Viruses

11 pages, 1203 KB

Open AccessArticle

Genomic Diversity of SARS-CoV-2 Omicron Sublineages and Co-Circulation with Respiratory Viruses in Pediatric Patients in Sao Paulo, Brazil

by Erick Gustavo Dorlass, Guilherme Pereira Scagion, Fabyano Bruno Leal de Oliveira, Bruna Larotonda Telezynski, Ana Karolina Antunes Eisen, Giovana Santos Caleiro, Isabela Barbosa de Assis, Camila Araújo Valério, Vanessa Nascimento Chalup, Cairo Monteiro de Oliveira, Camila Ohomoto de Morais, Marcelo Otsuka, Vera Bain, Mariana Pereira Soledade, Luciano Matsumiya Thomazelli, Carolina Sucupira, Luciana Becker Mau, Andressa Simões Aguiar, Flávia Jacqueline Almeida, Marco Aurélio Palazzi Safadi, João Renato Rebello Pinho, Danielle Bruna Leal de Oliveira, Jansen de Araujo and Edison Luiz Durigon Show full author list Hide full author list

Viruses 2025, 17(11), 1421; https://doi.org/10.3390/v17111421 (registering DOI) - 25 Oct 2025

Abstract

The SARS-CoV-2 Omicron variant caused a global surge in COVID-19 cases following its emergence in November 2021, rapidly diversifying in the subsequent months. Although many studies have documented Omicron’s diversification, few have explored its impact on pediatric populations or the seasonality of other [...] Read more.

The SARS-CoV-2 Omicron variant caused a global surge in COVID-19 cases following its emergence in November 2021, rapidly diversifying in the subsequent months. Although many studies have documented Omicron’s diversification, few have explored its impact on pediatric populations or the seasonality of other respiratory viruses in children. This study aims to investigate the diversity and circulation patterns of SARS-CoV-2 Omicron sublineages in pediatric patients in São Paulo, Brazil, and assess their co-circulation with other respiratory pathogens. Respiratory samples collected from patients under 18 years old across five hospitals between January 2022 and April 2023 were tested for different respiratory viruses using real-time RT-PCR. Whole-genome sequencing was performed on SARS-CoV-2-positive samples. Among the 7868 pediatric respiratory samples tested, 3902 were positive for viral pathogens. Respiratory Syncytial Virus accounted for the highest number of positive cases (n = 1248), exhibiting an atypical off-season peak in November 2022. SARS-CoV-2 was detected in 297 samples, of which 103 were sequenced. BA.1 and BA.5 sublineages had predominant genomic diversity and circulation time. These findings highlight the Omicron variant’s significant impact on the epidemiology and seasonal distribution of respiratory viruses in children, emphasizing the ongoing need for vaccination and robust surveillance efforts in pediatric populations. Full article

(This article belongs to the Special Issue Evolutionary Challenges of RNA Viruses: Insights from SARS-CoV-2 Variants and Emerging Respiratory Diseases)

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14 pages, 2098 KB

Open AccessArticle

Genetic Variability and Prediction of T Epitopes of the HPV16 E2 Gene in Asymptomatic Women from Cajamarca, Peru

by Eliezer Bonifacio-Velez de Villa, Deysi Aguilar-Luis, Dayana Denegri-Hinostroza, Miguel Angel Aguilar-Luis, Wilmer Silva-Caso, Yordi Tarazona-Castro, Lorena Becerra-Goicochea, Ronald Aquino-Ortega, Angela Cornejo-Tapia and Juana del Valle-Mendoza

Viruses 2025, 17(11), 1420; https://doi.org/10.3390/v17111420 (registering DOI) - 25 Oct 2025

Abstract

Background: The HPV16 E2 gene plays a crucial role in viral replication and oncogene regulation. This study aimed to assess the genetic variability of the E2 gene and to identify immunogenic epitopes of the E2 protein. Methods: The E2 gene was amplified and [...] Read more.

