Viruses

9 pages, 617 KB

Open AccessArticle

A Rapid, Cost-Effective RNA Recovery of Cowpea Mild Mottle Virus (CPMMV) Directly from PCR Tubes Adsorption for Routine-Scale Detection in Soybean

by Pedro Henrique Ribeiro, Marcos R. Ribeiro-Junior, Bárbara R. R. Silveira, Francisco M. Ochoa-Corona and Renate Krause-Sakate

Viruses 2026, 18(1), 41; https://doi.org/10.3390/v18010041 (registering DOI) - 25 Dec 2025

Abstract

This study describes an optimized plastic surface-based capsid protein adsorption/capturing method for detection of cowpea mild mottle virus (CPMMV) adapted from the direct antigen-capture method reported for the extraction of rose rosette virus (RRV) and other direct virus capturing attempts. Briefly, the method [...] Read more.

This study describes an optimized plastic surface-based capsid protein adsorption/capturing method for detection of cowpea mild mottle virus (CPMMV) adapted from the direct antigen-capture method reported for the extraction of rose rosette virus (RRV) and other direct virus capturing attempts. Briefly, the method starts with sap incubation, removal of unbound residual tissue and inhibitors by washing, and the viral RNA release using nuclease-free water and heat, in the presence of an RNase inhibitor. The protocol’s efficiency was assessed across different pH conditions, RNaseOUT concentrations, and reverse-transcriptase choices, and its performance was compared with commercial RNA-extraction methods. Three hundred thirty-two positive samples for CPMMV were processed using the optimized protocol (PBS-T, pH 7.4; RNaseOUT at 0.5 U/µL; and M-MLV reverse transcriptase). RT-PCR detection results were consistent with those obtained using the standard method. Cost estimates for tissue trapping indicate reductions of approximately 70% and 90% compared with the Qiagen RNeasy kit and the Bertheau method, respectively. The tissue-absorption protocol combines simplicity and low cost, making it particularly well suited for field diagnostics; by enabling rapid recovery of viral RNA without commercial kits and substantially reducing processing steps, it represents a practical, cost-effective alternative for routine CPMMV testing. Full article

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

15 pages, 1408 KB

Open AccessArticle

Redesigning Isolation Practices: Evaluation of a Comprehensive Protocol for Respiratory Virus Control Including Cycle Threshold (Ct) Value Dynamics

by Stefanie Lemmens, Kevin Janssen, Tine Nelis, Ahmed Elmahy, Noëlla Pierlet, Els Oris and Deborah Steensels

Viruses 2026, 18(1), 40; https://doi.org/10.3390/v18010040 (registering DOI) - 25 Dec 2025

Abstract

The recent literature has debunked the widespread hypothesis that viruses are primarily transmitted via droplets and not beyond 1.5 m, and transmission via contact has been downplayed. Hence, an evidence-based revision of the existing isolation guidelines for respiratory viruses was needed. Therefore, a [...] Read more.

The recent literature has debunked the widespread hypothesis that viruses are primarily transmitted via droplets and not beyond 1.5 m, and transmission via contact has been downplayed. Hence, an evidence-based revision of the existing isolation guidelines for respiratory viruses was needed. Therefore, a completely new protocol for respiratory virus isolation in terms of personal protective equipment and patient room air purification was evaluated. Isolation relief criteria based on Ct values in follow-up sampling were assessed. A Ct value of <28 was employed as a proxy for potential active replication and associated transmissibility. Between 25% and 50% of patients who tested positive for RSV, HRV, hMPV, or SARS-CoV-2 continued to exhibit high viral loads on day 7 post-initial diagnosis, underscoring the potential for sustained infectivity. Hence, the discontinuation of isolation measures for these patients without follow-up testing may carry a considerable risk of ongoing viral transmission. On the contrary, only 7% of patients positive for Flu and 14% for PIV had a follow-up sample on day 7 with a Ct value of less than 28. Ct values increased more rapidly in influenza, indicating faster viral clearance compared to other respiratory viruses. Based on these results, the policy of a standard 7-day isolation period without follow-up testing could be adopted for influenza-positive patients. Full article

(This article belongs to the Section General Virology)

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28 pages, 19507 KB

Open AccessArticle

Parvovirus B19 and Cellular Transcriptome Dynamics in Differentiating Erythroid Progenitor Cells

by Erika Fasano, Niccolò Guglietta, Federica Bichicchi, Ilaria Gasperini, Elisabetta Manaresi and Giorgio Gallinella

Viruses 2026, 18(1), 39; https://doi.org/10.3390/v18010039 (registering DOI) - 25 Dec 2025

Abstract

Parvovirus B19 (B19V) is a human ssDNA virus with ample pathogenic potential. It is characterized by a selective tropism for erythroid progenitor cells (EPC), exerting a cytotoxic effect with blockade of erythropoiesis. In our work, we investigated both viral and cellular expression profile [...] Read more.

