Viruses

16 pages, 1975 KiB

Open AccessReview

APOBEC3 Proteins: From Antiviral Immunity to Oncogenic Drivers in HPV-Positive Cancers

by Eliza Pizarro Castilha, Rosalba Biondo, Kleber Paiva Trugilo, Giulia Mariane Fortunato, Timothy Robert Fenton and Karen Brajão de Oliveira

Viruses 2025, 17(3), 436; https://doi.org/10.3390/v17030436 - 18 Mar 2025

Abstract

The human APOBEC superfamily consists of eleven cytidine deaminase enzymes. Among them, APOBEC3 enzymes play a dual role in antiviral immunity and cancer development. APOBEC3 enzymes, including APOBEC3A (A3A) and APOBEC3B (A3B), induce mutations in viral DNA, effectively inhibiting viral replication but also [...] Read more.

The human APOBEC superfamily consists of eleven cytidine deaminase enzymes. Among them, APOBEC3 enzymes play a dual role in antiviral immunity and cancer development. APOBEC3 enzymes, including APOBEC3A (A3A) and APOBEC3B (A3B), induce mutations in viral DNA, effectively inhibiting viral replication but also promoting somatic mutations in the host genome, contributing to cancer development. A3A and A3B are linked to mutational signatures in over 50% of human cancers, with A3A being a potent mutagen. A3B, one of the first APOBEC3 enzymes linked to carcinogenesis, plays a significant role in HPV-associated cancers by driving somatic mutagenesis and tumor progression. The A3A_B deletion polymorphism results in a hybrid A3A_B gene, leading to increased A3A expression and enhanced mutagenic potential. Such polymorphism has been linked to an elevated risk of certain cancers, particularly in populations where it is more prevalent. This review explores the molecular mechanisms of APOBEC3 proteins, highlighting their dual roles in antiviral defense and tumorigenesis. We also discuss the clinical implications of genetic variants, such as the A3A_B polymorphism, mainly in HPV infection and associated cancers, providing a comprehensive understanding of their contributions to both viral restriction and cancer development. Full article

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

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22 pages, 2316 KiB

Open AccessReview

Is the vIL-10 Protein from Cytomegalovirus Associated with the Potential Development of Acute Lymphoblastic Leukemia?

by Ruvalcaba-Hernández Pamela, Mata-Rocha Minerva, Cruz-Muñoz Mario Ernesto, Mejía-Aranguré Juan Manuel, Sánchez-Escobar Norberto, Arenas-Huertero Francisco, Melchor-Doncel de la Torre Silvia, Rangel-López Angélica, Jiménez-Hernández Elva, Nuñez-Enriquez Juan Carlos, Ochoa Sara, Xicohtencatl-Cortes Juan, Cruz-Córdova Ariadnna, Figueroa-Arredondo Paula and Arellano-Galindo José

Viruses 2025, 17(3), 435; https://doi.org/10.3390/v17030435 - 18 Mar 2025

Abstract

Leukemia is a hematologic malignancy; acute lymphoblastic leukemia (ALL) is the most prevalent subtype among children rather than in adults. Orthoherpesviridae family members produce proteins during latent infection phases that may contribute to cancer development. One such protein, viral interleukin-10 (vIL-10), closely resembles [...] Read more.

Leukemia is a hematologic malignancy; acute lymphoblastic leukemia (ALL) is the most prevalent subtype among children rather than in adults. Orthoherpesviridae family members produce proteins during latent infection phases that may contribute to cancer development. One such protein, viral interleukin-10 (vIL-10), closely resembles human interleukin-10 (IL-10) in structure. Research has explored the involvement of human cytomegalovirus (hCMV) in the pathogenesis of ALL. However, the limited characterization of its latent-phase proteins restricts a full understanding of the relationship between hCMV infection and leukemia progression. Studies have shown that hCMV induces an inflammatory response during infection, marked by the release of cytokines and chemokines. Inflammation may, therefore, play a role in how hCMV contributes to oncogenesis in pediatric ALL, possibly mediated by latent viral proteins. The classification of a virus as oncogenic is based on its alignment with cancer’s established hallmarks. Viruses can manipulate host cellular mechanisms, causing dysregulated cell proliferation, evasion of apoptosis, and genomic instability. These processes lead to mutations, chromosomal abnormalities, and chronic inflammation, all of which are vital for carcinogenesis. This study aims to investigate the role of vIL-10 during the latent phase of hCMV as a potential factor in leukemia development. Full article

(This article belongs to the Special Issue Molecular Biology of Human Cytomegalovirus)

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10 pages, 4954 KiB

Open AccessArticle

Conserved Cysteines of a Putative Zinc Finger Motif in p48 Are Important for the Nuclear Egress of Nucleocapsids and the Envelopment of Occlusion-Derived Virions

by Xiaoyan Ma, Jiang Li, Manli Wang, Zhihong Hu and Huanyu Zhang

Viruses 2025, 17(3), 434; https://doi.org/10.3390/v17030434 - 18 Mar 2025

Abstract

The open reading frame 103 (p48) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is one of the 38 core baculovirus genes. p48 has been shown to be essential for the production of infectious budded virions (BVs), nuclear egress of nucleocapsids, envelopment of [...] Read more.