Background: The HPV16 E2 gene plays a crucial role in viral replication and oncogene regulation. This study aimed to assess the genetic variability of the E2 gene and to identify immunogenic epitopes of the E2 protein. Methods: The E2 gene was amplified and sequenced. T-cell epitope prediction and evaluation were performed using IEDB, NetMHCpan v4.0, NetMHCIIpan v4.1, VaxiJen, ToxNet, and pLM4Alg. Results: Phylogenetic analysis of 47 E2 sequences demonstrated co-circulation of the D (n = 4) and A (n = 43) HPV16 lineages in Cajamarca. Twenty-eight Single Nucleotide Polymorphism (SNPs) were identified in E2, 21 of which were nonsynonymous. Seventeen variations were associated with positive Papanicolaou (Pap) test results. Epitope prediction identified 2 MHC class I and 27 MHC class II epitopes classified as potentially antigenic, non-toxic, and non-allergenic, with an overall global population coverage across both MHC classes of 99.78%. Conclusions: The A HPV16 lineage predominated among the women studied. The identified SNPs indicate substantial variability in the E2 gene and a relationship with endocervical lesions. In total, 29 E2-derived T-cell epitopes with immunogenic potential were identified. Full article

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

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17 pages, 3899 KB

Open AccessArticle

Genomic and Biological Characterization of a Novel Proteus mirabilis Phage with Anti-Biofilm Activity

by Yan Liang, Nana Li, Shenghui Wan, Yanfang Li, Yuwan Li and Yonggang Qu

Viruses 2025, 17(11), 1419; https://doi.org/10.3390/v17111419 (registering DOI) - 25 Oct 2025

Abstract

The emergence of multidrug-resistant (MDR) Proteus mirabilis poses a significant threat in porcine farming and public health, highlighting the need for alternative biocontrol agents. This study aimed to isolate and characterize a lytic bacteriophage with therapeutic potential against MDR P. mirabilis. Using [...] Read more.

The emergence of multidrug-resistant (MDR) Proteus mirabilis poses a significant threat in porcine farming and public health, highlighting the need for alternative biocontrol agents. This study aimed to isolate and characterize a lytic bacteriophage with therapeutic potential against MDR P. mirabilis. Using the clinical MDR P. mirabilis strain Pm 07 as host, a bacteriophage, vB_Pmc_P-07 (P-07), was successfully isolated from fecal and sewage samples via an enrichment protocol. Phage P-07 forms plaques surrounded by a distinct translucent “halo,” suggesting the production of depolymerase. It achieved high titers of up to 1.40 × 10⁸ PFU/mL and exhibited a narrow host range, high stability across a broad range of temperatures (40–60 °C) and pH (4–12), as well as considerable anti-biofilm activity. An optimal multiplicity of infection (MOI) of 0.001 was determined. Whole-genome sequencing revealed a linear double-stranded DNA genome of 58,582 bp with a GC content of 46.91%, encoding 63 open reading frames. Crucially, no virulence or antibiotic resistance genes were detected, supporting its safety profile. Phylogenetic analysis classified P-07 within the Casjensviridae family, closely related to phages PM87 and pPM01. These findings indicate that phage P-07 is a novel, safe, and effective lytic phage with strong potential as a biocontrol agent against biofilm-forming MDR P. mirabilis in swine. Full article

(This article belongs to the Section Bacterial Viruses)

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8 pages, 1274 KB

Open AccessBrief Report

Identification and Full-Genome Characterisation of Genomoviruses in Cassava Leaves Infected with Cassava Mosaic Disease

by Olabode Onile-ere, Oluwagboadurami John, Oreoluwa Sonowo, Pakyendou Estel Name, Ezechiel Bionimian Tibiri, Fidèle Tiendrébéogo, Justin Pita, Solomon Oranusi and Angela O. Eni

Viruses 2025, 17(11), 1418; https://doi.org/10.3390/v17111418 (registering DOI) - 25 Oct 2025

Abstract

This study identified and characterised three Genomoviruses during a circular DNA-enriched sequencing project aimed at assessing the evolution of Cassava mosaic begomoviruses in Nigeria. Using a combination of rolling circle amplification, Oxford Nanopore Sequencing and targeted amplicon sequencing, three full-length Genomovirus genomes were [...] Read more.

