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Viruses
Volume 17
Issue 3
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Viruses, Volume 17, Issue 3 (March 2025) – 165 articles

Cover Story (view full-size image): The persistence of latent HIV reservoirs remains a major obstacle to finding a cure for HIV infection. In this study, we investigated the potential of combination therapy using histone deacetylase (HDAC) and poly(ADP-ribose) polymerase (PARP) inhibitors to reactivate and reduce latent reservoirs in vitro. Our results demonstrate that this combinational approach effectively induces latent HIV, resulting in a significant reduction in reservoir size. Notably, both HDAC and PARP inhibitors are FDA-approved for cancer treatment, highlighting their strong potential for rapid clinical translation, contingent upon further validation of efficacy and safety in ongoing in vivo studies. View this paper
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12 pages, 777 KiB  
Communication
A Retrospective Study of Respiratory Viruses in a Four-Year Study of Nasal Swabs from Patients with Severe Influenza-like Symptoms in the Lazio Region, Italy
by Giuseppe Sberna, Licia Bordi, Cosmina Mija, Enrico Girardi, Fabrizio Maggi and Eleonora Lalle
Viruses 2025, 17(3), 452; https://doi.org/10.3390/v17030452 - 20 Mar 2025
Viewed by 297
Abstract
The global outbreak of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the strategies adopted by different nations have affected and altered the transmission of different respiratory pathogens around the world. We examined the impact of SARS-CoV-2 on the spread of respiratory viruses [...] Read more.
The global outbreak of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the strategies adopted by different nations have affected and altered the transmission of different respiratory pathogens around the world. We examined the impact of SARS-CoV-2 on the spread of respiratory viruses in the period between 2021 and 2024 in patients with severe influenza-like symptoms in the Lazio region using multiplex PCR tests for the identification of common seasonal respiratory viruses. Our data reveal a change in the transmission of respiratory viruses from 2021 to 2024, with a sharp decline in the transmission of SARS-CoV-2 and a rise in the transmission of other respiratory viruses, especially influenza viruses, and human rhinovirus/enterovirus in 2024. Moreover, viral co-infections, both those involving two viruses and those involving three viruses, have also increased. This work shows how the spread of SARS-CoV-2 influenced the spread of other respiratory viruses over four years in patients with severe influenza-like symptoms in the Lazio region. In conclusion, the resurgence and fluctuation of various respiratory viruses emphasize the dynamic nature of viral epidemiology in the post-pandemic context and highlight the ongoing need for vigilant public health monitoring and intervention strategies. Full article
(This article belongs to the Special Issue The Influence of COVID-19 Pandemic on the Epidemiology of Other Human Viral Infections)
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15 pages, 990 KiB  
Article
HIV-Helminth Co-Infections and Immune Checkpoints: Implications for Cancer Risk in South Africa
by Botle Precious Damane, Thanyani Victor Mulaudzi, Sayed Shakeel Kader, Pragalathan Naidoo, Zodwa Dlamini and Zilungile Lynette Mkhize-Kwitshana
Viruses 2025, 17(3), 451; https://doi.org/10.3390/v17030451 - 20 Mar 2025
Viewed by 453
Abstract
South Africa has the highest HIV prevalence globally, often co-occurring with helminth infections in impoverished regions. The coexistence of these infections leads to immunological interactions, potentially enhancing oncogenesis by upregulating immune checkpoint molecules (ICs) among other effects. Notably, most ICs are overexpressed in [...] Read more.