The open reading frame 103 (p48) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is one of the 38 core baculovirus genes. p48 has been shown to be essential for the production of infectious budded virions (BVs), nuclear egress of nucleocapsids, envelopment of the nucleocapsid, and embedding of occlusion-derived virions (ODVs) into occlusion bodies (OBs). However, the structure–function relationship of p48 remains unclear. In this study, we showed that four conserved cysteines (C127, C130, C138, and C141) in p48 may form a zinc finger motif based on a predicted structure analysis, and we investigated the roles of these cysteines in p48 function. AcMNPV bacmids lacking p48 or containing mutated p48 were generated. Transfection/infection assays showed that C127, C130, C138, and C141 in p48 were crucial for infectious BV production. Electron microscopy analysis further confirmed that these four cysteines played critical roles in the transport of nucleocapsids out of the nucleus for BV production, and in ODV envelopment. These results demonstrate that the conserved cysteines C127, C130, C138, and C141, related to the putative zinc finger motif, are critical for p48 function in baculovirus infection. Full article

(This article belongs to the Section Invertebrate Viruses)

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9 pages, 699 KiB

Open AccessBrief Report

Novel Rodent Coronavirus-like Virus Detected Among Beef Cattle with Respiratory Disease in Mexico

by Ismaila Shittu, Judith U. Oguzie, Gustavo Hernández-Vidal, Gustavo Moreno-Degollado, Diego B. Silva, Lyudmyla V. Marushchak, Claudia M. Trujillo-Vargas, John A. Lednicky and Gregory C. Gray

Viruses 2025, 17(3), 433; https://doi.org/10.3390/v17030433 - 18 Mar 2025

Abstract

In February 2024, while conducting surveillance for novel respiratory viruses, we studied four beef cattle farms near Monterrey, Mexico. Nasal swabs were collected from sick and healthy beef cattle along with 3 h aerosol samples. None of the samples had molecular evidence of [...] Read more.

In February 2024, while conducting surveillance for novel respiratory viruses, we studied four beef cattle farms near Monterrey, Mexico. Nasal swabs were collected from sick and healthy beef cattle along with 3 h aerosol samples. None of the samples had molecular evidence of influenza A viruses. Three (8%) of thirty-six nasal swabs collected from the four farms and four (33.3%) of the twelve bioaerosol specimens had molecular evidence of influenza D virus. Five sick cow nasal swabs and one bioaerosol sample on a single farm had molecular evidence of rodent coronavirus-like (RCoV), an alphacoronavirus. Three (60%) of the five RCoV-positive cattle nasal swabs also had molecular evidence of influenza D. Attempts to isolate the RCoV in Vero-E6, LLC-MK2, MDBK, and L-2 cells were unsuccessful. However, we were able to assemble ~60% of the RCoV genome using next-generation sequencing. The six RCoV-positive samples clustered with RCoV strains identified in China in 2021. During the last 12 months, we have studied an estimated 478 dairy and beef cattle nasal swabs on 11 farms in the US and Mexico, and these RCoV detections are the first we have encountered. While feed contamination cannot be ruled out, given the propensity of CoVs to jump species and that we detected RCoV only in the noses of sick cows on this one farm, we are concerned that these findings could represent an isolated RCoV spillover event. With this report, we are alerting veterinarians and cattle farm owners of our observations that RCoV may be a new cause of bovine respiratory disease. Full article

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

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19 pages, 17051 KiB

Open AccessArticle

Biosecurity Risk Factors and Predictive Index for Hepatitis E Virus Serological Status in Belgian Pig Farms: Conventional and Free-Range Systems

by Constance Wielick, Louisa Ludwig-Begall, Stefaan Ribbens, Étienne Thiry, Christel Faes and Claude Saegerman

Viruses 2025, 17(3), 432; https://doi.org/10.3390/v17030432 - 18 Mar 2025

Abstract

Hepatitis E viruses (HEV) cause hepatitis E in humans. In industrialized countries, sporadic HEV infections, typically caused by HEV genotypes 3 or 4, can become chronic and progress to liver cirrhosis in immunocompromised individuals. Pigs are a significant animal reservoir, implicating raw or [...] Read more.

