Simplex Virus type 2 (HSV-2), a double-stranded DNA virus. Silencing of DDX3 expression with siRNA significantly impaired HSV-2 replication, indicating that DDX3 supports viral propagation. Unexpectedly, HSV-2 infection led to a marked reduction in cellular DDX3 protein levels during in vitro replication in human cells, particularly at 24 h post-infection, corresponding to the peak of viral production. Notably, this decrease was not accompanied by a reduction in DDX3 mRNA levels, nor was it prevented by proteasome inhibition, suggesting an alternative mechanism of DDX3 depletion. Further analysis revealed substantial amounts of DDX3 protein within HSV-2 virions, supporting the hypothesis that DDX3 is packaged into viral particles during replication. We propose that HSV-2 exploits host DDX3 by incorporating it into progeny virions to facilitate early stages of infection in newly infected cells. However, no evidence linking DDX3 to the assembly process of HSV-2 particles was found. These findings expand the known functional repertoire of DDX3 and highlight its potential as a host factor co-opted by DNA viruses, suggesting a broader relevance in antiviral strategies. Full article

(This article belongs to the Section Animal Viruses)

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12 pages, 1465 KiB

Open AccessArticle

Development and Application of Mouse-Derived CD2v Monoclonal Antibodies Against African Swine Fever Virus from Single B Cells

by Litao Yu, Fangtao Li, Xingqi Zou, Lu Xu, Junjie Zhao, Yan Li, Guorui Peng, Yingju Xia, Qizu Zhao and Yuanyuan Zhu

Viruses 2025, 17(8), 1123; https://doi.org/10.3390/v17081123 - 15 Aug 2025

Abstract

African swine fever (ASF) is a highly pathogenic and hemorrhagic swine infectious disease caused by the African swine fever virus (ASFV). It encodes over 150 proteins, among which the CD2v protein plays multiple roles throughout the infection process. Single B-cell antibody technology is [...] Read more.

African swine fever (ASF) is a highly pathogenic and hemorrhagic swine infectious disease caused by the African swine fever virus (ASFV). It encodes over 150 proteins, among which the CD2v protein plays multiple roles throughout the infection process. Single B-cell antibody technology is a cutting-edge method for preparing monoclonal antibodies (mAbs), which has the advantages of rapid, efficient, and high yield in antibody production, while possessing natural conformations. In this study, by cloning and expressing antibody genes in vitro, 14 murine-derived mAbs were prepared using recombinant CD2v proteins as immunogenic sources, which brings sufficient enrichment and selectivity for the development of antibodies based on the single B-cell antibody technique. All 14 mAbs demonstrated reactivity with CD2v protein by indirect ELISA, whereas 8 mAbs successfully detected CD2v in ASFV-infected PAM cells by IFA, indicating the tested mAbs can effectively recognize and bind to ASFV CD2v. Finally, a blocking ELISA method for detecting CD2v antibodies using CD2v mAb C89 was established, which holds significant potential for broad application in the serological diagnosis of ASFV with determination of the CD2v-blocking ELISA specificity, sensitivity, reproducibility, and compliance rate. It could be used for the rapid clinical detection of ASFV CD2v protein to provide a powerful tool for the monitoring of epidemics. Full article

(This article belongs to the Special Issue Swine Viruses: Immunology and Vaccinology)

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28 pages, 3103 KiB

Open AccessArticle

First Complete Genome Sequence of Palo Verde Broom Emaravirus, Virus-Derived siRNA Signatures, and Phytohormone-Metabolite Profiling of Witches’ Broom-Affected Palo Verde Trees

by Raphael O. Adegbola, Muhammad Ilyas, Dinusha C. Maheepala, Ursula K. Schuch and Judith K. Brown

Viruses 2025, 17(8), 1122; https://doi.org/10.3390/v17081122 - 15 Aug 2025

Abstract

Witches’ broom disease of blue palo verde (Parkinsonia florida) was reported more than sixty years ago. Characteristic symptoms consist of dense clusters of shortened, brittle branches and stunted leaves. The suspect causal agent has been identified as palo verde broom virus [...] Read more.