South Africa has the highest HIV prevalence globally, often co-occurring with helminth infections in impoverished regions. The coexistence of these infections leads to immunological interactions, potentially enhancing oncogenesis by upregulating immune checkpoint molecules (ICs) among other effects. Notably, most ICs are overexpressed in cancer and correlated with its progression. Helminth infections trigger Th2-type immunity, increasing immunosuppressive M2 macrophages, regulatory T cells, and associated IC molecules. PD-L2 is reported to contribute to Th2-type immunity induced by helminth infections. Similarly, TIM-3, elevated during chronic viral infections, induces a similar immunosuppressive profile. CTLA-4 and PD-1 impact T-cell function by interacting with CD28, crucial for T-cell function. CD28 is downregulated in chronic infections and cancer. This study investigated the impact of HIV-helminth co-infection on co-stimulatory and co-inhibitory molecule profiles associated with antitumor immunity. Using 78 serum samples collected from March 2020 to May 2021, participants were categorized into uninfected control (no HIV and helminth infections), HIV-infected, helminth-infected, and HIV-helminth co-infected groups. Multiplex immune regulatory molecule assay analysis was conducted. The data were analyzed using multivariate regression analysis and adjusted for confounders (age, gender, BMI, ART, supplements, and other chronic diseases). The uninfected control group was used as the baseline reference group for analysis. HIV-infected individuals had higher PD-1 (adjusted β = 0.12, p = 0.034) and TIM-3 (adjusted β = 23.15, p = 0.052) levels, with the latter showing a trend toward significance. However, lower CD28 levels (adjusted β = −651.95, p = 0.010) were observed. Helminth-infected individuals had higher TIM-3 levels (adjusted β = 20.98, p = 0.020). The co-infected group had higher PD-1 (unadjusted β = 0.18, p = 0.0046) and PD-L2 (adjusted β = 7.95, p = 0.033) levels. A significant decrease in CD28 profile was observed across all infected groups: HIV-infected (adjusted β = −651.95, p = 0.010), helminth-infected (adjusted β = −674.32, p = 0.001), and co-infected (adjusted β = −671.55, p = 0.044). The results suggest that HIV-helminth co-infections alter immune checkpoint markers, potentially increasing cancer risk by promoting an immunosuppressive microenvironment that hinders anti-cancer immunity. CD28’s downregulation underscores immune inefficiency in chronic diseases. Addressing these co-infections is crucial for improving HIV care and potentially reducing cancer risks through targeted strategies. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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13 pages, 1251 KiB  
Article
Two Avastrovirus Species Discovered in Psittaciformes Expand the Host Range of the Family Astroviridae
by K9 Jenns, John-Sebastian Eden, Annabelle Olsson and David Phalen
Viruses 2025, 17(3), 450; https://doi.org/10.3390/v17030450 - 20 Mar 2025
Viewed by 329
Abstract
Metatranscriptomics has recently revealed greater species richness and host range of the Avastrovirus genus, quadrupling the number of avian orders known to host them in less than a decade. Despite this growing awareness of astrovirus presence in wild birds, limited attention has been [...] Read more.
Metatranscriptomics has recently revealed greater species richness and host range of the Avastrovirus genus, quadrupling the number of avian orders known to host them in less than a decade. Despite this growing awareness of astrovirus presence in wild birds, limited attention has been paid to these viruses in the context of disease in Australian avifauna. Here we used unbiased RNA sequencing of intestinal samples from a galah (Eolophus roseicapilla) and an Australian king parrot (Alisterus scapularis) with a chronic diarrhoeal and wasting disease to detect the entire genomes of two novel astrovirus species. We propose naming these viruses Avastrovirus eolorosei (PQ893528) and Avastrovirus aliscap (PQ893527). The phylogenetic positions of these viruses highlight the importance of current and future metatranscriptomic virus screening in investigations of avian host landscapes beyond Galloanserae. This is also the first documentation of avastrovirus infections in Psittaciformes and the first to report their potential role as disease agents in them. Full article
(This article belongs to the Section General Virology)
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7 pages, 168 KiB  
Case Report
Comparison of Nose Wipes, Stall Sponges, and Air Samples with Nasal Secretions for the Molecular Detection of Equine Influenza Virus in Clinically and Subclinically Infected Horses
by Nicola Pusterla, Kaila Lawton, Samantha Barnum and K. Gary Magdesian
Viruses 2025, 17(3), 449; https://doi.org/10.3390/v17030449 - 20 Mar 2025
Viewed by 288
Abstract
In recent years, the use of non-invasive host and environmental samples for the detection and monitoring of equine respiratory pathogens has shown promise and a high overall agreement with the gold standard of nasal secretions. The present study looked at comparing nose wipes, [...] Read more.