Hepatitis E viruses (HEV) cause hepatitis E in humans. In industrialized countries, sporadic HEV infections, typically caused by HEV genotypes 3 or 4, can become chronic and progress to liver cirrhosis in immunocompromised individuals. Pigs are a significant animal reservoir, implicating raw or undercooked pork products as potential sources of human infection. To better understand HEV dissemination in the Belgian pig population, potential risk factors were investigated by linking farm-level HEV serological status to biosecurity questionnaire data. Farrow-to-finish herd type, free-range systems, and poor boot hygiene were significantly associated with higher within-herd prevalences. This enabled an initial risk profiling of various farming types and the development of predictions for all Belgian pig farms. When combined with the census of the Belgian wild boar population, the predicted HEV status of all professional Belgian pig farms (based on these associations) does not suggest that the proximity of wild boars is a main source of HEV in free-ranging herds. Identifying risk factors for increased circulation of HEV between and within pig farms is critical to controlling its spread and reducing human infection. Full article

(This article belongs to the Special Issue Zoonotic Viral Diseases: Drivers, Causes, Prevention and Cure, 2nd Edition)

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14 pages, 2973 KiB

Open AccessArticle

Tegument Protein pUL47 Is Important but Not Essential for Horizontal Transmission of Vaccinal Strain SB-1 of Gallid Alphaherpesvirus 3

by Motoyuki Esaki, Mélanie Chollot, Sylvie Rémy, Katia Courvoisier-Guyader, Zoltan Penzes, David Pasdeloup and Caroline Denesvre

Viruses 2025, 17(3), 431; https://doi.org/10.3390/v17030431 - 18 Mar 2025

Abstract

The gallid alphaherpesvirus 3 (GaAHV3) SB-1, a Mardivirus used as a vaccine against Marek’s disease, has been proposed as an interesting viral vector for poultry vaccination. However, SB-1 is highly transmissible between chickens, a feature that may be a limitation for the use [...] Read more.

The gallid alphaherpesvirus 3 (GaAHV3) SB-1, a Mardivirus used as a vaccine against Marek’s disease, has been proposed as an interesting viral vector for poultry vaccination. However, SB-1 is highly transmissible between chickens, a feature that may be a limitation for the use of live recombinant vaccines. We have previously shown that UL47 is essential for horizontal transmission of the pathogenic Marek’s disease virus between chickens, but it is completely dispensable for replication and pathogenesis. In contrast, the role of UL47 in the biology of SB-1 remains unknown. To study that, we generated an SB-1 mutant lacking UL47 (∆47) from a commercial SB-1 isolate. This mutant replicated and spread like the WT in primary fibroblasts, indicating no growth defects in cell culture. In vivo, chickens inoculated with ∆47 had significantly reduced viral loads in the blood and the spleen, and transport to the skin was delayed compared to WT inoculated chickens. Strikingly, the ∆47 mutant was present in 66% of contact birds. As expected, 100% of contact birds were positive for the WT. In conclusion, our findings reveal that UL47 facilitates GaAHV3 SB-1 replication in vivo, which is important for latency establishment but is not essential for horizontal transmission, unlike for MDV. Full article

(This article belongs to the Special Issue Marek's Disease Virus)

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12 pages, 2162 KiB

Open AccessArticle

Phylogenetic Analysis of Chikungunya Virus Eastern/Central/South African-Indian Ocean Epidemic Strains, 2004–2019

by Alessandra Lo Presti, Claudio Argentini, Giulia Marsili, Claudia Fortuna, Antonello Amendola, Cristiano Fiorentini and Giulietta Venturi

Viruses 2025, 17(3), 430; https://doi.org/10.3390/v17030430 - 18 Mar 2025

Abstract

CHIKV infection is transmitted by Aedes mosquitoes spp., with Ae. aegypti considered as the primary vector and Ae. Albopictus playing an important role in sustaining outbreaks in Europe. The ECSA-Indian Ocean Lineage (IOL) strain emerged in Reunion, subsequently spreading to areas such as [...] Read more.

CHIKV infection is transmitted by Aedes mosquitoes spp., with Ae. aegypti considered as the primary vector and Ae. Albopictus playing an important role in sustaining outbreaks in Europe. The ECSA-Indian Ocean Lineage (IOL) strain emerged in Reunion, subsequently spreading to areas such as India, the Indian Ocean, and Southeast Asia, also causing outbreaks in naive countries, including more temperate regions, which originated from infected travelers. In Italy, two authocthounous outbreaks occurred in 2007 (Emilia Romagna region) and 2017 (Lazio and Calabria regions), caused by two different ECSA-IOL strains. The phylogenetics, evolution, and phylogeography of ECSA-IOL-CHIKV strains causing the 2007 and 2017 outbreaks in Italy were investigated. The mean evolutionary rate and time-scaled phylogeny were performed through BEAST. Specific adaptive vector mutations or key signature substitutions were also investigated. The estimated mean value of the CHIKV E1 evolutionary rate was 1.313 × 10⁻³ substitution/site/year (95% HPD: 8.709 × 10⁻⁴–1.827 × 10⁻³). The 2017 CHIKV Italian sequences of the outbreak in Lazio and of the secondary outbreak in Calabria were located inside a sub-clade dating back to 2015 (95% HPD: 2014–2015), showing an origin in India. Continued genomic surveillance combined with phylogeographic analysis could be useful in public health, as a starting point for future risk assessment models and early warning. Full article

(This article belongs to the Section General Virology)

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14 pages, 226 KiB

Open AccessArticle

Risk Factors Affecting the Severity, Mortality, and Intensive Care Unit Admission of COVID-19 Patients: A Series of 1075 Cases

by Ecem Narin Çopur, Dilek Ergün, Recai Ergün, Serap Atik, Hatice Türk Dağı and Muslu Kazım Körez

Viruses 2025, 17(3), 429; https://doi.org/10.3390/v17030429 - 17 Mar 2025

Abstract

Background: The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is broad; it can range from asymptomatic cases to mild upper respiratory tract illness, respiratory failure, and severe multiorgan failure resulting in death. Therefore, it is important to identify the [...] Read more.