Witches’ broom disease of blue palo verde (Parkinsonia florida) was reported more than sixty years ago. Characteristic symptoms consist of dense clusters of shortened, brittle branches and stunted leaves. The suspect causal agent has been identified as palo verde broom virus (PVBV), genus, Emaravirus, family, Fimoviridae. Here, the first complete PVBV genome sequence was determined, and virus small interfering RNAs (vsiRNAs), primary metabolites, and phytohormone profiles were characterized from infected palo verde leaves, adventitious shoots, flowers, and seeds. Based on pairwise distances, PVBV RNAs 1–4 shared 54–65% nucleotide identity and 19–51% amino acid similarity, respectively, with other emaraviruses, while PVBV RNA 5 shared no sequence homology with any emaravirus. The 21–24-nt virus-derived vsiRNAs, indicative of post-transcriptional gene silencing (PTGS), represented nearly the entire PVBV genome in flowers, leaves, seeds, and adventitious shoots; however, PVBV RNA 3 and RNA 4 were most heavily targeted in all plant parts. Evidence that six major phytohormones were altered in PVBV-infected compared to virus-free trees indicated that emaravirus-infected trees mount classical defense responses to virus infection and/or eriophyid mite infestations. Detection of PVBV RNA genome segments 1–5, accumulation of predominantly 21-nt vsiRNAs, homologous to the PVBV genome and transcripts, and altered levels of phytohormones and metabolites in PVBV-infected trees strongly implicate PVBV as the causal agent of witches’ broom disease. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Plant Viruses and Vector Complexes: Advances in Characterization, Surveillance, and Mitigation)

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15 pages, 455 KiB

Open AccessArticle

White-Tailed Deer Prion Protein Gene Variability Suggests Selection Against Chronic Wasting Disease in Canada’s Prairies

by William Pilot, Maria I. Arifin, Antanas Staskevicius, Nicholas J. Haley, Gordon Mitchell and Jiewen Guan

Viruses 2025, 17(8), 1121; https://doi.org/10.3390/v17081121 - 15 Aug 2025

Abstract

Chronic wasting disease (CWD), a transmissible spongiform encephalopathy that targets cervids, has become a significant threat to both free-ranging and captive populations of Canadian white-tailed deer. In an effort to mitigate its spread, research in the past 20 years has demonstrated that the [...] Read more.

Chronic wasting disease (CWD), a transmissible spongiform encephalopathy that targets cervids, has become a significant threat to both free-ranging and captive populations of Canadian white-tailed deer. In an effort to mitigate its spread, research in the past 20 years has demonstrated that the genetic background of deer may influence the pathogenesis of CWD. Specifically, variants located on the 95-, 96-, 116- and 226-codon of the prion protein gene seem to attenuate disease progression in white-tailed deer. The influence of these alleles on the likelihood of being found CWD-positive on Saskatchewan and Albertan farms was assessed using a Bayesian logistic regression model. To assess the presence of selection for favourable prion protein gene alleles, shifts in variant genotype frequencies were examined over the last seventeen years. Our results show that deer harboring the G96S allele have significantly lowered odds of infection within Canadian herds. Furthermore, the prevalence of this allele has increased significantly in farmed deer over the past seventeen years. Establishing the dynamic genetic background of Canadian deer populations will inform future disease management initiatives. Full article

(This article belongs to the Special Issue Chronic Wasting Disease: From Pathogenesis to Prevention)

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17 pages, 18176 KiB

Open AccessArticle

Identification and Structural Characterization of Viroporins from Deadly Hemorrhagic Viruses

by Hiya Lahiri, Kingshuk Basu and Isaiah T. Arkin

Viruses 2025, 17(8), 1120; https://doi.org/10.3390/v17081120 - 14 Aug 2025

Abstract

Crimean–Congo hemorrhagic fever virus (CCHF-V) and Ebola virus are lethal pathogens that cause widespread outbreaks of hemorrhagic fever. Both diseases can be transmitted through contact with the bodily fluids of infected individuals, but as an arbovirus, CCHF-V is primarily transmitted through tick bites. [...] Read more.

Crimean–Congo hemorrhagic fever virus (CCHF-V) and Ebola virus are lethal pathogens that cause widespread outbreaks of hemorrhagic fever. Both diseases can be transmitted through contact with the bodily fluids of infected individuals, but as an arbovirus, CCHF-V is primarily transmitted through tick bites. Both of these viruses are classified as Risk Group 4 due to the appreciable health threat they pose. To date, there are few effective treatments available to combat these deadly hemorrhagic fevers. Consequently, identifying and characterizing ion channels (viroporins) encoded in the viral genomes may lead to potential targeted drug development. Therefore, using bacteria-based genetic assays, two viroporin candidates from CCHF-V and Ebola have been examined, and their proposed structures have been modeled to aid in further drug discovery. The results indicate that CCHF-V-gp exhibits channel activity, which is indistinguishable from established viroporins found in other viruses. In contrast, our experimental approach was unable to uncover a viroporin candidate in the Ebola virus. Full article

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

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12 pages, 821 KiB

Open AccessArticle

The Clinical and Laboratory Predictors of Intensive Care Unit Admission in Romanian Measles Cases: A Retrospective Cohort Analysis (2023–2025)

by Aneta-Rada Dobrin, Tamara Mirela Porosnicu, Islam Ragab, Lucian-Flavius Herlo, Voichita Elena Lazureanu, Alexandra Herlo, Felix Bratosin, Cristian Iulian Oancea, Silvia Alda and Monica Licker

Viruses 2025, 17(8), 1119; https://doi.org/10.3390/v17081119 - 14 Aug 2025

Abstract

Background and Objectives: Romania has experienced the highest measles incidence rate in the European Union since late 2023, driven by suboptimal measles–mumps–rubella (MMR) uptake. Contemporary data on bedside predictors of clinical deterioration are scarce. The objective was to characterise demographic, clinical and [...] Read more.