This study identified and characterised three Genomoviruses during a circular DNA-enriched sequencing project aimed at assessing the evolution of Cassava mosaic begomoviruses in Nigeria. Using a combination of rolling circle amplification, Oxford Nanopore Sequencing and targeted amplicon sequencing, three full-length Genomovirus genomes were recovered. The recovered genomes ranged from 2090 to 2188 nucleotides in length, contained two open reading frames (Rep and CP) in an ambisense orientation and shared between 84.81 and 95.37% nucleotide similarity with isolates in the NCBI GenBank repository. Motif analyses confirmed the presence of conserved rolling circle replication (RCR) and helicase motifs in all three isolates; however, one isolate lacked the RCR II motif. Phylogenetic inference using Rep and CP nucleotide sequences suggested that the isolates belonged to a divergent lineage within the Genomovirus family. These findings expand current knowledge of Genomovirus diversity and highlight the potential of cassava as a source for identifying novel CRESS-DNA viruses. Full article

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

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12 pages, 454 KB

Open AccessArticle

Efficacy and Safety of Cabotegravir–Rilpivirine in PLWH: A Real-World Study

by Giuseppe Nicolò Conti, Serena Spampinato, Andrea De Vito, Andrea Marino, Teresa Cirelli, Viviana Coco, Alessia Mirabile, Rossella Fontana del Vecchio, Antonina Franco, Arturo Montineri, Chiara Frasca, Chiara Gullotta, Michele Salvatore Paternò Raddusa, Ylenia Russotto, Sonia Sofia, Grazia Pantò, Claudia Calì, Roberto Bruno, Eugenia Pistarà, Nunziatina Villari, Carmelo Iacobello, Bruno Cacopardo, Benedetto Maurizio Celesia, Giovanni F. Pellicanò, Francesco P. Antonucci, Sergio Lo Caputo, Giordano Madeddu, Giuseppe Nunnari and Emmanuele Venanzi Rullo Show full author list Hide full author list

Viruses 2025, 17(11), 1417; https://doi.org/10.3390/v17111417 (registering DOI) - 24 Oct 2025

Abstract

Background: Long-acting injectable antiretroviral therapy (LA-ART) with cabotegravir and rilpivirine (CAB + RPV) has emerged as a promising alternative to daily oral regimens for people living with HIV (PLWH), particularly those facing adherence challenges. While clinical trials have demonstrated its efficacy, real-world evidence [...] Read more.

Background: Long-acting injectable antiretroviral therapy (LA-ART) with cabotegravir and rilpivirine (CAB + RPV) has emerged as a promising alternative to daily oral regimens for people living with HIV (PLWH), particularly those facing adherence challenges. While clinical trials have demonstrated its efficacy, real-world evidence remains limited. Methods: This retrospective, multicenter study evaluated the efficacy and safety of CAB + RPV in 160 virologically suppressed PLWH across eight Italian infectious disease units. Participants received intramuscular CAB (600 mg) and RPV (900 mg) every eight weeks without an oral lead-in phase. Clinical, immunological, and biochemical parameters were assessed at baseline and after 24 weeks. Results: At week 24, 96.25% of participants maintained virological suppression, and the proportion of individuals with target-not-detected viral load increased from 71% to 76%. Only one case of virological failure was observed. Significant immunological improvements included an increase in the CD4+/CD8+ ratio (p = 0.0038) and a reduction in CD8+ T-cell count (p = 0.0150). Biochemical analysis showed a decrease in serum creatinine (p < 0.0001) and an increase in HDL cholesterol (p = 0.0223). Treatment discontinuation occurred in 3.75% of participants, primarily due to adverse events or psychological factors. Conclusions: CAB + RPV demonstrated high efficacy and tolerability in a real-world setting, with favorable immunological and metabolic outcomes. These findings support its use as a viable therapeutic option for PLWH, especially those with adherence barriers. Further long-term studies are warranted to confirm these results across broader populations. Full article

(This article belongs to the Special Issue Advances in Research on HIV Drug Resistance and Other Determinants of Treatment Success: 3rd Edition)

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14 pages, 1184 KB

Open AccessArticle

IL-2 and IL-7 Contribution to Immune Response: Effects of Vaccination Against COVID-19 in Adults

by Dominika Siedlecka, Lena Bielawska, Aleksandra Ludziejewska, Aleksandra Baszczuk and Ewa Wysocka

Viruses 2025, 17(11), 1416; https://doi.org/10.3390/v17111416 - 24 Oct 2025

Abstract

Background: Cytokines participate in regulating the immune response of lymphocytes. Interleukin 2 (IL-2) is the main modulator of T lymphocyte development, homeostasis, and function, whereas interleukin 7 (IL-7) regulates the development and homeostasis of immune cells and plays a crucial role in the [...] Read more.