Background: The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is broad; it can range from asymptomatic cases to mild upper respiratory tract illness, respiratory failure, and severe multiorgan failure resulting in death. Therefore, it is important to identify the clinical course of the disease and the factors associated with mortality. Objective: The aim of this study is to identify the risk factors associated with the severity of the disease, intensive care unit admission, and mortality in COVID-19 patients. Methods: A total of 1075 patients with clinical and radiological findings compatible with COVID-19 pneumonia and positive SARS-CoV-2 PCR were selected and retrospectively screened. All included patients were classified according to the 7th edition of the 2019 Coronavirus Disease Guidelines published by the National Health Commission of China. Results: It was observed that elevated white blood count (WBC) increased the severity of COVID-19 by 3.26 times and the risk of intensive care unit (ICU) admission by 3.47 times. Patients with high D-dimer levels had a 91% increased risk, and those with high fibrinogen levels had a 2.08 times higher risk of severe disease. High C-reactive protein (CRP) values were found to increase disease severity by 6.89 times, mortality by 12.84 times, and ICU admission by 3.37 times. Conclusions: Identifying the factors associated with disease severity, ICU admission, and mortality in COVID-19 patients could help reduce disability and mortality rates in pandemics. Full article

(This article belongs to the Special Issue COVID-19 and Pneumonia, 3rd Edition)

20 pages, 3704 KiB

Open AccessArticle

Exploring the Contribution of TLR7 to Sex-Based Disparities in Respiratory Syncytial Virus (RSV)-Induced Inflammation and Immunity

by Mark A. Miles, Thomas D. Huttmann, Stella Liong, Felicia Liong, John J. O’Leary, Doug A. Brooks and Stavros Selemidis

Viruses 2025, 17(3), 428; https://doi.org/10.3390/v17030428 - 16 Mar 2025

Abstract

TLR7 plays a key role in recognizing viral RNA to initiate an immune response. Sex-based differences in the severity of RSV respiratory infections have been noted, and this may be related to higher expression of X-linked toll-like receptor 7 (TLR7) in female immune [...] Read more.

TLR7 plays a key role in recognizing viral RNA to initiate an immune response. Sex-based differences in the severity of RSV respiratory infections have been noted, and this may be related to higher expression of X-linked toll-like receptor 7 (TLR7) in female immune cells. Indeed, TLR7 has been shown to influence sex differences in responses to other respiratory viruses; however, its role in RSV infection remains underexplored. We infected adult C57Bl/6 or TLR7 knockout mice with RSV and compared the specific lung immune responses between different sexes. Gene expression analysis revealed that infected female mice had elevated levels of type I and II interferons, proinflammatory cytokines, chemokines, and viral transcripts in their lungs compared to males. Additionally, females exhibited increased numbers of macrophages and higher antibody responses in the airways. Deletion of TLR7 diminished the sex differences in certain cytokine and antibody responses. Furthermore, ex vivo infection of male alveolar macrophages with RSV resulted in greater production of proinflammatory cytokines and viral transcripts than in female macrophages, suggesting inherent sex differences in macrophage responses. These findings provide new insights into the mechanisms underlying sex differences in RSV pathophysiology and suggest that TLR7 contributes to an enhanced inflammatory response in females. Full article

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

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14 pages, 1459 KiB

Open AccessArticle

A New Approach to the Etiology of Syncope: Infection as a Cause

by Branislav Milovanovic, Nikola Markovic, Masa Petrovic, Vasko Zugic, Milijana Ostojic, Milica Dragicevic-Antonic and Milovan Bojic

Viruses 2025, 17(3), 427; https://doi.org/10.3390/v17030427 - 15 Mar 2025

Abstract

Background/Objectives: Syncope is a common clinical occurrence, with neurally mediated and orthostatic types accounting for about 75% of cases. The exact pathophysiological mechanisms remain unclear, with recent evidence suggesting autonomic nervous system damage and a potential infectious etiology. This study aimed to examine [...] Read more.