In recent years, the use of non-invasive host and environmental samples for the detection and monitoring of equine respiratory pathogens has shown promise and a high overall agreement with the gold standard of nasal secretions. The present study looked at comparing nose wipes, stall sponges, and air samples with nasal swabs collected from 27 horses involved in an equine influenza (EI) outbreak. The outbreak involved 5 clinical, 6 subclinical, and 16 uninfected horses. Samples sets were collected at the onset of the index case and retested every 2–3 days thereafter until all horses tested qPCR-negative for EI virus (EIV). Nose wipes and stall sponges identified EIV in all clinical cases, and air samples identified EIV in 4/5 clinical horses. The overall agreement with all nasal swabs collected from clinical cases was 89% for nose wipes, 78% for stall sponges, and 44% for air samples. Due to the shorter shedding time in subclinical cases, nose wipes and stall sponges detected EIV in 5/6 and 4/6 subclinical horses, respectively. Only one single air sample tested qPCR-positive for EIV in a subclinical shedder. When compared to the gold standard of nasal secretions in subclinically infected horses, the overall agreement was 54% for stall sponges, 50% for air samples, and 45% for nose wipes. The collection of non-invasive contact and environmental samples is a promising alternative to nasal swabs for the detection of EIV in clinically and subclinically infected horses. However, they should always be considered as a second-choice sample type to the more accurate nasal swabs and used to test refractory horses or large populations during outbreaks. Further, the pooling of identical or different samples collected from the same horse for the qPCR testing of EIV increases the accuracy of detecting EIV, especially in subclinically infected horses. Full article
(This article belongs to the Section Animal Viruses)
14 pages, 2256 KiB  
Article
Development of IgY-Based Passive Immunization Against Tilapia Lake Virus: Development and In Vitro Neutralization Assays
by Piyathip Setthawong, Jidapa Yamkasem, Matepiya Khemthong, Puntanat Tattiyapong, Pornphimon Metheenukul, Noppadol Prasertsincharoen, Tuchakorn Lertwanakarn, Naris Thengchaisri and Win Surachetpong
Viruses 2025, 17(3), 448; https://doi.org/10.3390/v17030448 - 20 Mar 2025
Viewed by 367
Abstract
Tilapia lake virus (TiLV) poses a major threat to global tilapia aquaculture and contributes to significant economic losses due to the absence of effective vaccines and treatments. Given the high mortality rates and severe pathological effects of TiLV on tilapia, alternative strategies, such [...] Read more.
Tilapia lake virus (TiLV) poses a major threat to global tilapia aquaculture and contributes to significant economic losses due to the absence of effective vaccines and treatments. Given the high mortality rates and severe pathological effects of TiLV on tilapia, alternative strategies, such as immunoglobulin-based therapies, are being considered for disease control. In this study, we developed specific immunoglobulin Y (IgY) antibodies against TiLV and evaluated their neutralization activity. Laying hens were immunized via intramuscular injections of recombinant TiLV segment 4 protein, and IgY antibodies were extracted and purified from their egg yolks using polyethylene glycol precipitation. Western blot analysis confirmed the specificity of the IgY, which demonstrated no cross-reactivity with nontarget proteins. Neutralization assays revealed a dose-dependent reduction in TiLV infectivity, which declined from 5.01 × 106 TCID50/mL to 5.01 × 104–1.26 × 105 TCID50/mL, with the highest efficacy observed at a 1:2 dilution. Despite the variability in neutralization infectivity among the different hens, IgY effectively inhibited TiLV-induced cytopathic effects. Immunofluorescence assays further confirmed a significant reduction in the TiLV antigen levels in IgY-treated RHTiB cells. Our findings highlight IgY as a promising strategy for TiLV control and suggest its potential application in the prevention of emerging viruses. Full article
(This article belongs to the Special Issue Aquatic Animal Viruses and Antiviral Immunity)
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19 pages, 3982 KiB  
Article
Comparative Interactome Profiling of Nonstructural Protein 3 Across SARS-CoV-2 Variants Emerged During the COVID-19 Pandemic
by Valeria Garcia Lopez and Lars Plate
Viruses 2025, 17(3), 447; https://doi.org/10.3390/v17030447 - 20 Mar 2025
Viewed by 405
Abstract
SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and [...] Read more.
SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and manipulation of host protein interactions. We focus on nonstructural protein 3 (nsp3), with multiple domains with different activities, including viral polyprotein cleavage, host deubiquitylation, de-ISGylation, and double-membrane vesicle formation. Using affinity purification–mass spectrometry (AP-MS), we identify differential protein interactions in nsp3 caused by mutations found in variants identified between 2019 and 2024: Alpha 20I, Beta 20H, Delta 21I, Delta 21J, Gamma 20J, Kappa 21B, Lambda 21G, Omicron 21K, and Omicron 21L. A small set of amino acid substitutions in the N-terminal region of nsp3 (nsp3.1) could be traced to increased interactions with RNA-binding proteins, which are vital in viral replication. Meanwhile, variants of the central region of nsp3 (nsp3.2) were found to share interactions with protein quality control machinery, including ER-associated degradation. In this construct, shared trends in interactor enrichment are observed between Omicron 21K and Delta 21I. These results underscore how minor mutations reshape host interactions, emphasizing the evolutionary arms race between the host and virus. We provide a roadmap to track the interaction changes driven by SARS-CoV-2 variant evolution. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants, Vaccines, and Immune Responses)
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3 pages, 168 KiB  
Commentary
Human T-Cell Lymphotropic Virus (HTLV 1/2) in Ecuador: Time for Action
by Miguel Angel Garcia-Bereguiain, Solon Alberto Orlando, Melissa Joseth Carvajal Capa and Manuel Gonzalez
Viruses 2025, 17(3), 446; https://doi.org/10.3390/v17030446 - 20 Mar 2025
Viewed by 273
Abstract
The human T-cell lymphotropic viruses of type 1 and 2 (HTLV 1/2) are retroviruses with estimations of 10 million people infected worldwide. HTLV 1/2 viruses are endemic in South America where Indigenous and Afro American populations are considered of high risk. Although several [...] Read more.
The human T-cell lymphotropic viruses of type 1 and 2 (HTLV 1/2) are retroviruses with estimations of 10 million people infected worldwide. HTLV 1/2 viruses are endemic in South America where Indigenous and Afro American populations are considered of high risk. Although several case reports of HTLV 1/2 associated pathologies and some prevalence studies have been reported in Ecuador, the country lacks a national surveillance and control program, and no screening of blood or organ donors is currently done. We discuss the problems associated to HTLV 1/2 in Ecuador and propose a strategy to improve a surveillance and control program. Full article
(This article belongs to the Special Issue HIV and HTLV Infections and Coinfections)
2 pages, 351 KiB  
Correction
Correction: Gao et al. Effects of the NF-κB Signaling Pathway Inhibitor BAY11-7082 in the Replication of ASFV. Viruses 2022, 14, 297
by Qi Gao, Yunlong Yang, Yongzhi Feng, Weipeng Quan, Yizhuo Luo, Heng Wang, Jiachen Zheng, Xiongnan Chen, Zhao Huang, Xiaojun Chen, Runda Xu, Guihong Zhang and Lang Gong
Viruses 2025, 17(3), 445; https://doi.org/10.3390/v17030445 - 20 Mar 2025
Viewed by 218
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue African Swine Fever Virus 2021)
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9 pages, 184 KiB  
Article
Liver Scores in the Prognostication of COVID-19 Patients
by Thilo Gambichler, Dominic König, Nadine Schuleit, Laura Susok, Wolfgang Schmidt and Nessr Abu Rached
Viruses 2025, 17(3), 444; https://doi.org/10.3390/v17030444 - 19 Mar 2025
Viewed by 336
Abstract
The implementation of easily accessible prognostic biomarkers for patients with COVID-19 remains an important area of clinical research. In this large monocentric study at a German tertiary care hospital, we determined the prognostic performance of different liver scores in 605 patients with COVID-19. [...] Read more.