Background and Objectives: Romania has experienced the highest measles incidence rate in the European Union since late 2023, driven by suboptimal measles–mumps–rubella (MMR) uptake. Contemporary data on bedside predictors of clinical deterioration are scarce. The objective was to characterise demographic, clinical and laboratory differences between severe and non-severe measles and derive a multivariable model for intensive-care-unit (ICU) admission. Methods: We undertook a retrospective cohort study at the “Victor Babeș” University Hospital for Infectious Diseases, Timișoara. All admissions from 1 November 2023 to 15 May 2025 with serological or RT-PCR confirmation and a complete baseline laboratory panel were included. Descriptive statistics compared ward-managed versus ICU-managed patients; independent predictors of ICU transfer were identified through logistic regression that incorporated age, vaccination status, leukocyte count, C-reactive protein (CRP) and interleukin-6 (IL-6). Results: Among 455 patients (median age 3.0 y, interquartile range [IQR] 1.0–7.0), 17 (3.7%) required ICU care. Vaccine coverage was 18.0% overall and 0% among ICU cases. Compared with ward peers, ICU patients exhibited higher leukocyte counts (8.1 × 10⁹ L vs. 6.0 × 10⁹ L; p = 0.003) and a near-five-fold elevation in IL-6 (18 pg mL vs. 4 pg mL; p < 0.001), while CRP, procalcitonin and fibrinogen were similar. ICU admission prolonged median length of stay from 5 days (IQR 4–7) to 8 days (5–12; p = 0.004). In multivariable modelling, IL-6 remained the sole independent predictor (odds ratio [OR] 1.07 per pg mL; 95% confidence interval [CI] 1.03–1.12; p = 0.001); the model’s AUC was 0.83, indicating good discrimination. Complete separation precluded reliable estimation of the protective effect of vaccination, but no vaccinated child required ICU care. Conclusions: A simple admission panel centred on IL-6 accurately identified Romanian measles patients at risk of critical deterioration, whereas traditional markers such as CRP and leukocyte count added little incremental value. Even a single documented MMR dose was associated with the complete absence of ICU transfers, underscoring the urgent need for catch-up immunisation campaigns. Integrating IL-6-guided triage with intensified vaccination outreach could substantially reduce measles-related morbidity and health-system strain in low-coverage EU settings. Full article

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

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8 pages, 1623 KiB

Open AccessCase Report

First Use of Phage Therapy in Canada for the Treatment of a Life-Threatening, Multidrug-Resistant Staphylococcus epidermidis Periprosthetic Joint Infection

by Melissa T. Cammuso, Bradley W. M. Cook, D. William Cameron, Stephen Ryan, Marielou Tamayo, Melissa J. Peters, Tia Arnaud, Stephanie Lau, Henrik Almblad, Nicolas Fournier, Karen LoVetri, Tasia J. Lightly, Yuen Ming Chung, Riya Roy, Natasha Theriault, Steven S. Theriault, Gina A. Suh and Marisa A. Azad

Viruses 2025, 17(8), 1118; https://doi.org/10.3390/v17081118 - 14 Aug 2025

Abstract

We describe the first use of phage therapy in Canada for the treatment of a life-threatening periprosthetic joint infection (PJI), with successful outcome. PJI is a devastating complication of joint replacement surgery, with high morbidity and mortality. Our patient presented with early sepsis [...] Read more.

We describe the first use of phage therapy in Canada for the treatment of a life-threatening periprosthetic joint infection (PJI), with successful outcome. PJI is a devastating complication of joint replacement surgery, with high morbidity and mortality. Our patient presented with early sepsis from a chronic recalcitrant multidrug-resistant (MDR) Staphylococcus epidermidis hip PJI which had repeatedly failed standard therapy. She had previously undergone 10 operations of the right hip, and only three weeks after completing a prolonged course of daptomycin following her most recent hip revision, she developed a draining sinus tract. Given the high burden of disease, inability to achieve surgical source control, and lack of antibiotic treatment options for long-term suppressive therapy, bacteriophage (phage) therapy was pursued. The patient underwent irrigation and debridement with complex flap reconstruction: intraoperative tissue cultures again yielded MDR S. epidermidis. We developed a novel phage therapy protocol for this patient, with twice daily, intra-articular and intravenous (7 × 10⁹ PFU/dose) phage delivery over a planned 14-day course. Complete healing of the wound with cessation of drainage occurred within one month after treatment. A marked improvement in right hip pain and mobility occurred within three months after treatment. Twelve months following phage treatment, there is normalization of serum inflammatory markers with diminished pain, increased mobility, and no recurrent surgery. Our patient continues to improve and is currently living independently at home, with sustained clinical control of infection. Full article