Background/Objectives: Syncope is a common clinical occurrence, with neurally mediated and orthostatic types accounting for about 75% of cases. The exact pathophysiological mechanisms remain unclear, with recent evidence suggesting autonomic nervous system damage and a potential infectious etiology. This study aimed to examine the role of infection in the development of syncope and orthostatic hypotension (OH). Methods: The cross-sectional study included 806 patients from the Neurocardiological Laboratory of the Institute for Cardiovascular Diseases “Dedinje”. Patients were divided into three groups: unexplained recurrent syncope (n = 506), syncope with OH during the head-up tilt test (HUTT) (n = 235), and OH without a history of syncope (n = 62). All participants underwent the HUTT, and 495 underwent serological testing for various microorganisms. Data were analyzed using chi-squared tests and binary and multinomial logistic regression. Results: The HUTT was positive in 90.6% of patients with syncope and OH, compared with 61.6% with syncope alone (p < 0.001). Serological testing revealed that 57.85% of syncope patients, 62.9% of syncope with OH patients, and 78% of OH patients had positive IgM antibodies to at least one microorganism. Multivariate analysis indicated that IgM antibodies to Coxsackievirus and Epstein–Barr virus were significant predictors of OH. Conclusions: This study demonstrated a potential association between infections and syncope/OH. Further investigation into the role of infectious agents in autonomic dysfunction is warranted to clarify the underlying mechanisms of syncope and OH. Full article

(This article belongs to the Special Issue Beyond Acute: Navigating Long COVID and Post-Viral Complications)

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14 pages, 2364 KiB

Open AccessArticle

Deletion of the Human Cytomegalovirus US2 to US11 Gene Family Members Impairs the Type-I Interferon Response

by Inessa Penner, Nadine Krämer, Julia Hirsch, Nicole Büscher, Hanno Schmidt and Bodo Plachter

Viruses 2025, 17(3), 426; https://doi.org/10.3390/v17030426 - 15 Mar 2025

Abstract

Infection of cells with the human cytomegalovirus (HCMV) triggers the expression of interferon-stimulated genes (ISGs). ISGs encode proteins with antiviral functions, such as inhibiting viral replication, promoting cell death of infected cells and enhancing immune responses. HCMV has evolved mechanisms to evade the [...] Read more.

Infection of cells with the human cytomegalovirus (HCMV) triggers the expression of interferon-stimulated genes (ISGs). ISGs encode proteins with antiviral functions, such as inhibiting viral replication, promoting cell death of infected cells and enhancing immune responses. HCMV has evolved mechanisms to evade the antiviral effects of ISGs. The viral proteins encoded by the viral genes US7, US8, and US9 have been shown to interfere with interferon induction. US7 to US9 are embedded in a cluster of HCMV genes, termed US2 to US11. The individual members of this gene family interfere on multiple levels with innate and adaptive immune responses to HCMV infection. Using viral mutants with different deletions in US2 to US11, we addressed the question if genes other than US7 to US9 would also influence the IFN responses. Surprisingly, deletion of the complete US2 to US11 gene region led to reduced levels of selected ISGs. Cells infected with viruses in which individual US2 to US11 genes were deleted showed a less pronounced reduction of the selected ISGs. The experiments including RNA-seq analyses indicate that genes of the US2 to US11 gene family have a complex interaction with the IFN-ISG response which is likely regulated on the level of ISG protein stability. As US2–US11 are dispensable for replication in cell culture, the genomic region was frequently used for the insertion of bacterial artificial chromosome vectors in the process of cloning the complete HCMV genome. The results shown here must be considered when viruses derived from BACs with US2–US11 deletions are used and whether appropriate controls must be applied. Full article

(This article belongs to the Section Animal Viruses)

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12 pages, 3680 KiB

Open AccessArticle

Surveillance and Genomic Evolution of Infectious Precocity Virus (IPV) from 2011 to 2024

by Chengyan Zhou, Guohao Wang, Qingqing Zhou, Fanzeng Meng, Shufang Liu, Jie Huang and Xuan Dong

Viruses 2025, 17(3), 425; https://doi.org/10.3390/v17030425 - 15 Mar 2025

Abstract

Infectious precocity virus (IPV) poses a significant economic threat to the aquaculture industry by causing sexual precocity and slow growth in Macrobrachium rosenbergii. In this study, we conducted an in-depth investigation into the genetic evolution of IPV from 2011 to 2024 by [...] Read more.

Infectious precocity virus (IPV) poses a significant economic threat to the aquaculture industry by causing sexual precocity and slow growth in Macrobrachium rosenbergii. In this study, we conducted an in-depth investigation into the genetic evolution of IPV from 2011 to 2024 by collecting 31 IPV variants through epidemiological surveys and public databases, including 29 variants with complete genomic sequences. The phylogenetic analysis revealed that these complete genomic sequences clustered into two distinct phylogenetic clades as follows: the Southeast Asian clade and the Chinese clade. Nucleotide and protein variation analyses demonstrated a high degree of similarity, with nucleotide identity ranging from 98.5% to 100% and protein identity from 99.4% to 100%. Further analysis of protein variations within the putative coding region identified two distinct variation patterns. The average dN/dS ratio of 0.12 highlights the strong purifying selection acting on IPV, particularly on structural proteins. In conclusion, this study significantly expands the genomic database of IPV and provides valuable insights into its genetic evolution. These findings offer critical scientific evidence to enhance detection protocols and support sustainable M. rosenbergii aquaculture practices. Full article