The implementation of easily accessible prognostic biomarkers for patients with COVID-19 remains an important area of clinical research. In this large monocentric study at a German tertiary care hospital, we determined the prognostic performance of different liver scores in 605 patients with COVID-19. We evaluated the Fibrosis-4 (FIB-4) index, the Aspartate Aminotransferase-to-Platelet Ratio Index (APRI), the Model for End-Stage Liver Disease (MELD) score, and the De Ritis ratio (DRR; AST/ALT ratio). The 30-day mortality was used as primary COVID-19 outcome measure. The need for intensive care unit (ICU) treatment and overall mortality were secondary endpoints. Univariable analyses showed that most of the investigated liver-related scores (FIB-4, MELD, and DRR), but not APRI for overall mortality, were significantly associated with key outcomes in COVID-19 patients. Concurrently, well-known risk factors—such as advanced age, diabetes, and cardiac or pulmonary comorbidities—were also linked to worse outcomes, except for the female sex having a preventive effect against ICU admission. A history of liver disease was rarely documented among the patients and showed no significant impact on the examined endpoints. Multivariable analyses further revealed that advanced age, DRR, and MELD were independent predictors of both 30-day and overall mortality, while FIB-4 emerged as an independent predictor specifically for overall mortality. Regarding ICU admission, obesity, underlying lung disease, and elevated APRI and MELD scores were identified as independent risk factors, whereas the female sex appeared to be protective. Overall, MELD demonstrated the strongest prognostic value for mortality and ICU admission, with DRR also exhibiting independent predictive power for mortality. These findings suggest that scores originally developed for chronic liver disease assessment—namely FIB-4, APRI, MELD, and DRR—hold promise as prognostic tools in COVID-19. In particular, MELD and DRR emerged as the most powerful biomarkers for predicting severe disease and mortality, highlighting the potential for incorporating these indices into risk stratification models for COVID-19 management. Further prospective multicenter studies are warranted to confirm these observations. Full article
(This article belongs to the Section Coronaviruses)
19 pages, 2878 KiB  
Article
Analysis of Morbidity and Mortality Due to Yellow Fever in Brazil
by Luisa Sousa Machado, Antonio Francisco Marinho Sobrinho, Andrielly Gomes De Jesus, Juarez Antônio Simões Quaresma and Helierson Gomes
Viruses 2025, 17(3), 443; https://doi.org/10.3390/v17030443 - 19 Mar 2025
Viewed by 346
Abstract
Introduction: Yellow fever (YF) is a viral hemorrhagic fever transmitted by mosquitoes, characterized by a high mortality due to kidney and liver failure, massive coagulation disorders, and hemorrhages. With no specific treatment, prevention through vaccination and vector control is essential. This study investigates [...] Read more.
Introduction: Yellow fever (YF) is a viral hemorrhagic fever transmitted by mosquitoes, characterized by a high mortality due to kidney and liver failure, massive coagulation disorders, and hemorrhages. With no specific treatment, prevention through vaccination and vector control is essential. This study investigates the epidemiology of YF in Brazil from 2011 to 2020, focusing on its trends and distribution across the territory. Methods: This ecological time-series study analyzed confirmed YF cases in Brazil’s 27 federative units between 2011 and 2020. Data were sourced from DATASUS, IBGE, and IPEA. Incidence rates per 100,000 inhabitants were calculated, and various sociodemographic and health indicators were analyzed. Prais–Winsten autoregressive models assessed the trends, while a spatial analysis identified the risk areas using global and local Moran’s I statistics. The data were processed using Stata and GeoDa® software, version 1.12. Results: YF cases were concentrated in the Amazon and Atlantic Forest biomes. The majority of the cases occurred in males (83.3%), non-white individuals (94.3%), and rural workers. Pará showed an increasing trend in incidence. A higher vaccination coverage correlated with a lower YF incidence, though endemic areas with good vaccination coverage still exhibited high rates. Health and socioeconomic indicators were inversely related to incidence, highlighting disparities in regional development. Conclusion: Effective YF control requires multidisciplinary strategies, including expanded vaccination coverage, intensified vector control, and active surveillance. Research should focus on developing better vaccines, monitoring immunity, and improving the global response coordination. Full article
(This article belongs to the Special Issue Arboviruses and Global Health: A PanDengue Net Initiative)
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17 pages, 962 KiB  
Review
Understanding HIV-Exposed Uninfected Children: A Narrative Review
by Martina Salvi, Benedetta Fioretti, Maria Alberti, Irene Scarvaglieri, Stefania Arsuffi, Giorgio Tiecco, Francesco Castelli and Eugenia Quiros-Roldan
Viruses 2025, 17(3), 442; https://doi.org/10.3390/v17030442 - 19 Mar 2025
Viewed by 428
Abstract
The widespread implementation of antiretroviral therapy has significantly reduced HIV-related mortality and mother-to-child transmission. Despite being HIV-uninfected, HIV-exposed children (HEU) seem to face heightened risks of immune dysfunction, cardiometabolic diseases, growth delays, reduction in bone mineral density, and neurocognitive impairments compared to HIV-unexposed [...] Read more.