(This article belongs to the Section Bacterial Viruses)

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16 pages, 2236 KiB

Open AccessArticle

Avian Influenza Surveillance Among Migratory Birds, Poultry, and Humans Around Nansi Lake, China, 2021–2024

by Sheng Zhang, Yu-Min Liang, Dong-Mei Wang, Chao Shang, Wang-Qian Wei, Xin-Jing Zhao, Li-Bo Li, Wen-Guo Jiang, Bao-Jin Guo, Bo-Yan Jiao, Jun Ma, Yun-Bo Qiu, Yong-Biao Cui, Guo-Qiang Wang, Jin-Jin Chen, Qiang Xu, Chen-Long Lv, Feng Hong, Guo-Lin Wang and Li-Qun Fang

Viruses 2025, 17(8), 1117; https://doi.org/10.3390/v17081117 - 14 Aug 2025

Abstract

Avian influenza A viruses (AIVs) pose a significant pandemic threat due to their cross-species transmission potential. However, AIV surveillance at the critical “migratory birds–poultry-exposed population” interface remains limited. Between 2021 and 2024, we implemented a prospective One Health surveillance program around Nansi Lake, [...] Read more.

Avian influenza A viruses (AIVs) pose a significant pandemic threat due to their cross-species transmission potential. However, AIV surveillance at the critical “migratory birds–poultry-exposed population” interface remains limited. Between 2021 and 2024, we implemented a prospective One Health surveillance program around Nansi Lake, monitoring AIVs in migratory birds, poultry, and environmental samples, as well as serological investigations against representative AIVs among migratory birds or poultry-exposed subjects. AIVs were detected in 2.1% (30/1417) of migratory bird samples and 10.2% (100/978) of poultry samples. Among these, we identified ten highly pathogenic avian influenza (HPAI) H5 subtype viruses, one HPAI H7N9 virus, and five low pathogenic avian influenza (LPAI) H9N2 viruses. Phylogenetic analysis revealed evidence of frequent genomic reassortment events involving H5 subtype viruses among migratory birds, poultry, and humans. Serological investigation also suggested that both migratory birds and the poultry-exposed population had a higher risk of getting AIV infection than the general control population, especially against the H9N2 virus. Our study emphasizes the importance of strengthening continuous prospective surveillance of AIVs among migratory birds, poultry, and their exposed individuals to prevent and control potential outbreaks. Full article

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

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25 pages, 451 KiB

Open AccessReview

T Cell Responses to Influenza Infections in Cattle

by Akanksha Hada and Zhengguo Xiao

Viruses 2025, 17(8), 1116; https://doi.org/10.3390/v17081116 - 14 Aug 2025

Abstract

Influenza viruses are major threats to global health, with potential to cause widespread disease in both humans and animals. Cattle, once considered resistant, are susceptible hosts for multiple influenza viruses, including influenza A, C and D, while no evidence currently supports infection with [...] Read more.

Influenza viruses are major threats to global health, with potential to cause widespread disease in both humans and animals. Cattle, once considered resistant, are susceptible hosts for multiple influenza viruses, including influenza A, C and D, while no evidence currently supports infection with influenza B virus. Cattle serve not only as natural reservoirs for influenza D virus but also as emerging spillover hosts for highly pathogenic avian influenza A strains like H5N1. Their role in sustaining viral circulation, facilitating interspecies transmission, and potentially contributing to viral evolution raises significant concerns about future global outbreaks. As host immunity controls viral clearance and spread, understanding how cattle respond to influenza is essential. While most research has focused on antibody-mediated immunity, T cells play indispensable roles in controlling influenza infections by regulating antibody response, clearing infected cells, and providing long-term protection. However, bovine T cell responses to influenza remain poorly characterized. Given that most research has focused on mice and humans, this review outlines current knowledge of bovine T cell responses to influenza viruses in comparison to these well-characterized models. Cross-species comparative studies are essential to identify species-specific immunity, guide cattle vaccine development, and build predictive models to evaluate future pandemic potential. Full article

(This article belongs to the Special Issue Bovine Influenza)

24 pages, 7887 KiB

Open AccessArticle

Dissection of Emerging Shrimp Viruses Through Scientometric Assessment: Insights into Infectious Myonecrosis Virus (IMNV) and Decapod Iridescent Virus 1 (DIV1)

by Kandasamy Saravanan, Rajesh Bharathi Rathinam, Sounder Abuthagir Iburahim, Jayasimhan Praveenraj, Rajendran Kiruba-Sankar and Gokhlesh Kumar

Viruses 2025, 17(8), 1115; https://doi.org/10.3390/v17081115 - 13 Aug 2025

Abstract

Viral diseases pose significant threats to global aquaculture, particularly in shrimp farming, which has suffered substantial economic losses due to pathogens such as Infectious Myonecrosis Virus (IMNV) and Decapod Iridescent Virus 1 (DIV1). This study presents a comprehensive scientometric analysis of the research [...] Read more.