Background: Cytokines participate in regulating the immune response of lymphocytes. Interleukin 2 (IL-2) is the main modulator of T lymphocyte development, homeostasis, and function, whereas interleukin 7 (IL-7) regulates the development and homeostasis of immune cells and plays a crucial role in the maintenance of memory cells. The study aims to assess the blood IL-2 and IL-7 concentration in relation to the obtained cellular and humoral response in adults, six months after vaccination against COVID-19. Methods: We measured the concentration of IL-2 and IL-7 with ELISA, CoV2-IgG with an indirect chemiluminescence test, and the levels of IFN-γ with interferon gamma release assay (IGRA) post SARS-CoV-2 antigen stimulation. The study group (n = 76; F = 66, M = 10) was divided into 41 individuals, who did not report any chronic disorder (ChrD-Neg), and 35, who did (ChrD-Pos). Results: ChrD-Pos group presented higher IL-7 compared to ChrD-Neg (p = 0.023). Negative correlations were observed in the entire study population between IL-2 and age (R = −0.252, p = 0.028), as well as between IL-7 and IFN-γ (R = −0.295, p = 0.010). We found a positive correlation between IL-2 and IL-7 concentrations in the entire study population (R = 0.305, p = 0.007) and the ChrD-Pos group (R = 0.358, p = 0.035), and people with a positive IGRA result (R = 0.359, p = 0.005). Conclusions: The interaction of IL-2 and IL-7 may be important for achieving post-vaccination immunity, especially in adults with chronic diseases. Age is a factor modifying the post-vaccination response (decreased IL-2), whereas IL-7 may be an important factor in achieving a satisfactory post-vaccine response in people with chronic diseases. Full article

(This article belongs to the Special Issue SARS-CoV-2, COVID-19 Pathologies, Long COVID, and Anti-COVID Vaccines)

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10 pages, 667 KB

Open AccessArticle

Pre-Clade IIb Mpox Virus Exposure in Ghana: A Retrospective Serological Analysis

by Christopher Dorcoo, Grace Opoku Gyamfi, Franziska Kaiser, Elvis Suatey Lomotey, Jeffrey Gabriel Sumboh, Robert J. Fischer, Claude Kwe Yinda, Vincent J. Munster, Joseph H. K. Bonney and Irene Owusu Donkor

Viruses 2025, 17(11), 1415; https://doi.org/10.3390/v17111415 - 24 Oct 2025

Abstract

Monkeypox virus (MPXV), a zoonotic Orthopox virus endemic to West and Central Africa, causes mpox disease. Although Ghana had no confirmed human cases before 2022, the 2003 U.S. mpox outbreak was traced to rodents exported from Ghana, suggesting potential undetected exposure in the [...] Read more.

Monkeypox virus (MPXV), a zoonotic Orthopox virus endemic to West and Central Africa, causes mpox disease. Although Ghana had no confirmed human cases before 2022, the 2003 U.S. mpox outbreak was traced to rodents exported from Ghana, suggesting potential undetected exposure in the local population. This study assessed mpox exposure prior to the emergence of Clade IIb in humans. We tested 457 serum samples collected across 14 regions of Ghana using a commercial anti-MPXV IgG ELISA. These samples comprised 365 archived sera from 2021 SARS-CoV-2 surveillance and 92 sera from suspected mpox cases during the 2022 outbreak. Multivariable logistic regression was performed to examine associations between MPXV seropositivity and demographic factors, including age, sex, region, urban/rural status and inferred smallpox vaccination status. Overall MPXV seroprevalence was 6.6%. Participants from the Western Region had significantly increased odds of seropositivity (aOR = 6.70, 95% CI: 1.75–25.62, p = 0.005), whereas those from Greater Accra had decreased odds (aOR = 0.28, 95% CI: 0.09–0.90, p = 0.033). The findings suggest localized MPXV circulation or repeated zoonotic spillover may have occurred undetected, challenging the prevailing assumption that Ghana was unaffected by human mpox prior to 2022, underscoring the importance of strengthened surveillance and preparedness in Ghana. Full article