Parvovirus B19 (B19V) is a human ssDNA virus with ample pathogenic potential. It is characterized by a selective tropism for erythroid progenitor cells (EPC), exerting a cytotoxic effect with blockade of erythropoiesis. In our work, we investigated both viral and cellular expression profile in the course of infection of EPCs cultures via mRNA high throughput sequencing technology (HTS) and a dedicated bioinformatic pipeline, reconstructing both the viral and cellular transcriptome and their variations. A productive infection was confirmed as restricted to EPCs expressing mature differentiation markers and the specific receptor for virus VP1u region. mRNA HTS reconstructed the viral transcriptome in terms of localization and abundance of the different mRNA species, detailing the differential expression profile of B19V among early or late times in the course of infection. Analysis of cellular transcriptome indicated that variation was mainly driven by the cellular differentiation process, with the virus impacting to a lesser level, but still clearly separating infected vs. non-infected profiles. At early times post-infection, variations were typical of cellular sensing of viral infection and aimed at the induction of an antiviral state. At later times in the course of infection, the cellular population showed induction of an inflammatory response, related to TNF and IL-10, and a transition to adaptive immunity with evidence of upregulation of genes involved in MHC-II presentation. This dual-transcriptome analysis on infected EPCs population can lay the ground for future research aimed at a better definition of the pathogenetic mechanisms of B19V. Full article

(This article belongs to the Collection Parvoviridae)

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27 pages, 3445 KB

Open AccessReview

The Forgotten History of Bacteriophages in Bulgaria: An Overview and Molecular Perspective on Their Role in Addressing Antibiotic Resistance and Therapy

by Nikolay Kalvatchev, Tannaz Khanbabapour, Arit Sakkeer, Iliya Tsekov, Yancho Delchev and Tanya Strateva

Viruses 2026, 18(1), 38; https://doi.org/10.3390/v18010038 (registering DOI) - 25 Dec 2025

Abstract

Bacteriophages, often referred to as “bacteria eaters,” have gained renewed interest as a powerful alternative to traditional antibiotics, particularly in addressing antibiotic-resistant bacterial infections. The present review summarizes data collected in Bulgaria during the 1960s, 1970s, and 1980s, drawing connections between past findings [...] Read more.

Bacteriophages, often referred to as “bacteria eaters,” have gained renewed interest as a powerful alternative to traditional antibiotics, particularly in addressing antibiotic-resistant bacterial infections. The present review summarizes data collected in Bulgaria during the 1960s, 1970s, and 1980s, drawing connections between past findings and present-day understanding of cytotoxicity and the clinical validation of bacteriophage applications. Its sections describe phage structure, mechanisms of action, and historical findings both globally and within the Bulgarian context, while also highlighting emerging trends and applications. The cited studies delve into the past through contemporary research contributions related to “Bulgarian phages”, a topic that remains underexplored in existing literature. The role of phages in medical microbiology is discussed alongside the challenges of therapeutic implementation, with particular focus on insights gained from the Bulgarian experience. In conclusion, by fostering international collaborations, investing in infrastructure, and establishing supportive policies, bacteriophage therapy can emerge as a critical tool for managing bacterial infections and reducing the global burden of antibiotic resistance in the future. Full article

(This article belongs to the Section Bacterial Viruses)

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4 pages, 176 KB

Open AccessEditorial

Preparing for the Next Potential Pandemic—Chikungunya, Dengue, Zika and Other Viruses

by Zoltan Vajo and Csaba Laszlofy

Viruses 2026, 18(1), 37; https://doi.org/10.3390/v18010037 (registering DOI) - 25 Dec 2025

Abstract

Pandemics have claimed millions of lives over millennia [...] Full article

(This article belongs to the Special Issue Preparation for the Next Potential Pandemic—Chikungunya, Dengue, Zika and Other Viruses)

22 pages, 651 KB

Open AccessReview

Crucial Obstacles and Strategies for Human RSV Pediatric Vaccine Development

by Chen Ling, Yuya Wang, Rui Xiong, Yong Wu, Susu Liu, Weijia Li, Yining Wang, Yuwei Zhao and Changfa Fan

Viruses 2026, 18(1), 36; https://doi.org/10.3390/v18010036 - 24 Dec 2025

Abstract

Human respiratory syncytial virus (RSV) remains a leading cause of severe lower respiratory tract infections in infants and immunocompromised populations, causing approximately 160,000 annual deaths globally. Despite recent approvals of prefusion F (pre-F) protein-based vaccines (Arexvy, Abrysvo) for older adults and pregnant women, [...] Read more.