(This article belongs to the Section Animal Viruses)

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19 pages, 1197 KiB

Open AccessArticle

COVID-19 Disease Burden in the Omicron Variant-Dominated Endemic Phase: Insights from the ROUTINE-COV19 Study Using Real-World German Statutory Health Insurance Data

by Sabrina Müller, Andrea Schmetz, Julia K. Knaul, Thomas Wilke, Jingyan Yang, Sabine Dornig, Clara Lehmann and Christoph D. Spinner

Viruses 2025, 17(3), 424; https://doi.org/10.3390/v17030424 - 14 Mar 2025

Abstract

The ROUTINE-COV19 study explores the burden of COVID-19 in Germany during the early endemic phase, assessing disease patterns and their impact on the healthcare system from 1 July 2022 to 30 June 2023. Using anonymized statutory health insurance data from over 3 million [...] Read more.

The ROUTINE-COV19 study explores the burden of COVID-19 in Germany during the early endemic phase, assessing disease patterns and their impact on the healthcare system from 1 July 2022 to 30 June 2023. Using anonymized statutory health insurance data from over 3 million individuals in Thuringia and Saxony, COVID-19 cases were identified through diagnostic codes, with severe and critical cases defined by hospitalization and intensive care criteria. The study focused on high-risk populations as identified by the German Immunization Technical Advisory Group. During the study period, 414,648 new COVID-19 cases were documented, with peaks in October 2022 and March 2023. Severe cases occurred at a rate of 241.6 per 100,000 persons, with in-hospital mortality exceeding 12%. Critical cases requiring intensive care had an in-hospital mortality rate of 32.2%. COVID-19-related hospitalizations averaged 9.94 days, generating direct costs of EUR 64.9 million, while indirect costs from work absenteeism amounted to EUR 454.3 million, representing 7.5% of all-cause absenteeism costs. Despite entering an endemic phase, COVID-19 continues to pose a substantial burden, particularly among older adults and those with pre-existing cardiovascular conditions. Full article

(This article belongs to the Section Coronaviruses)

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20 pages, 8925 KiB

Open AccessArticle

A New Human SCARB2 Knock-In Mouse Model for Studying Coxsackievirus A16 and Its Neurotoxicity

by Haiting Wu, Ziou Wang, Yiwei Zhang, Lingfeng Hu, Jinling Yang, Caixing Zhang, Mumeng Lou, Na Pi, Qiyan Wang, Shengtao Fan and Zhangqiong Huang

Viruses 2025, 17(3), 423; https://doi.org/10.3390/v17030423 - 14 Mar 2025

Abstract

Hand, Foot, and Mouth Disease (HFMD) is a viral illness caused by enterovirus infections. While the introduction of the enterovirus 71 (EV71) vaccine has significantly reduced the number of EV71-related cases, the continued spread of Coxsackievirus A16 (CVA16) remains a major public health [...] Read more.

Hand, Foot, and Mouth Disease (HFMD) is a viral illness caused by enterovirus infections. While the introduction of the enterovirus 71 (EV71) vaccine has significantly reduced the number of EV71-related cases, the continued spread of Coxsackievirus A16 (CVA16) remains a major public health threat. Previous studies have shown that human SCARB2 (hSCARB2) knock-in (KI) mice, generated using embryonic stem cell (ESC) technology, are susceptible to CVA16. However, these models have failed to reproduce the clinical pathology and neurotoxicity after CVA16 infection. Therefore, there is an urgent need for a more reliable and effective animal model to study CVA16. In this study, we successfully created a hSCARB2 KI mouse model targeting the ROSA26 locus using CRISPR/Cas9 gene editing technology. The application of CRISPR/Cas9 enabled stable and widespread expression of hSCARB2 in the model. After infection, the KI mice exhibited a clinical pathology that closely mimics human infection, with prominent limb weakness and paralysis. The virus was detectable in multiple major organs of the mice, with peak viral load observed on day 7 post-infection, gradually clearing thereafter. Further analysis revealed widespread neuronal necrosis and infiltration of inflammatory cells in the brain and spinal cord of the KI mice. Additionally, significant activation of astrocytes (GFAP-positive) and microglia (IBA1-positive) was observed in the brain, suggesting that CVA16 infection may induce limb paralysis by attacking neuronal cells. Overall, this model effectively replicates the neuropathological changes induced by CVA16 infection and provides a potential experimental platform for studying CVA16-associated pathogenesis and neurotoxicity. Full article

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

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13 pages, 1010 KiB

Open AccessBrief Report

Prevalence of EBV, HHV6, HCMV, HAdV, SARS-CoV-2, and Autoantibodies to Type I Interferon in Sputum from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients

by Ulf Hannestad, Annika Allard, Kent Nilsson and Anders Rosén

Viruses 2025, 17(3), 422; https://doi.org/10.3390/v17030422 - 14 Mar 2025

Abstract

An exhausted antiviral immune response is observed in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and post-SARS-CoV-2 syndrome, also termed long COVID. In this study, potential mechanisms behind this exhaustion were investigated. First, the viral load of Epstein–Barr virus (EBV), human adenovirus (HAdV), human cytomegalovirus [...] Read more.