Viral diseases pose significant threats to global aquaculture, particularly in shrimp farming, which has suffered substantial economic losses due to pathogens such as Infectious Myonecrosis Virus (IMNV) and Decapod Iridescent Virus 1 (DIV1). This study presents a comprehensive scientometric analysis of the research landscape, knowledge structure, and emerging trends related to these two pivotal critical shrimp viruses. Using bibliometric data extracted from the Scopus database, we evaluated publication trends, key contributing countries, institutions, authors, co-authorship networks, and keyword co-occurrence patterns. IMNV-related research demonstrated more established collaborative networks, whereas DIV1 studies have surged only recently, reflecting its status as an emerging pathogen and underscoring the urgent need for intensified research efforts. Thematic clusters reveal molecular characterization, host–pathogen interactions, and viral diagnostics as central areas of focus. This analysis identifies research hotspots, collaborative gaps, and leading contributors, offering guidance for future shrimp disease research. However, challenges persist, including limited cross-border collaboration and the underrepresentation of certain regions. Our findings offer valuable insights for researchers, funding agencies, and policymakers, highlighting the opportunities for interdisciplinary and international collaboration to mitigate the impact of these viral threats in aquaculture systems. Full article

(This article belongs to the Section Animal Viruses)

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15 pages, 2268 KiB

Open AccessArticle

The Differences in the Evolutionary Dynamics of MERS and SARS Coronaviruses

by Yushan Ding, Jiameng Liu, Jamal S. M. Sabir, Xinyuan Cui, Xuejuan Shen, Nahid H. Hajrah, Mohamed M. M. Ahmed, Meshaal J. Sabir, Onaizan Godian Al-Zogabi, David M. Irwin and Yongyi Shen

Viruses 2025, 17(8), 1114; https://doi.org/10.3390/v17081114 - 13 Aug 2025

Abstract

SARS-CoV and MERS-CoV are two coronaviruses that have received significant attention due to their high pathogenicity and mortality rates in human populations. In this study, we compared their evolutionary dynamics to provide a One Health perspective on their differences in terms of the [...] Read more.

SARS-CoV and MERS-CoV are two coronaviruses that have received significant attention due to their high pathogenicity and mortality rates in human populations. In this study, we compared their evolutionary dynamics to provide a One Health perspective on their differences in terms of the results of disease control. The phylogenetic network of SARS-CoVs showed that human isolates gathered into a “super-spreader” cluster and were distinct from civet isolates. In contrast, dromedary camel- and human-isolated MERS-CoVs were clustered together. Thus, most clades of MERS-CoV can infect humans, and MERS-CoVs seem to more easily spill over the animal-to-human interface. Additionally, the civet can be easily controlled, while the intermediate host (dromedary camels) of MERS-CoV is an important livestock species, so it is impossible to eliminate all animals. This further leads to difficulties in disease control in MERS. Although MERS-CoVs are endemic to dromedary camels in both the Middle East and Africa, human infections are mainly linked to the Middle East. The nucleotide sequences of the MERS-CoV receptor gen (dipeptidyl peptidase 4 (DPP4)) from 30 Egyptians, 36 Sudanese, and 34 Saudi Arabians showed little difference. These findings suggest that the observed disparities in MERS prevalence between populations in the Middle East and Africa may be more strongly attributed to inadequate disease surveillance and the limited camel-to-human transmission of clade C MERS-CoV in Africa, rather than variations in DPP4 gene. Full article

(This article belongs to the Special Issue Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination)

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17 pages, 3414 KiB

Open AccessArticle

Acute Febrile Illness Associated with an Emerging Dengue 4 GIIb Variant Causing Epidemic in León, Nicaragua 2022

by Omar Zepeda, Edwing C. Cuadra, Daniel O. Espinoza, Yerun Zhu, Hernán Vanegas, Alexis Domeracki, Rodrigo A. Mora-Rodríguez, Anne Piantadosi, Jesse J. Waggoner, Armando J. Matute, Lakshmanane Premkumar, Aravinda M. de Silva, Matthew H. Collins, Megan E. Reller and Filemón Bucardo

Viruses 2025, 17(8), 1113; https://doi.org/10.3390/v17081113 - 13 Aug 2025

Abstract

Historically, DENV-4 has been rarely associated with epidemics and has been less well-studied than DENV-1 to -3. Epidemic dengue struck several South and Central American countries in 2022, with Nicaragua reporting the highest incidence. In an acute febrile illness (AFI) cohort enrolled from [...] Read more.