Human respiratory syncytial virus (RSV) remains a leading cause of severe lower respiratory tract infections in infants and immunocompromised populations, causing approximately 160,000 annual deaths globally. Despite recent approvals of prefusion F (pre-F) protein-based vaccines (Arexvy, Abrysvo) for older adults and pregnant women, pediatric vaccine development faces unique challenges including enhanced respiratory disease (ERD) risks, maternal antibody interference, and immature infant immune responses. Meanwhile, G protein glycosylation variability and NS1/NS2-mediated interferon suppression remain the outstanding difficulties in structure-based vaccine design. Additionally, current animal models demonstrate notable constraints in virus replication, host susceptibility, immune responses, clinical symptoms, and ERD phenomena. This review synthesizes current obstacles and innovative strategies, highlighting that the selection of multi-antigen strategies, appropriate adjuvants, and the development of more precise preclinical animal models are critical elements that will determine the efficacy and safety of future RSV vaccines. Full article

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

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3 pages, 138 KB

Open AccessEditorial

Research Progress on Porcine Reproductive and Respiratory Syndrome Virus

by Xingyang Cui, Suzhen Liu and Tongqing An

Viruses 2026, 18(1), 35; https://doi.org/10.3390/v18010035 - 24 Dec 2025

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant diseases affecting the global swine industry, characterized by reproductive failure and late-term abortion in sows and respiratory diseases in all age of pigs [...] Full article

(This article belongs to the Special Issue Research Progress on Porcine Reproductive and Respiratory Syndrome Virus)

20 pages, 1468 KB

Open AccessArticle

Knowledge, Attitudes, and Biosecurity Practices Regarding African Swine Fever Among Small-Scale Pig Farmers in the Lao People’s Democratic Republic and Cambodia

by Véronique Renault, Ariane Masson, Paeng Xaphokame, Outhen Phommasack, Borin Sear, Samnang Ven and Claude Saegerman

Viruses 2026, 18(1), 34; https://doi.org/10.3390/v18010034 - 24 Dec 2025

Abstract

African swine fever (ASF) is a transboundary viral disease that has heavily impacted Southeast Asia since its introduction in 2019. Smallholder pig production systems in Cambodia and the Lao People’s Democratic Republic (the Lao PDR), characterized by low biosecurity, free-ranging practices, and limited [...] Read more.

African swine fever (ASF) is a transboundary viral disease that has heavily impacted Southeast Asia since its introduction in 2019. Smallholder pig production systems in Cambodia and the Lao People’s Democratic Republic (the Lao PDR), characterized by low biosecurity, free-ranging practices, and limited veterinary oversight, remain particularly vulnerable. To assess farmers’ awareness and practices regarding ASF, a knowledge, attitudes, and practices (KAP) survey was implemented between March and September 2023 by Agronomes et Vétérinaires Sans Frontières within the framework of the Biosecurity in Pig Farming (BIG) project. A total of 471 pig farmers, including 56% women, were interviewed across eight provinces using a standardized questionnaire (188 in Cambodia and 283 in the Lao PDR). Results showed that ASF awareness was generally high (92% in Cambodia, 66% in the Lao PDR), yet 15% of Cambodian and 30% of Lao respondents expressed doubts about the presence of ASF in their country. While recognition of ASF symptoms was moderate and positively correlated with farmers’ perceived capacity to identify the disease, knowledge of transmission pathways was low and often misaligned with perceptions. Airborne transmission was frequently cited as a risk, and the risks related to visitors and fomites were underestimated by more than 50% of the farmers. Implementation of biosecurity measures (BSM) was limited, with mean scores of 43% in Cambodia and 27% in the Lao PDR. Risky practices such as swill feeding, free-ranging, sharing of boars, traders, and inadequate carcass disposal remained widespread. Statistical analysis identified education level, herd size, knowledge, perceived risks, and perceived benefits of BSM as the main determinants of biosecurity implementation. Farmers with larger herds or stronger commercial orientation demonstrated higher biosecurity adoption, while misconceptions and knowledge gaps remained frequent among smallholder farmers. Strengthening awareness, promoting low-cost and feasible biosecurity practices, and integrating farmer-centred approaches are essential for reducing ASF transmission risks and improving the resilience of smallholder pig production systems in the region. Full article

(This article belongs to the Special Issue New Findings in Animal Biosecurity Related to Viral Diseases)

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15 pages, 1921 KB

Open AccessArticle

Anti-HIV-1 Activity of the Integrase Strand Transfer Inhibitor ACC017

by Meng-Di Ma, Rong-Hua Luo, Chun-Yan Li, Guan-Cheng Huang, Xin-Yan Long, Feng-Ying He, Liu-Meng Yang, He-Liang Fu and Yong-Tang Zheng

Viruses 2026, 18(1), 33; https://doi.org/10.3390/v18010033 - 24 Dec 2025

Abstract

HIV-1 integrase strand transfer inhibitors (INSTIs) are pivotal to antiretroviral therapy. However, the emergence of drug-resistant mutations necessitates the development of new agents. Here, we present ACC017 as a novel INSTI candidate. ACC017 demonstrated potent activity against the laboratory-adapted HIV-1_IIIB strain (EC [...] Read more.