An exhausted antiviral immune response is observed in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and post-SARS-CoV-2 syndrome, also termed long COVID. In this study, potential mechanisms behind this exhaustion were investigated. First, the viral load of Epstein–Barr virus (EBV), human adenovirus (HAdV), human cytomegalovirus (HCMV), human herpesvirus 6 (HHV6), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was determined in sputum samples (n = 29) derived from ME/CFS patients (n = 13), healthy controls (n = 10), elderly healthy controls (n = 4), and immunosuppressed controls (n = 2). Secondly, autoantibodies (autoAbs) to type I interferon (IFN-I) in sputum were analyzed to possibly explain impaired viral immunity. We found that ME/CFS patients released EBV at a significantly higher level compared to controls (p = 0.0256). HHV6 was present in ~50% of all participants at the same level. HAdV was detected in two cases with immunosuppression and severe ME/CFS, respectively. HCMV and SARS-CoV-2 were found only in immunosuppressed controls. Notably, anti-IFN-I autoAbs in ME/CFS and controls did not differ, except in a severe ME/CFS case showing an increased level. We conclude that ME/CFS patients, compared to controls, have a significantly higher load of EBV. IFN-I autoAbs cannot explain IFN-I dysfunction, with the possible exception of severe cases, also reported in severe SARS-CoV-2. We forward that additional mechanisms, such as the viral evasion of IFN-I effect via the degradation of IFN-receptors, may be present in ME/CFS, which demands further studies. Full article

(This article belongs to the Special Issue Saliva in the Diagnosis of Viral Diseases)

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8 pages, 169 KiB

Open AccessCommunication

Dual Resistance to Maribavir and Ganciclovir in Transplant Recipients

by Steven B. Kleiboeker

Viruses 2025, 17(3), 421; https://doi.org/10.3390/v17030421 - 14 Mar 2025

Abstract

Background: Human cytomegalovirus (CMV) remains an important pathogen, especially for immunocompromised patients such as solid organ and hematopoietic stem cell recipients. Viral genomic mutations conferring drug resistance are an important impediment to effective CMV management and frequently lead to use of alternative antiviral [...] Read more.

Background: Human cytomegalovirus (CMV) remains an important pathogen, especially for immunocompromised patients such as solid organ and hematopoietic stem cell recipients. Viral genomic mutations conferring drug resistance are an important impediment to effective CMV management and frequently lead to use of alternative antiviral drugs to treat CMV disease. Methods: Results from 1459 de-identified patient samples with both UL54 and UL97 sequencing results were analyzed for ganciclovir (GCV) and maribavir (MBV) resistance mutations. Genomic sequencing was performed by the Sanger method and resistance mutations were identified by comparison to CMV reference strain AD169. Results: Ganciclovir resistance was identified in 379 of 1459 (25.98%) of the samples tested, with most resistance-conferring mutations present in viral gene UL97. A total of 121 of 1459 (8.29%) samples had MBV resistance mutations, and 84 (69.42%) of the 121 samples with MBV resistance also had GCV resistance mutations. Of the 84 samples with resistance to both MBV and GCV, 35 (41.67%) had a single UL97 mutation conferring resistance to both drugs, either C480F or F342Y. The overall prevalence of C480F was increased relative to an earlier analysis of samples from this reference laboratory. Conclusions: Although a high prevalence of CMV resistance mutations was identified, this must be taken in the context of healthcare providers submitting samples from patients with suspected CMV resistance. Most MBV-resistant samples were also resistant to GCV, suggesting that use of MBV as an alternative to GCV may benefit from genotypic resistance testing to achieve the effective control of CMV disease. Full article

(This article belongs to the Special Issue Human Cytomegalovirus Therapeutic Strategies and Clinical Applications)

19 pages, 3118 KiB

Open AccessArticle

Bunyaviral Cap-Snatching Endonuclease Activity and Inhibition with Baloxavir-like Inhibitors in the Context of Full-Length L Proteins

by Arlo J. Loutan, Baiuyan Yang, Gabrielle Connolly, Adam Montoya, Robert J. Smiley, Arnab K. Chatterjee and Matthias Götte

Viruses 2025, 17(3), 420; https://doi.org/10.3390/v17030420 - 14 Mar 2025

Abstract

The Bunyavirales order includes a range of zoonotic viruses, which can cause severe disease in humans. The viral replication machinery is a logical target for the development of direct-acting antivirals. Inhibition of the cap-snatching endonuclease activity of related influenza viruses provides a proof [...] Read more.