The widespread implementation of antiretroviral therapy has significantly reduced HIV-related mortality and mother-to-child transmission. Despite being HIV-uninfected, HIV-exposed children (HEU) seem to face heightened risks of immune dysfunction, cardiometabolic diseases, growth delays, reduction in bone mineral density, and neurocognitive impairments compared to HIV-unexposed uninfected peers. These vulnerabilities can be attributed to maternal immune dysregulation during pregnancy, antiretroviral (ART) toxicity, HIV exposure, and adverse socioeconomic and nutritional environments. Emerging evidence highlights the impact of antiviral therapy exposure, particularly tenofovir disoproxil fumarate, on HEU mitochondrial dysfunction, bone resorption, neurocognitive delays, and zidovudine on cardiac abnormalities. This narrative review explores the multisystem effects of ART exposure in HEU children, focusing on immune function, neurodevelopment, cardiovascular health, growth, and bone metabolism. By synthesizing findings from diverse studies, the review aims to provide a comprehensive understanding of the potential risks associated with ART regimens and identify future research priorities to improve outcomes for HEU children. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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33 pages, 1407 KiB  
Article
Detection and In Vivo Validation of Dichorhavirus e-Probes in Meta-Transcriptomic Data via Microbe Finder (MiFi®) Discovers a Novel Host and a Possible New Strain of Orchid Fleck Virus
by Avijit Roy, Jonathan Shao, Andres S. Espindola, Daniel Ramos Lopez, Gabriel Otero-Colina, Yazmín Rivera, Vessela A. Mavrodieva, Mark K. Nakhla, William L. Schneider and Kitty Cardwell
Viruses 2025, 17(3), 441; https://doi.org/10.3390/v17030441 - 19 Mar 2025
Viewed by 302
Abstract
Dichorhavirus is a recently accepted plant virus genus within the family Rhabdoviridae. Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by Brevipalpus spp. Currently, there are five recognized species and two unclassified members in [...] Read more.
Dichorhavirus is a recently accepted plant virus genus within the family Rhabdoviridae. Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by Brevipalpus spp. Currently, there are five recognized species and two unclassified members in the genus Dichorhavirus. Four out of seven-orchid fleck virus (OFV), citrus leprosis virus N, citrus chlorotic spot virus, and citrus bright spot virus-can infect citrus and produce leprosis disease-like symptoms. The E-probe Diagnostic for Nucleic Acid Analysis (EDNA) was developed to reduce computational effort and then integrated within Microbe-Finder (MiFi®) online platform to design and evaluate e-probes in raw High Throughput Sequencing (HTS) data. During this study, Dichorhavirus genomes were downloaded from public databases and e-probes were designed using the MiProbe incorporated into the MiFi® platform. Three different sizes of e-probes, 40, 60, and 80 nucleotides, were developed and selected based on whole genome comparisons with near-neighbor genomes. For curation, each e-probe was searched in the NCBI nucleotide sequence database using BLASTn. All the e-probes that had hits with non-target species with ≥90% identities were removed. The sensitivity and specificity of Dichorhavirus genus, species, strain, and variant-specific e-probes were validated in vivo using HTS meta-transcriptomic libraries generated from Dichorhavirus-suspected citrus, orchid, and ornamentals. Through downstream analysis of HTS data, EDNA not only detected the known hosts of OFV but also discovered an unknown host leopard plant (Farfugium japonicum), and the possible existence of a new ornamental strain of OFV in nature. Full article
(This article belongs to the Special Issue The World of Rhabdoviruses)
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16 pages, 1351 KiB  
Article
Switching to Bictegravir/Emtricitabine/Tenofovir Alafenamide Fumarate Regimen and Its Effect on Liver Steatosis Assessed by Fibroscan
by Marcello Trizzino, Roberta Gaudiano, Dalila Mimì Arena, Luca Pipitò, Claudia Gioè and Antonio Cascio
Viruses 2025, 17(3), 440; https://doi.org/10.3390/v17030440 - 19 Mar 2025
Viewed by 805
Abstract
Background: Antiretroviral therapy has transformed HIV infection from a fatal disease to a chronic and manageable condition, but increasing health issues beyond acquired immunodeficiency syndrome, such as metabolic, liver, and cardiovascular diseases, have been observed. Furthermore, the increasing prevalence of HIV strains resistant [...] Read more.