HIV-1 integrase strand transfer inhibitors (INSTIs) are pivotal to antiretroviral therapy. However, the emergence of drug-resistant mutations necessitates the development of new agents. Here, we present ACC017 as a novel INSTI candidate. ACC017 demonstrated potent activity against the laboratory-adapted HIV-1_IIIB strain (EC₅₀ = 0.59 nM; SI > 34,525) and maintained efficacy against a panel of drug-resistant strains (EC₅₀ range from 0.34 to 9.12 nM) and clinical isolated strains (EC₅₀ range from 0.11 to 1.78 nM). Mechanism of action studies confirmed its ability to inhibit the integrase enzyme (IC₅₀ = 9.19 nM) and effectively block viral genome integration. Notably, in vitro resistance selection primarily yielded D232N and R263K mutations, without the emergence of G140S/A/C/R or Q148H/R/K. This promising profile, combined with synergistic interactions with other antiretroviral drugs, positions ACC017 as a potential therapeutic option. Full article

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

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24 pages, 6486 KB

Open AccessArticle

Resistance Mutations to Broadly Neutralizing Antibodies Destabilize Hemagglutinin and Attenuate H1N1 Influenza Virus

by Guohua Yang, Po-Ling Chen, Samuel W. Rovito, Karine Minari, Haley N. Writt, Jennifer DeBeauchamp, Jeri Carol Crumpton, Lisa Kercher, Rebecca M. DuBois, Richard J. Webby and Charles J. Russell

Viruses 2026, 18(1), 32; https://doi.org/10.3390/v18010032 - 24 Dec 2025

Abstract

Because antigenic drift primarily generates amino-acid changes in the membrane-distal hemagglutinin (HA) head, broadly neutralizing antibodies (bNAbs) are being developed to target conserved epitopes in the membrane-proximal stem. Mutations to HA2 residue A44, a buried residue beneath the central stem epitope, in 2009 [...] Read more.

Because antigenic drift primarily generates amino-acid changes in the membrane-distal hemagglutinin (HA) head, broadly neutralizing antibodies (bNAbs) are being developed to target conserved epitopes in the membrane-proximal stem. Mutations to HA2 residue A44, a buried residue beneath the central stem epitope, in 2009 H1N1 viruses have been shown to cause resistance to stem-binding bNAbs. Here, we introduced A44V and A44T mutations into A/Tennessee/1-560/2009 (TN09) and A/Puerto Rico/15/2018 (PR18) and investigated their effects in cell culture, mice, and ferrets. In both virus strains, the mutations decreased HA and virus stability and decreased bNAb binding and neutralization in vitro. The mutations reduced pathogenicity and lung replication in DBA/2J mice. Ferrets were inoculated with PR18 wild-type (WT) or A44V virus, and the A44V mutation reduced day-1 and peak nasal virus titers. Airborne transmission in the A44V group occurred only after genotypic reversion (HA2-V44A) or acquisition of a distal re-stabilizing mutation (HA2-I77M). Compared to WT, an engineered PR18 virus containing both HA2 mutations (A44V and I77M) had similar growth and pathogenicity in mice in addition to decreased binding and neutralization by bNAbs. Overall, this work provides insight into the role of HA stability during HA stem-epitope remodeling that results in virus resistance to stem-binding bNAbs. Full article

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

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24 pages, 3923 KB

Open AccessArticle

Invertebrate Iridescent Viruses (Iridoviridae) from the Fall Armyworm, Spodoptera frugiperda

by Birmania Rodríguez-Heredia, Jesús Alejandro Zamora-Briseño, Leonardo Velasco and Trevor Williams

Viruses 2026, 18(1), 31; https://doi.org/10.3390/v18010031 - 24 Dec 2025

Abstract

Invertebrate iridescent viruses (IIVs, family Iridoviridae) are icosahedral double-stranded DNA viruses that infect a wide range of invertebrates, particularly in humid and aquatic environments. During field trials in Chiapas, southern Mexico, larvae of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), displayed an [...] Read more.