(This article belongs to the Special Issue Mpox (Monkeypox): From Neglected Tropical Disease to Emerging Global Pathogen)

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16 pages, 1674 KB

Open AccessArticle

Detection of West Nile Virus, Usutu Virus and Insect-Specific Bunyaviruses in Culex spp. Mosquitoes, Greece, 2024

by Katerina Tsioka, Konstantina Stoikou, Vasilis Antalis, Elissavet Charizani, Styliani Pappa, Sandra Gewehr, Stella Kalaitzopoulou, Spiros Mourelatos and Anna Papa

Viruses 2025, 17(11), 1414; https://doi.org/10.3390/v17111414 - 23 Oct 2025

Abstract

Greece is one of the countries in Europe most affected by West Nile virus (WNV), and since 2010, when the virus caused a large outbreak with 197 human neuroinvasive cases, outbreaks occur almost every year. Mosquito surveillance is an indirect sign of virus [...] Read more.

Greece is one of the countries in Europe most affected by West Nile virus (WNV), and since 2010, when the virus caused a large outbreak with 197 human neuroinvasive cases, outbreaks occur almost every year. Mosquito surveillance is an indirect sign of virus circulation; therefore, the purpose of the study was the molecular detection of WNV in 45,988 C. pipiens s.l. mosquitoes collected during 2024 in four Regions of Greece and the genetic characterization of the virus strains. WNV was detected in 41 of 1316 (3.12%) Culex spp. mosquito pools. Next-generation sequencing was applied to the WNV-positive samples that had a high viral load. All WNV sequences belong to Cluster B of the sub-lineage Europe WNV-2A presenting a temporal clustering. The WNV infection rates varied highly across the Regions, regional units and months, being higher in Thessaly and Central Macedonia Regions, especially in July and September. All mosquito pools were also tested for Usutu virus (USUV), and one pool was found positive, with sequence clustering into the EU-2 lineage. A subset of mosquitoes (737 pools) was tested for additional viruses, and bunya-like viruses were detected in 6 pools with sequences clustering into four distinct subclades. The prompt detection of pathogenic viruses is helpful for the design of control measures, while the detection of insect-specific viruses provides insights into viral diversity and evolution. Full article

(This article belongs to the Section Invertebrate Viruses)

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17 pages, 4229 KB

Open AccessArticle

Genetic and Statistical Study of Anelloviruses and Gyroviruses in Diarrheic Cats and Their Co-Occurrence Patterns

by Turhan Turan, Hakan Işıdan, Selda Duran-Yelken, Mustafa Ozan Atasoy, Remziye Özbek, Rania F. El Naggar and Mohammed A. Rohaim

Viruses 2025, 17(11), 1413; https://doi.org/10.3390/v17111413 - 23 Oct 2025

Abstract

Members of the Anelloviridae family are increasingly being recognized for their role in veterinary and public health, with domestic cats identified as potential carriers of anelloviruses and gyroviruses. This study aimed to investigate the prevalence and genetic characteristics of these viruses in diarrheic [...] Read more.

Members of the Anelloviridae family are increasingly being recognized for their role in veterinary and public health, with domestic cats identified as potential carriers of anelloviruses and gyroviruses. This study aimed to investigate the prevalence and genetic characteristics of these viruses in diarrheic cats from Sivas, Türkiye. A total of 91 fecal samples were analysed, initially for feline panleukopenia virus using conventional PCR, followed by screening with our Anelloviridae panel. The results revealed that 19 (20.9%) samples were positive for TTFeV1, 32 (35.2%) for CAV, 67 (73.6%) for Avian gyrovirus 2, four (4.4%) for Gyrovirus 3, and three (3.3%) for Gyrovirus 4. Statistical analyses revealed frequent co-infections among parvoviruses, anelloviruses, and gyroviruses, with a significant association between Gyrovirus chickenanemia (CAV) and Gyrovirus galga1 (AvGyV2). Notably, Gyrovirus 4 (Gyrovirus homsa3) was identified in feline stool for the first time. Phylogenetic and genomic analyses, based on partial TATA box-ORF2 sequences for anelloviruses and VP1 sequences for gyroviruses, provided further insights into viral diversity. These findings expand current knowledge of anellovirus and gyrovirus circulation in feline populations, underscoring the importance of continued surveillance for feline and public health. Full article