Background: Antiretroviral therapy has transformed HIV infection from a fatal disease to a chronic and manageable condition, but increasing health issues beyond acquired immunodeficiency syndrome, such as metabolic, liver, and cardiovascular diseases, have been observed. Furthermore, the increasing prevalence of HIV strains resistant to older antiretroviral regimens has necessitated a re-evaluation of treatment strategies. Methods: We performed a retrospective, observational study to evaluate the long-term outcomes of an antiretroviral switch from a non-nucleoside reverse transcriptase inhibitor-based to bictegravir-based regimen; this study aimed to assess the impact of this antiretroviral switch on treatment adherence, the safety profile, and virologic outcomes. The secondary objectives were to analyze the changes in lipid, kidney function, liver function, and anthropometric parameters after switching. Results: A total of 25 patients were included in this analysis; virologic suppression was maintained over time, with 100% of patients demonstrating undetectable viral loads at 6, 12, 24, and 36 months. In parallel, a significant increase in CD4+ cell count was observed after switching. No significant differences were observed compared to the previous therapy regarding anthropometric parameters or laboratory parameters. However, a significant reduction in liver steatosis, as assessed by Fibroscan, was observed. Conclusions: bictegravir-based regimens are a valid therapeutic option for people living with HIV, particularly for those with metabolic comorbidities. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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18 pages, 1778 KiB  
Review
A Comprehensive Review of the Neglected and Emerging Oropouche Virus
by Fengwei Bai, Prince M. D. Denyoh, Cassandra Urquhart, Sabin Shrestha and Donald A. Yee
Viruses 2025, 17(3), 439; https://doi.org/10.3390/v17030439 - 19 Mar 2025
Viewed by 946
Abstract
Oropouche virus (OROV) is a neglected and emerging arbovirus that infects humans and animals in South and Central America. OROV is primarily transmitted to humans through the bites of infected midges and possibly some mosquitoes. It is the causative agent of Oropouche fever, [...] Read more.
Oropouche virus (OROV) is a neglected and emerging arbovirus that infects humans and animals in South and Central America. OROV is primarily transmitted to humans through the bites of infected midges and possibly some mosquitoes. It is the causative agent of Oropouche fever, which has high morbidity but low mortality rates in humans. The disease manifests in humans as high fever, headache, myalgia, arthralgia, photophobia, and, in some cases, meningitis and encephalitis. Additionally, a recent report suggests that OROV may cause fetal death, miscarriage, and microcephaly in newborns when women are infected during pregnancy, similar to the issues caused by the Zika virus (ZIKV), another mosquito-borne disease in the same regions. OROV was first reported in the mid-20th century in the Amazon basin. Since then, over 30 epidemics and more than 500,000 infection cases have been reported. The actual case numbers may be much higher due to frequent misdiagnosis, as OROV infection presents similar clinical symptoms to other co-circulating viruses, such as dengue virus (DENV), chikungunya virus (CHIKV), ZIKV, and West Nile virus (WNV). Due to climate change, increased travel, and urbanization, OROV infections have occurred at an increasing pace and have spread to new regions, with the potential to reach North America. According to the World Health Organization (WHO), over 10,000 cases were reported in 2024, including in areas where it was not previously detected. There is an urgent need to develop vaccines, antivirals, and specific diagnostic tools for OROV diseases. However, little is known about this surging virus, and no specific treatments or vaccines are available. In this article, we review the most recent progress in understanding virology, transmission, pathogenesis, diagnosis, host–vector dynamics, and antiviral vaccine development for OROV, and provide implications for future research directions. Full article
(This article belongs to the Special Issue Oropouche Virus (OROV): An Emerging Peribunyavirus (Bunyavirus))
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7 pages, 1455 KiB  
Article
The Effect of Immunosuppressive Treatment on Torque Teno Virus Load in Lung Transplant Recipients: A Preliminary Study
by Marek Ochman, Dagmara Galle, Anna Kowal, Magdalena Królikowska, Fryderyk Zawadzki, Anita Stanjek-Cichoracka, Anna Łaszewska, Elżbieta Chełmecka and Tomasz Hrapkowicz
Viruses 2025, 17(3), 438; https://doi.org/10.3390/v17030438 - 19 Mar 2025
Viewed by 366
Abstract
After transplantation, systematically monitoring and assessing the risk of transplanted organ rejection is crucial. Current methods involving immunosuppressant monitoring, the assessment of organ function, and biopsies are insufficient for predicting rejection. However, regular determination of torque teno virus (TTV) load after transplantation may [...] Read more.