Invertebrate iridescent viruses (IIVs, family Iridoviridae) are icosahedral double-stranded DNA viruses that infect a wide range of invertebrates, particularly in humid and aquatic environments. During field trials in Chiapas, southern Mexico, larvae of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), displayed an unexpected lavender iridescence, leading to the discovery of novel IIV isolates from this major agricultural pest. Restriction endonuclease analysis revealed evident diversity among isolates from individual infected larvae. Although one field experiment yielded inconclusive results, a second experiment revealed a positive association between IIV disease and SfMNPV infection, compared to a negative association with the prevalence of parasitoids, and no association with entomopathogenic nematodes (probably Hexamermis sp.). These findings require further investigation to determine the distinct ecological routes through which the virus may transmit across host species. IIV infection of S. frugiperda was also identified in Veracruz State, Mexico, and northern Argentina, revealing a previously unrecognized geographic and host range for these viruses. The genomic and evolutionary features of the three isolates from S. frugiperda were compared with those of two other lepidopteran isolates from Helicoverpa zea (IIV30C obtained from CSIRO) and Anticarsia gemmatalis (AgIIV). Genome sizes ranged between 196.1 and 205.4 kbp (~28% GC content), with several large inversions, and were rich in tandem repeats. The average amino acid identity of the complete genomes and phylogenetic analyses of 26 core gene sequences placed all five isolates within the genus Chloriridovirus, closely related to IIV22 and IV22a isolated from blackflies (Diptera) in Wales and a previously sequenced isolate of IIV30 from the USA. We conclude that these lepidopterans are all infected by closely related strains of the virus species Chloriridovirus simulium1 across their native geographical range. These findings highlight the unexpected ecological breadth and evolutionary adaptability of IIVs. Full article

(This article belongs to the Section Invertebrate Viruses)

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31 pages, 2327 KB

Open AccessReview

Hidden in Plain Sight: Alphavirus Persistence and Its Potential for Driving Chronic Pathogenesis

by Maria del Mar Villanueva Guzman, Zhenlan Yao, Melody M. H. Li and Maria Gabriela Noval

Viruses 2026, 18(1), 30; https://doi.org/10.3390/v18010030 - 24 Dec 2025

Abstract

Alphaviruses have historically been viewed as acute, self-limiting pathogens. However, growing evidence shows that viral RNA and antigens can persist in vertebrate hosts long after the resolution of acute infection, a phenomenon known as viral persistence. Viral persistence reflects a dynamic interplay between [...] Read more.

Alphaviruses have historically been viewed as acute, self-limiting pathogens. However, growing evidence shows that viral RNA and antigens can persist in vertebrate hosts long after the resolution of acute infection, a phenomenon known as viral persistence. Viral persistence reflects a dynamic interplay between viral replication—including shifts from lytic to non-lytic infection—and host defenses, which together establish cellular and tissue niches that enable evasion of immune-mediated clearance. Within vertebrate hosts, alphaviruses exhibit broad tissue tropism, infecting diverse cell types that may differentially support long-term persistence. Emerging evidence suggests that viral persistence arises through three interconnected processes: (i) selective infection of specific cellular niches, (ii) reprogramming of host cellular pathways, and (iii) modulation of immune responses. Yet, the extent to which viral or host determinants shape this balance, and how persistence contributes to chronic disease, remains unresolved. Here, we synthesize current in vitro and in vivo evidence of alphavirus persistence in vertebrate hosts and discuss potential mechanisms by which alphaviruses establish and maintain persistent infection beyond the acute phase. We further underscore critical gaps in current knowledge and outline future research avenues essential for elucidating the mechanisms underlying alphavirus pathogenesis. Full article

(This article belongs to the Special Issue Advances in Understanding Viral Pathogenesis and Host Immune Responses to Arboviruses and Respiratory Viruses)

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13 pages, 884 KB

Open AccessArticle

The Role of mTOR Inhibitors in COVID-19 Outcomes Among Heart Transplant Recipients

by Agnieszka Kuczaj, Szymon Warwas, Mikołaj Tyrka, Błażej Skotnicki, Daniel Szymecki, Oliwia Jewuła, Szymon Pawlak, Piotr Przybyłowski and Tomasz Hrapkowicz

Viruses 2026, 18(1), 29; https://doi.org/10.3390/v18010029 - 24 Dec 2025

Abstract

Background: Heart failure (HF) remains a major global health challenge, with orthotopic heart transplantation (OHT) serving as the gold-standard therapy for end-stage disease. Chronic immunosuppression required to prevent graft rejection increases the risk of infections and malignancies. The COVID-19 pandemic underscored the particular [...] Read more.