(This article belongs to the Section Animal Viruses)

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14 pages, 1992 KB

Open AccessArticle

LAIV Mutations Selectively Alter Influenza Viral RNA Polymerase Function, Favoring Transcription over Genome Synthesis

by Justin R. Leach, Adrian Oo, Aitor Nogales, Sebastian I. Bosch, Luis Martínez-Sobrido, Changyong Feng, Baek Kim and Stephen Dewhurst

Viruses 2025, 17(11), 1412; https://doi.org/10.3390/v17111412 - 23 Oct 2025

Abstract

Influenza viruses cause mild to severe lower respiratory infections, sometimes resulting in hospitalization and death. Vaccination remains the primary prophylactic strategy. Live attenuated influenza vaccines (LAIVs) efficiently induce antiviral immune responses and contain temperature-sensitive and cold-adapted mutations that render them safe. These mutations [...] Read more.

Influenza viruses cause mild to severe lower respiratory infections, sometimes resulting in hospitalization and death. Vaccination remains the primary prophylactic strategy. Live attenuated influenza vaccines (LAIVs) efficiently induce antiviral immune responses and contain temperature-sensitive and cold-adapted mutations that render them safe. These mutations are principally located in the PB1 and PB2 subunits of the viral RNA polymerase, but the mechanism by which they attenuate the virus is unclear. We introduced the PB1 and PB2 mutations from two LAIV backbones, A/Ann Arbor/6/1960 H2N2 (AA) and A/Leningrad/134/17/1957 H2N2 (Len), into the model influenza strain A/Puerto Rico/8/1934 H1N1 (PR8). In contrast to the wild-type (WT) PR8 polymerase, the two “PR8-LAIV” polymerase complexes demonstrated maximal activity at cold temperatures (30–32 °C) and greatly reduced activity at elevated temperatures (>37 °C). To further understand the impact of the LAIV mutations, we infected MDCK cells with WT and mutated PR8 viruses that contain the Len and AA LAIV mutations in PB1 and PB2. The PR8-LAIV mutant viruses exhibited a selective, temperature-dependent defect in the replicase activity of the viral RNA polymerase relative to WT PR8, while also demonstrating a temperature-dependent enhancement in the transcriptional activity of the enzyme. In addition, the PR8-LAIV mutant viruses produced similar levels of viral proteins to WT PR8 at 37 °C, but greatly (2–3 log₁₀) reduced levels of infectious viral progeny. Collectively, these data show that LAIV mutations selectively alter influenza viral RNA polymerase function, favoring transcription over genome synthesis at 37 °C, thereby preserving viral antigen production while also contributing to viral attenuation. Full article

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

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13 pages, 2124 KB

Open AccessArticle

First Detection of an Alphaherpesvirus Gene in Humpback Whale Blow Samples Collected Noninvasively Using Unmanned Aerial Vehicles

by Wataru Sekine, Junna Kawasaki, Kosuke Ohira, Kaixin Li, Misa Katayama, Ayano Ichikawa, Yuta Wakabayashi, Akiko Takenaka-Uema, Shin Murakami and Taisuke Horimoto

Viruses 2025, 17(11), 1411; https://doi.org/10.3390/v17111411 - 23 Oct 2025

Abstract

Viral infections have a significant impact on wildlife health, population dynamics, and ecosystem stability. Studies of cetaceans—key species in marine ecosystems—are challenging for viral infection research, owing to difficulties in collecting conventional biological samples. In this study, unmanned aerial vehicles (UAVs) were used [...] Read more.