The Bunyavirales order includes a range of zoonotic viruses, which can cause severe disease in humans. The viral replication machinery is a logical target for the development of direct-acting antivirals. Inhibition of the cap-snatching endonuclease activity of related influenza viruses provides a proof of concept. Using the influenza B virus (IBV) RNA-dependent RNA polymerase complex as a benchmark, we conducted a comparative analysis of endonuclease activities of recombinant full-length bunyaviral L proteins using gel-based assays. The IBV complex demonstrates specific endonucleolytic cleavage and a clear preference for capped substrates. In contrast, severe fever with thrombocytopenia syndrome, Sin Nombre, and Hantaan virus L proteins readily cleave capped and uncapped RNAs to a broader spectrum of RNA fragments. Active site mutants further help to control for the potential of contaminating nucleases, exonuclease activity, and RNA hydrolysis. The influenza cap-snatching inhibitor baloxavir and derivatives have been used to validate this approach. In conclusion, the results of this study demonstrate the importance of assays with single nucleotide resolution and the use of full-length L proteins as a valuable experimental tool to identify selective endonuclease inhibitors. Full article

(This article belongs to the Special Issue Viral Replication Inhibitors)

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10 pages, 2185 KiB

Open AccessArticle

Testing the Tenacity of Small Ruminant Lentiviruses In Vitro to Assess the Potential Risk of Indirect Fomites’ Transmission

by Maksym Samoilenko, Vitalii Nedosekov and Giuseppe Bertoni

Viruses 2025, 17(3), 419; https://doi.org/10.3390/v17030419 - 14 Mar 2025

Abstract

In 2011–2013, we isolated and characterized small ruminant lentiviruses (SRLVs) from two flocks, one of goats and the other of sheep, that had never been in direct contact. Phylogenetic analysis of these viruses indicated a common origin, which led us to hypothesize indirect [...] Read more.

In 2011–2013, we isolated and characterized small ruminant lentiviruses (SRLVs) from two flocks, one of goats and the other of sheep, that had never been in direct contact. Phylogenetic analysis of these viruses indicated a common origin, which led us to hypothesize indirect transmission of these viruses between the two flocks. Since, to our knowledge, there are no published data on the tenacity of these viruses, we started this work. In the first part, we monitored the loss of infectivity of two prototypic SRLV strains, MVV 1514 and CAEV-CO, over time, in liquid suspension. As expected, the suspensions stored at 4 °C better preserved the infectivity of the viruses. Additionally, viruses resuspended in milk, the medium mirroring the in vivo situation, proved more tenacious than those maintained in a cell culture medium. These viruses, subjected to harsh treatments such as drying and resuspending, partially maintained their replication capacity. After an immediate loss of nearly 1 log₁₀ TCID₅₀ immediately after desiccation, the viruses maintained their replication capacity for at least three weeks when desiccated in milk. These results suggest that fomites, clothing, or pastures contaminated with secretions or milk from infected animals might mediate the infection of animals independently of direct contact. Full article

(This article belongs to the Special Issue Viral Diseases of Livestock and Diagnostics, 2nd Edition)

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19 pages, 3368 KiB

Open AccessArticle

Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification with Xylenol Orange Targeting Nucleocapsid Gene for Detection of Feline Coronavirus Infection

by Kotchaporn Khumtong, Witsanu Rapichai, Wichayet Saejung, Piyamat Khamsingnok, Nianrawan Meecharoen, Siriluk Ratanabunyong, Hieu Van Dong, Supansa Tuanthap, Amonpun Rattanasrisomporn, Kiattawee Choowongkomon, Oumaporn Rungsuriyawiboon and Jatuporn Rattanasrisomporn

Viruses 2025, 17(3), 418; https://doi.org/10.3390/v17030418 - 14 Mar 2025

Abstract

Feline infectious peritonitis (FIP), a devastating disease with near-complete mortality, is caused by the feline coronavirus (FCoV) and affects domestic cats worldwide. Herein, we report the development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay incorporating xylenol orange (XO) as a visual [...] Read more.

Feline infectious peritonitis (FIP), a devastating disease with near-complete mortality, is caused by the feline coronavirus (FCoV) and affects domestic cats worldwide. Herein, we report the development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay incorporating xylenol orange (XO) as a visual indicator for FCoV detection. The assay employed six oligonucleotide primers targeting regions of the nucleocapsid (N) gene. Under optimized conditions (65 °C, 60 min), amplification products were detected through pH-dependent colour changes in the XO dye. The RT-LAMP-XO assay exhibited high specificity for FCoV, with no cross-reactivity against other common feline viral pathogens. While the detection limit (1.7 × 10¹ copies/µL) was an order of magnitude higher than that of qPCR, the method offered advantages in simplicity and speed compared to existing diagnostic approaches. Although less sensitive than qPCR, the RT-LAMP-XO assay may serve as a rapid screening tool when used in combination with additional primer sets. These findings demonstrate the potential utility of XO-based RT-LAMP as a simple, visual detection method for FCoV infection. Full article

(This article belongs to the Special Issue Viral Diseases of Domestic Animals)

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