Background: Heart failure (HF) remains a major global health challenge, with orthotopic heart transplantation (OHT) serving as the gold-standard therapy for end-stage disease. Chronic immunosuppression required to prevent graft rejection increases the risk of infections and malignancies. The COVID-19 pandemic underscored the particular vulnerability of transplant recipients to severe SARS-CoV-2 infection. Specific immunosuppressive agents used in OHT patients may differentially affect SARS-CoV-2 infection. In particular, mTOR inhibitors may modulate viral replication and immune responses, potentially influencing disease severity. Objectives: This study evaluated the impact of immunosuppressive regimens—particularly mTOR inhibitors—on COVID-19 outcomes in heart transplant recipients, comparing mTOR-based therapy (with or without calcineurin inhibitors, CNIs) to non-mTOR-based regimens. Methods: This single-center retrospective observational study included 556 orthotopic heart transplant recipients (76.3% male; median age, 58 years) followed from March 2020 to March 2024. To compare patients receiving mTOR inhibitors with similar non-mTOR recipients, 3:1 propensity score matching was performed based on age, sex, and body mass index. Among the study population, 88 patients (15.8%) received mTOR inhibitors (everolimus or sirolimus), of whom 66 were concomitantly treated with calcineurin inhibitors and 22 without. Data were obtained from the National Health Fund database and clinical follow-ups. Results: Overall mortality was 13.5%, and COVID-19-related mortality 3.2%. COVID-19 incidence was 33% in the mTOR group versus 36.7% in the non-mTOR group (p = 0.52). Hospitalization rates were 3.4% and 6.4% (p = 0.29), respectively. All-cause mortality was higher among mTOR users (21.6% vs. 11.7%, p = 0.02), especially in the mTOR+CNI subgroup. Notably, no COVID-19-related deaths occurred in the mTOR CNI-free group. Conclusions: mTOR-based immunosuppression was non-inferior to standard therapy for COVID-19 outcomes. The absence of COVID-19-related deaths in patients on mTOR CNI-free regimens suggests potential protective effects that merit further investigation. Full article

(This article belongs to the Section Coronaviruses)

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12 pages, 238 KB

Open AccessArticle

Seven Strategies Implemented in Response to the 16th Ebola Virus Disease Outbreak in the Democratic Republic of Congo: Lessons Learned over a Three-Month Period

by Dieudonné K. Mwamba, Karl B. Angendu, Waly Diouf, Marie-Claire Mikobi, Olive Leonard, Danny Kalala, Nella Ntumba, Deogratias Kakule, David K. Kayembe, Emilia Sana, Bienvenu Kabasele, Jack Katya, Alice Montoyo, Béatrice Serra, Henriette Bulambo, John Otshudiema, Serge Kapanga, Olea Balayulu, Jeanpie Muya, Erick Kamangu, Richard Kitenge, Gaston Tshapenda, Cris Kasita, Mory Keita, Francis K. Kabasubabo, John Kombe, Mathias Mossoko, Christian B. Ngandu, Célestin Manianga, Gregory Moullec, Christina Zarowsky and Pierre Z. Akilimali Show full author list Hide full author list

Viruses 2026, 18(1), 28; https://doi.org/10.3390/v18010028 - 24 Dec 2025

Abstract

The 2025 Ebola outbreak that ravaged the Bulape Health District (HD) in Kasai, Democratic Republic of Congo (DRC), was tackled using the incident management system (IMS) model. The Bulape HD is located in the Mweka territory, which has experienced two Ebola epidemics: one [...] Read more.

The 2025 Ebola outbreak that ravaged the Bulape Health District (HD) in Kasai, Democratic Republic of Congo (DRC), was tackled using the incident management system (IMS) model. The Bulape HD is located in the Mweka territory, which has experienced two Ebola epidemics: one in 2007 and another in 2008. The IMS comprises seven strategies recommended for an effective response to an Ebola outbreak: (i) thorough investigation, (ii) strengthening infection prevention and control measures in the community, (iii) ensuring that medical care is provided by experienced professionals, (iv) strengthening risk communication and community engagement (RCCE), (v) ring vaccination, (vi) operational research, and (vii) anchoring interventions in the existing health system. We share our experience implementing these seven strategies and compare them with those utilized during three previous Ebola outbreaks. This paper describes our achievements, the resulting benefits, and the factors that facilitated the implementation of the aforementioned strategies. A literature review and interviews were conducted. The atlas.ti 22 software was used for data analysis. Implementing these seven strategies contributed to an effective response, largely due to the experience and expertise of those involved but also thanks to the support of technical and financial partners (TFPs) and the engagement of the local community. Challenges such as geographical accessibility, the fragile health system, the community’s strong attachment to traditional practices, and negative reactions to healthcare—which was widely discredited, with many of those involved expressing a lack of faith in its effectiveness—were major obstacles. To overcome these challenges, an integrated approach was utilized, combining a rapid comprehensive response with deep and respectful community engagement. The support and alignment of TFPs were invaluable during this process. The RCCE pillar proved key to successful IMS implementation. Our experiences will be useful during the next Ebola outbreak in the DRC; additionally, they may also help to inform the response to similar outbreaks in other countries. Full article

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

9 pages, 214 KB

Open AccessOpinion

Natural Hepacivirus Infection in Tree Shrews: A Call for Routine Screening in Hepatitis Virus Research

by Mohammad Enamul Hoque Kayesh, Takahiro Sanada, Michinori Kohara and Kyoko Tsukiyama-Kohara

Viruses 2026, 18(1), 27; https://doi.org/10.3390/v18010027 (registering DOI) - 23 Dec 2025

Abstract

Hepatitis viruses continue to pose major global health challenges, necessitating the development of reliable and well-characterized experimental models. Tree shrews are increasingly recognized as a valuable small animal model because of their natural susceptibility to hepatitis viruses and close phylogenetic relationship with primates. [...] Read more.