Historically, DENV-4 has been rarely associated with epidemics and has been less well-studied than DENV-1 to -3. Epidemic dengue struck several South and Central American countries in 2022, with Nicaragua reporting the highest incidence. In an acute febrile illness (AFI) cohort enrolled from June to September 2022, 58 (34%) of 172 patients had PCR-confirmed dengue, of which 46 (79%) were serotyped as DENV-4. In this cohort, acute dengue, as a proportion of AFI, increased from 8% in June to a peak of 58% in August. Genome sequencing and phylogenetic analysis identified a lineage of DENV-4 Genotype IIb (GIIb) with six amino acid substitutions on the surface-exposed regions of the envelope (E) protein as compared to a reference sequence from 2005. Indeed, two of these mutations appear to be novel and located at G172E or near N174K, an antigenic epitope on domain I. Most (90%, 43/48) DENV-4 patients had pre-existing DENV IgG (secondary dengue), at the acute phase. Secondary dengue was associated with the male sex (prevalence ratio (PR)), 6.88) and being younger than 11 years of age (PR, 8.38). Further analysis showed no association between past Zika exposure and DENV-4 acute illness in older subjects (≥12 years of age). In conclusion, our study describes an epidemic of DENV-4 in León, Nicaragua, associated with a novel lineage of genotype GIIb, which contains two amino acid changes not observed in DENV-4 before 2022. Full article

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

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13 pages, 1807 KiB

Open AccessArticle

Imaging Retroviral RNA Genome Heterodimers Using Bimolecular Fluorescence Complementation (BiFC)

by Eunice C. Chen, Rebecca K. Maldonado and Leslie J. Parent

Viruses 2025, 17(8), 1112; https://doi.org/10.3390/v17081112 - 13 Aug 2025

Abstract

Retroviruses are single-stranded RNA viruses that package two copies of their positively stranded RNA genomes as a non-covalent dimer into newly formed virions. This process is evolutionarily conserved, and disruption of genome dimerization results in production of non-infectious virus particles. Genome dimers can [...] Read more.

Retroviruses are single-stranded RNA viruses that package two copies of their positively stranded RNA genomes as a non-covalent dimer into newly formed virions. This process is evolutionarily conserved, and disruption of genome dimerization results in production of non-infectious virus particles. Genome dimers can be packaged as homodimers, containing two identical RNAs, or heterodimers, consisting of two genetically distinct copies. Genome dimerization generates genetic diversity, and different retroviruses have preferences for the type of genome dimers packaged into virions. We developed a novel imaging approach to specifically label and detect retroviral genome heterodimers in cells using a modified bimolecular fluorescence complementation (BiFC) technique. This method utilizes viral genomes encoding two different RNA stem-loop cassettes that each specifically binds to an RNA-binding protein conjugated to a split fluorophore. When two genetically different genomes are within close proximity, the fluorophore halves come together to reconstitute fluorescence. These BiFC-labeled RNA dimers can be visualized and tracked in living cells and interact with retroviral Gag proteins. This method has the advantage of low background fluorescence and can be applied to the study of dimeric or double-stranded RNAs of viruses and other organisms. Full article

(This article belongs to the Special Issue Microscopy Methods for Virus Research)

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18 pages, 445 KiB

Open AccessArticle

Thirty-Five Years of IBV Evolution in Chile Reveals a Novel Lineage and Evidence of Vaccine-Driven Recombination

by Miguel Guzmán, Leandro Cádiz, Leonardo Sáenz, Héctor Hidalgo and Claudio Verdugo

Viruses 2025, 17(8), 1111; https://doi.org/10.3390/v17081111 - 13 Aug 2025

Abstract

Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 [...] Read more.

Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile—GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31. The latter, identified in isolates from 1986 to 1988, is highly divergent (22–24%) from other known lineages, representing a previously unreported South American IBV variant. Despite widespread Mass vaccination, genetically distinct field strains circulated during the 1980s, facilitating potential recombination with GI-1 vaccine-derived strains, including evidence of shared ancestry with GI-11, an endemic lineage from Brazil. Non-recombinant GI-16, likely introduced from Asia, was detected in isolates from 2009. Notably, a recombinant strain emerged in 2015, four years after 4/91 vaccine introduction, indicating vaccine–field-strain genetic exchange. By 2017, isolates with >99% identity to the 4/91 strain were recovered, suggesting vaccine-derived variants. In 2021, GI-1 re-emerged, showing recombination signatures between GI-1 and GI-13 (4/91-derived) strains, likely reflecting suboptimal or inconsistent vaccination strategies. Selection analyses showed strong purifying selection across most of the S1 gene, with limited sites under positive selection in the receptor-binding domain. Phylodynamic reconstruction revealed time-structured evolution and multiple introduction events over 35 years, with lineage-specific tMRCA estimates. Collectively, these findings highlight the emergence of a novel lineage in South America and demonstrate that vaccine use, while mitigating disease, has significantly shaped the evolution of IBV in Chile. Our results underscore the importance of continuous genomic surveillance to inform vaccine strategies and limit recombinant emergence. Full article