After transplantation, systematically monitoring and assessing the risk of transplanted organ rejection is crucial. Current methods involving immunosuppressant monitoring, the assessment of organ function, and biopsies are insufficient for predicting rejection. However, regular determination of torque teno virus (TTV) load after transplantation may prove to be a useful parameter for monitoring immunosuppression efficacy. Therefore, we aimed to evaluate TTV load in patients before and after lung transplantation and the kinetics of TTV growth in relation to immunosuppression strength. We included 14 patients (mean age: 49.4 ± 14.0 years) undergoing lung transplantation and determined TTV copy numbers using the commercial ARGENE TTV-R-GENE kit from BioMerieux from the day of transplantation to 180 days post-transplantation. We also developed an empirical immunosuppression unit scale to calculate immunosuppression strength. We observed an average positive correlation between log10 TTV and immunosuppression strength, with significant increases in log10 TTV depending on the duration of immunosuppression. These results indicate the potential of TTV as a new parameter to assess the possibility of transplanted organ rejection. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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23 pages, 1995 KiB  
Article
Adapting Next-Generation Sequencing to in Process CRISPR-Cas9 Genome Editing of Recombinant AcMNPV Vectors: From Shotgun to Tiled-Amplicon Sequencing
by Madhuja Chakraborty, Lisa Nielsen, Delaney Nash, Jozef I. Nissimov, Trevor C. Charles and Marc G. Aucoin
Viruses 2025, 17(3), 437; https://doi.org/10.3390/v17030437 - 18 Mar 2025
Viewed by 325
Abstract
The alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most commonly used virus in the Baculovirus Expression Vector System (BEVS) and has been utilized for the production of many human and veterinary biologics. AcMNPV has a large dsDNA genome that [...] Read more.
The alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most commonly used virus in the Baculovirus Expression Vector System (BEVS) and has been utilized for the production of many human and veterinary biologics. AcMNPV has a large dsDNA genome that remains understudied, and relatively unmodified from the wild-type, especially considering how extensively utilized it is as an expression vector. Previously, our group utilized CRISPR-Cas9 genome engineering that revealed phenotypic changes when baculovirus genes are targeted using either co-expressed sgRNA or transfected sgRNA into a stable insect cell line that produced the Cas9 protein. Here, we describe a pipeline to sequence the recombinant AcMNPV expression vectors using shotgun sequencing, provide a set of primers for tiled-amplicon sequencing, show that untargeted baculovirus vector genomes remain relatively unchanged when amplified in Sf9-Cas9 cells, and confirm that AcMNPV gp64 gene disruption can minimize baculovirus contamination in cell cultures. Our findings provide a robust baseline for analyzing in process genome editing of baculoviruses. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research 2024)
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16 pages, 1975 KiB  
Review
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
Viewed by 436
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  
Review
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
Viewed by 454
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, 4944 KiB  
Article
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
Viewed by 244
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  
Brief 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
Viewed by 1144
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  
Article
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
Viewed by 250
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  
Article
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
Viewed by 264
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  
Article
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
Viewed by 311
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  
Article
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
Viewed by 400
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  
Article
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
Viewed by 523
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  
Article
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
Viewed by 573
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  
Article
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
Viewed by 424
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  
Article
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
Viewed by 473
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  
Article
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
Viewed by 552
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  
Article
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
Viewed by 494
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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