Hepatitis viruses continue to pose major global health challenges, necessitating the development of reliable and well-characterized experimental models. Tree shrews are increasingly recognized as a valuable small animal model because of their natural susceptibility to hepatitis viruses and close phylogenetic relationship with primates. Recent identification of a high prevalence of natural hepacivirus infections in tree shrews underscores the urgent need for routine viral screening of the animals used in hepatitis studies. Undetected infections may confound experimental results, undermine data integrity, and pose risks to laboratory biosecurity. Integrating systematic screening and standardized reporting practices will minimize these risks, enhance reproducibility, and safeguard the integrity of research findings. Moreover, a consistent assessment of the infection status will enhance the translational potential of tree shrews for studying viral hepatitis pathogenesis and evaluating antiviral interventions. This opinion paper emphasizes that ensuring the virological status of tree shrews is not merely a procedural recommendation but also a methodological standard essential for advancing hepatitis virus research. Full article

(This article belongs to the Section Animal Viruses)

20 pages, 3794 KB

Open AccessArticle

Tracking Respiratory Viruses in Pakistan (2022–2025): Genomic and Epidemiologic Insights from Sentinel Surveillance of Influenza, SARS-CoV-2, and RSV

by Nazish Badar, Abdul Ahad, Hamza Ahmed Mirza, Fazal Hanan, Asghar Javaid, Aamir Amanat, Zunira Saghir and Muhammad Salman

Viruses 2026, 18(1), 26; https://doi.org/10.3390/v18010026 - 23 Dec 2025

Abstract

Influenza and other respiratory viruses pose significant public health threats among SARI patients, yet comprehensive surveillance data remain limited in Pakistan. This prospective, multi-center study characterized the burden, distribution, and molecular evolution of respiratory viruses among hospitalized SARI patients across seven tertiary hospitals [...] Read more.

Influenza and other respiratory viruses pose significant public health threats among SARI patients, yet comprehensive surveillance data remain limited in Pakistan. This prospective, multi-center study characterized the burden, distribution, and molecular evolution of respiratory viruses among hospitalized SARI patients across seven tertiary hospitals from November 2022 to June 2025. Specimens were tested using RT-PCR for influenza, SARS-CoV-2, and RSV, with 375 samples sequenced via Oxford Nanopore Technology. Among 11,451 specimens, 2818 (24.6%) tested positive: RSV (1648, 14.4%), influenza (855, 7.5%; 45% H1N1pdm09, 35% H3N2, 20% influenza B), and SARS-CoV-2 (315, 2.8%). RSV predominantly affected children under 2 years (63%), while influenza and SARS-CoV-2 primarily impacted adults aged 15–40 years. Male predominance (65–79%) reflected healthcare access barriers. Strong winter seasonality (December–February) was observed for influenza and RSV. ICU admission rates were 17% for influenza, 16% for RSV, and 4% for SARS-CoV-2. Shortness of breath was associated with influenza (OR = 1.62) and RSV (OR = 1.27), while malaise (OR = 2.24) and myalgia (OR = 3.87) was associated with SARS-CoV-2. Phylogenetic analysis revealed vaccine-matched influenza clades and rapid SARS-CoV-2 variant succession (3–4 months). RSV is the primary SARI pathogen in young children, necessitating maternal vaccines and nirsevimab implementation. Sustained genomic surveillance remains essential for pandemic preparedness. Full article

(This article belongs to the Special Issue RSV Epidemiological Surveillance: 2nd Edition)

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19 pages, 1789 KB

Open AccessArticle

Effects of Orthonairovirus hazaraense Nucleoprotein on Gene Expression Profiles in Infected Cells

by Keisuke Ohta and Machiko Nishio

Viruses 2026, 18(1), 25; https://doi.org/10.3390/v18010025 - 23 Dec 2025

Abstract

Nucleoprotein (N) of Orthonairovirus hazaraense (HAZV) not only encapsidates viral genomic RNA but also has the potential to regulate functions of host factors. To screen for host factors affected by HAZV N protein, we investigated the effects of HAZV N protein on the [...] Read more.