Viral infections have a significant impact on wildlife health, population dynamics, and ecosystem stability. Studies of cetaceans—key species in marine ecosystems—are challenging for viral infection research, owing to difficulties in collecting conventional biological samples. In this study, unmanned aerial vehicles (UAVs) were used in 2024 to noninvasively sample exhaled breath condensates (blows) from five groups of humpback whales (Megaptera novaeangliae) along the coastline of an island in the Pacific Ocean south of Japan. Comprehensive virome analysis revealed viral sequences related to 39 known virus species across 18 families, including nine that infect mammals. Notably, partial sequences of the UL20 gene similar to an alphaherpesvirus previously identified in beluga whales were detected for the first time in the blows from these humpback whales. Our study demonstrates that UAV-based blow sampling is an effective tool for virological surveillance in cetaceans. Moreover, our findings aid in advancing our understanding of the diversity of viruses in marine mammals and supporting the development of noninvasive monitoring strategies that are critical for ensuring the conservation and health of these creatures. Full article

(This article belongs to the Section Animal Viruses)

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16 pages, 4434 KB

Open AccessArticle

Two Decades Later: Long-Term Multisystem Sequelae and Subclinical Organ Dysfunction in Sudan Ebola Virus (SUDV) Survivors of the 2000 Outbreak

by Raymond Ernest Kaweesa, Joseph Ssebwana Katende, Geoffrey Odoch, Annie Daphine Ntabadde, Raymond Reuel Wayesu, Deborah Mukisa, Peter Ejou, on behalf of the FiloStudy Team, Pontiano Kaleebu and Jennifer Serwanga

Viruses 2025, 17(11), 1410; https://doi.org/10.3390/v17111410 - 23 Oct 2025

Abstract

Background: Despite repeated re-emergence of Sudan ebolavirus (SUDV), its long-term human toll remains under-characterised. We assessed multisystem clinical, biochemical, and psychosocial outcomes ~25 years after the 2000 Gulu outbreak. Methods: We conducted a cross-sectional evaluation of 45 survivors of laboratory-confirmed SUDV [...] Read more.

Background: Despite repeated re-emergence of Sudan ebolavirus (SUDV), its long-term human toll remains under-characterised. We assessed multisystem clinical, biochemical, and psychosocial outcomes ~25 years after the 2000 Gulu outbreak. Methods: We conducted a cross-sectional evaluation of 45 survivors of laboratory-confirmed SUDV and 30 age- and gender-matched community controls from the same region. Symptoms were assessed as current at the study visit using a structured checklist; for each symptom present, we recorded severity and duration from onset to the visit date. Standardised clinical examinations, haematological and biochemical assessments, anxiety and depression screening, and structured interviews on social support and stigma were performed. Group comparisons were assessed with Wilcoxon rank-sum and χ²/Fisher’s exact tests; correlations were assessed with Spearman’s ρ. Findings: Core physiological indices (vital signs, BMI, blood pressure, and body temperature) and mental health were comparable between survivors and controls. Nevertheless, survivors reported ongoing symptoms, including joint pain and visual impairment each in 36% (16/45), fatigue in 18% (8/45), and neurological symptoms in 13% (6/45). Subclinical laboratory deviations centred on hepatic and platelet biology: elevated total bilirubin occurred in 14% of survivors versus 6.7% of controls; thrombocytopenia or platelet morphological abnormalities in 12% versus 3.3%; haemoglobin abnormalities in 6% versus 0%. Among survivors, albumin and mean platelet volume declined with age (both p ≤ 0.03). Psychological morbidity was low (normal anxiety 82% (37/45; and normal depression 80% (36/45). Yet a social paradox emerged, despite universal post-outbreak support, 98% (44/45) described enduring stigma. To minimise differential recall bias, symptom inventories were not collected from controls; consequently, between-group comparisons for symptom prevalence were not performed, and symptom inferences are restricted to survivors and framed descriptively. Interpretation: A quarter-century after infection, SUDV survivors show preserved systemic physiology but carry chronic musculoskeletal, sensory, and neurological sequelae, alongside a discrete subclinical profile implicating hepatic function and platelet biology. Psychological resilience coexists with near-universal, persistent stigma, indicating that material support did not achieve full psychosocial reintegration. Given the lack of virological and deep immune profiling, proposed pathogenetic mechanisms, such as antigen persistence or immune-mediated injury, remain speculative and hypotheses-generating only. These findings argue for survivor-centred long-term care, embedded with epidemic preparedness frameworks that integrate musculoskeletal rehabilitation, ophthalmic and neurological services with comprehensive mental health care, and sustained anti-stigma community engagement. This dissociation, including short-lived support alongside enduring stigma, indicates that humanitarian relief alone does not secure durable psychosocial reintegration and should be complemented by long-horizon, survivor-centred services and community engagement. Funding: This study was supported by the Coalition for Epidemic Preparedness Innovations (CEPI) under the Universal Protocol for Standardising Assays and Advancing Vaccine Immunogenicity Assessments for Emerging and Re-emerging Viral Threats, implemented through the Uganda Virus Research Institute (UVRI) as part of CEPI’s Centralised Laboratory Network (CLN). Full article