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

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12 pages, 925 KiB

Open AccessArticle

Genetic and Antigenic Diversity of Bubaline alphaherpesvirus 1

by Rocío Lucía Tau, Ana Eugenia Marandino, Fátima Torales, Fabrício Souza Campos, Paulo Michel Roehe, José Luis Konrad, Sonia Alejandra Romera, Ruben Pérez and Silvina Soledad Maidana

Viruses 2025, 17(8), 1110; https://doi.org/10.3390/v17081110 - 13 Aug 2025

Abstract

Bubaline alphaherpesvirus 1 (BuHV-1) is a virus that belongs to the Varicellovirus genus within the Alphaherpesvirinae subfamily. While BuHV-1 infections in water buffaloes (Bubalus bubalis) are often subclinical, clinical manifestations have been reported. This study provides complete genome sequences of five [...] Read more.

Bubaline alphaherpesvirus 1 (BuHV-1) is a virus that belongs to the Varicellovirus genus within the Alphaherpesvirinae subfamily. While BuHV-1 infections in water buffaloes (Bubalus bubalis) are often subclinical, clinical manifestations have been reported. This study provides complete genome sequences of five BuHV-1 strains isolated in Argentina, marking the first genomic characterization of BuHV-1 from the Americas. Phylogenetic reconstructions based on whole-genome and coding sequences, along with analyses of glycoproteins C, D, and E, identified a distinct clade and divergent strains. Comparative genomic analyses with publicly available BuHV-1 and Bovine alphaherpesvirus 5 (BoHV-5) sequences showed nucleotide divergence of up to 1.3% among BuHV-1 strains, indicating significant intraspecific genetic diversity. Cross-neutralization assays revealed variable relationships between BuHV-1 and BoHV-5 strains. Some Argentinian BuHV-1 strains exhibited significant antigenic subtype differences compared to Bovine alphaherpesvirus 1 (BoHV-1). Recombination analyses uncovered events between BuHV-1 and bovine herpesviruses, suggesting a complex evolutionary history within mixed farming systems. The findings indicate that the monophyletic BuHV-1 clade, including the reference BuHV-1 isolate, is representative of the BuHV-1 species. The remaining strains, provisionally classified as BuHV-1 indeterminate (BuHV-1i), can be categorized based on specific clinical and antigenic properties. The identified heterogeneity has significant implications for diagnostic accuracy, vaccine development, and disease management strategies in buffalo populations worldwide. Full article

(This article belongs to the Special Issue Animal Herpesvirus 2025)

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20 pages, 1605 KiB

Open AccessArticle

Latent Human Cytomegalovirus Infection Activates the STING Pathway but p-IRF3 Translocation Is Limited

by Wang Ka Lee, Zuodong Ye and Allen Ka Loon Cheung

Viruses 2025, 17(8), 1109; https://doi.org/10.3390/v17081109 - 12 Aug 2025

Abstract

Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus that establishes lifelong latent infection in CD34⁺ haematopoietic stem and progenitor cells. A unique subset of viral genes is expressed during latency, which functions to modulate cellular mechanisms without supporting viral replication. One potential function [...] Read more.

Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus that establishes lifelong latent infection in CD34⁺ haematopoietic stem and progenitor cells. A unique subset of viral genes is expressed during latency, which functions to modulate cellular mechanisms without supporting viral replication. One potential function of these genes is to regulate the differentiation state of latently infected CD34⁺ cells, thereby preventing their progression into antigen-presenting cells, e.g., dendritic cells. In this study, we first compared CD34⁺ cells that supported productive and latent infections using the RV-TB40-BAC_KL7-SE-EGFP virus. Over a seven-day time course, the proportion of latently infected CD34⁺ cell subsets within the myeloid progenitor population remained similar to that in the mock-infected control. However, starting from day 3 post-infection, there was an increase in the proportion of the early progenitor subsets, including haematopoietic stem cells (HSCs) and multipotent progenitors (MPPs). In contrast, productively infected cells, which constituted less than 1% of the population, only accounted for a small portion of the myeloid progenitors. Importantly, our data revealed that the innate immune STING/p-TBK1/p-IRF3 pathway was activated in latently infected CD34⁺ cells, yet type I interferon (IFN) expression was decreased. This decrease was attributed to impaired p-IRF3 nuclear translocation, limiting the induction of an autocrine type I IFN response. However, treatment with IFN-β could induce myelopoiesis in latently infected cells. In summary, HCMV modulates a key component of the STING pathway to inhibit antiviral immune responses by decreasing the type I IFN-mediated cell differentiation of CD34⁺ progenitor cells. This study uncovered a new mechanism of latent HCMV-mediated regulation of the host cell differentiation response. Full article