Nucleoprotein (N) of Orthonairovirus hazaraense (HAZV) not only encapsidates viral genomic RNA but also has the potential to regulate functions of host factors. To screen for host factors affected by HAZV N protein, we investigated the effects of HAZV N protein on the gene expression profile by transcriptome analysis of a HAZV-infected SW13 cell line constitutively expressing HAZV N protein (SW13/N). The gene expression profile of HAZV-infected SW13/N was quite different from that of HAZV-infected SW13 cells. Notably, HAZV infection up-regulated many immune-response-related genes in SW13 cells, but not in SW13/N. This clearly indicates the suppression of host immune response by N protein. Among immune-response-related genes, the myeloid differentiation factor 88 (MyD88) gene was uniquely down-regulated in SW13/N, despite its up-regulation by HAZV infection. Furthermore, MyD88 was also down-regulated at the protein level in SW13/N. N protein was also found to potentially down-regulate cell adhesion, cell cycle, apoptosis and cytoskeleton-related genes. HAZV N protein is suggested to have a great impact on the gene expression profile in infected cells. This is the first report of comprehensive analysis of host gene expression that is manipulated by nairovirus protein. Full article

(This article belongs to the Section General Virology)

16 pages, 4787 KB

Open AccessArticle

Stable Population, Shifting Clades: A 17-Year Phylodynamic Study of IBV GI-19-like Strains in Spain Reveals the Relevance of Frequent Introduction Events, Local Dispersal and Recombination Events

by Giovanni Franzo, Francesca Poletto, Matteo Legnardi, Riccardo Baston, Cristina Andolfatto, Laura Ramon, Marta Becerra, Mar Biarnés, Mattia Cecchinato and Claudia Maria Tucciarone

Viruses 2026, 18(1), 24; https://doi.org/10.3390/v18010024 - 23 Dec 2025

Abstract

Infectious bronchitis virus (IBV) remains a common pathogen in poultry production. Although its clinical and economic impact in Europe has markedly declined in recent decades due to extensive vaccination, ongoing viral circulation continues to pose risks to animal health and provides opportunities for [...] Read more.

Infectious bronchitis virus (IBV) remains a common pathogen in poultry production. Although its clinical and economic impact in Europe has markedly declined in recent decades due to extensive vaccination, ongoing viral circulation continues to pose risks to animal health and provides opportunities for viral evolution. In this study, we investigated the molecular epidemiology of GI-19 and related strains in Spain using samples collected between 2008 and 2025. Partial S1 sequencing revealed a complex scenario involving three major clades and several minor ones, the latter likely resulting from independent introduction events from north-western Europe, particularly Denmark. Six distinct recombination events involving GI-13 and GI-19 parental strains—some apparently vaccine derived—were also identified, several of which showed wide geographical spread and long-term persistence. Both recombinant and non-recombinant variants were detected across multiple regions and production systems, indicating strong epidemiological connectivity among broilers, layers, and breeders. Although overall viral population size appeared stable over time, shifts in the predominance of specific clades and recombinant groups were observed, possibly reflecting fitness advantages of newly introduced or evolved variants and reduced cross-protection from existing immunity. These findings highlight the susceptibility of the poultry sector to repeated introductions, mixing, and the dissemination of IBV variants. Strengthened molecular surveillance and tailored control strategies, together with the periodic evaluation of vaccination practices and population immunity, are needed to limit viral circulation, reduce recombination opportunities, and mitigate the impact of IBV. Full article

(This article belongs to the Section Animal Viruses)

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13 pages, 819 KB

Open AccessReview

Key Challenges in Screening Blood Donors for Hepatitis B Virus

by Maha A. Badawi, Sahar Eldakhakhny, Mohamed Ali, Mazen Badawi, Jaffar Khiariy, Yagoub Bin-Taleb and Salwa I. Hindawi

Viruses 2026, 18(1), 23; https://doi.org/10.3390/v18010023 - 23 Dec 2025

Abstract

Technological advancements in blood donor screening have significantly improved blood safety. However, certain testing challenges and limitations continue to face blood banks in donor screening for the hepatitis B virus, resulting in occasional cases of transfusion transmission. These cases are mostly related to [...] Read more.

Technological advancements in blood donor screening have significantly improved blood safety. However, certain testing challenges and limitations continue to face blood banks in donor screening for the hepatitis B virus, resulting in occasional cases of transfusion transmission. These cases are mostly related to donors presenting within the window period and donors with occult hepatitis B infection. There are several other challenges that professionals in transfusion medicine, infectious diseases, gastroenterology, and public health must be aware of. Maintaining the highest test sensitivity is a key parameter for enhancing blood safety, and the review describes current recommendations in this regard, along with relevant advancements. The diversity of viral genotypes and the potential for mutations affecting the surface antigen may negatively affect the performance of both serologic and nucleic acid tests. Serologic tests may also be affected by several interferences, endogenous or exogenous to the sample. A clear understanding of these challenges is necessary to create effective policies and procedures and to properly manage atypical cases. Full article

(This article belongs to the Section General Virology)

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