(This article belongs to the Special Issue Viral Infections and Immune Dysregulation 2024–2025)

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15 pages, 453 KiB

Open AccessReview

Safety, Tolerability, and Metabolic Effects of Long-Acting Cabotegravir and Rilpivirine in HIV Care: A Comprehensive Review

by Martina Bottanelli, Antonella Castagna and Camilla Muccini

Viruses 2025, 17(8), 1108; https://doi.org/10.3390/v17081108 - 12 Aug 2025

Abstract

The use of long-acting cabotegravir and rilpivirine (LA CAB/RPV) is a novel approach to manage human immunodeficiency virus (HIV). This injectable regimen offers benefits such as an improved quality of life, reduced stigma and enhanced treatment satisfaction by minimising the need for daily [...] Read more.

The use of long-acting cabotegravir and rilpivirine (LA CAB/RPV) is a novel approach to manage human immunodeficiency virus (HIV). This injectable regimen offers benefits such as an improved quality of life, reduced stigma and enhanced treatment satisfaction by minimising the need for daily medication adherence. This review summarises the findings of clinical trials and real-world studies on the safety, tolerability and metabolic effects of LA CAB/RPV, which are areas that have received less extensive coverage in previous reviews. Clinical trial data suggest that LA CAB/RPV is generally safe and well tolerated. The most common side effects were injection site reactions, affecting 70–97% of participants. However, these were typically mild and short lived, rarely leading to treatment discontinuation in fewer than 2–3% of cases. Systemic side effects were minimal and comparable to those observed with traditional oral antiretroviral therapy. Real-world studies corroborated these findings, reporting low discontinuation rates due to adverse events. Regarding metabolic impact, clinical trials showed minimal weight gain (an average increase of 1–2 kg over 48–96 weeks) with no significant differences or impact on lipid and glucose levels. Although real-world data are still emerging, they suggest similar trends, including a possible improvement in lipid profiles. Overall, LA CAB/RPV appears to be a safe, well-tolerated and effective treatment option, although longer-term follow-up is needed. Full article

(This article belongs to the Special Issue Long-Acting Antiretrovirals)

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11 pages, 328 KiB

Open AccessArticle

Seroprevalence of Human Immunodeficiency Virus (HIV), Hepatitis B Virus (HBV), and Hepatitis C Virus (HCV) Among Blood Donors in Borgou, Benin in 2023: A Cross-Sectional Study

by Kamel-Dine Djaliri, Brice Boris Legba, Victorien Dougnon, Abdelsalam Tidjani and Lamine Baba-Moussa

Viruses 2025, 17(8), 1107; https://doi.org/10.3390/v17081107 - 12 Aug 2025

Abstract

Blood transfusion remains vital in healthcare but poses risks, particularly from transfusion-transmissible viral infections (TTVIs). This study aims to determine the seroprevalence of HIV, HBV, and HCV among blood donors in Borgou (Benin) in 2023. This prospective, cross-sectional study involved voluntary, non-remunerated blood [...] Read more.

Blood transfusion remains vital in healthcare but poses risks, particularly from transfusion-transmissible viral infections (TTVIs). This study aims to determine the seroprevalence of HIV, HBV, and HCV among blood donors in Borgou (Benin) in 2023. This prospective, cross-sectional study involved voluntary, non-remunerated blood donors recruited via mobile campaigns and at a fixed site from January to December 2023. Screening for HIV, HBV, and HCV was performed using fourth-generation ELISA (Biorad^®). Data analysis used SPSS with Chi-square test of independence (p < 0.05), and multiple logistic regression identified independent risk factors. Among 9646 donors, 87.80% were male (sex ratio 7.19), mostly aged 18–24 (55.93%), with students forming the largest group (58.67%). Mobile units collected 70.80% of donations; 52.60% were repeat donors. Overall TTVI seroprevalence was 9.35%, with HBV (6.29%) most common, followed by HCV (1.78%) and HIV (1.28%). Chi-square tests revealed significant associations between serostatus and donor status, donation site, and occupation, but not sex. Logistic regression identified independent risk factors: age, donor status, and donation site were significantly associated with HIV infection; male sex, older age, occupation, and donor status predicted HBV infection; and only donor status was significantly associated with HCV infection. These findings highlight the need for targeted recruitment and awareness strategies to improve transfusion safety. Full article

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

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