(This article belongs to the Special Issue Advancing Understanding of Filoviruses)

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17 pages, 987 KB

Open AccessReview

Chromatin Regulation of HSV Gene Transcription

by Yuxuan Zheng, Juncheng Zhang and Dongli Pan

Viruses 2025, 17(11), 1409; https://doi.org/10.3390/v17111409 - 23 Oct 2025

Abstract

Herpes simplex virus (HSV) has a complicated life cycle including stages of primary lytic infection, latent infection, and reactivation. Although the HSV genomic DNA within the viral capsid is devoid of histones, it rapidly associates with histones upon entering the nucleus to form [...] Read more.

Herpes simplex virus (HSV) has a complicated life cycle including stages of primary lytic infection, latent infection, and reactivation. Although the HSV genomic DNA within the viral capsid is devoid of histones, it rapidly associates with histones upon entering the nucleus to form viral chromatin. This chromatin is not integrated into the host chromosome and displays features distinct from the cellular chromatin. The composition, structure, and post-translational modifications of the HSV chromatin change over the course of infection due to the actions of numerous viral and host molecules. In turn, the chromatin states influence the transcription profiles of viral genes at all stages of the viral life cycle and may dictate the outcomes of the lytic-latent balance. These mechanisms may be exploited to develop new antiviral therapeutics. This review summarizes current knowledge about the formation, regulation, and functions of the HSV chromatin and discusses the questions remaining to be answered. Full article

(This article belongs to the Special Issue Herpesvirus Transcriptional Control)

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19 pages, 1366 KB

Open AccessArticle

Characterization of Chemically-Induced Endogenous Retroviral Particles in the CHO-K1 Cell Line

by Nicholas B. Mattson, Trent J. Bosma, Yamei Gao, Sandra M. Fuentes, Pei-Ju Chin and Arifa S. Khan

Viruses 2025, 17(11), 1408; https://doi.org/10.3390/v17111408 - 23 Oct 2025

Abstract

The Chinese hamster ovary K1 cell line (CHO-K1) constitutively produces retroviral-like particles (RVLPs) containing reverse transcriptase (RT) activity, which, thus far, have not been shown to be infectious. Since infectious retroviruses have been reported in other rodent species, this study was undertaken to [...] Read more.

The Chinese hamster ovary K1 cell line (CHO-K1) constitutively produces retroviral-like particles (RVLPs) containing reverse transcriptase (RT) activity, which, thus far, have not been shown to be infectious. Since infectious retroviruses have been reported in other rodent species, this study was undertaken to investigate the presence of latent, infectious, endogenous retroviruses (ERVs) in CHO-K1 cells by using chemical induction assays and detection of activated virus using the highly sensitive, product-enhanced RT (PERT) assay, with subsequent infectivity analysis in cell lines of different species, including human. The results demonstrated activation of A-type and C-type retroviral particles based on transmission electron microscopy and increased production of cell-free RT-particles after treatment of the cells with 5-iodo-2′-deoxyuridine and 5-azacytidine, which was greater with dual treatment than with each inducer alone. Induction of A- and C-type particles was confirmed in dual-drug-treated CHO-K1 cells by long-read high-throughput sequence (HTS) analysis. Infectivity studies performed by inoculating human A549, HEK-293, and MRC-5 cells; African green monkey Vero cells; Mus dunni cells; and CHO-K1 cells with supernatant containing RT-particles from dual-treated CHO-K1 cells indicated the absence of a replicating retrovirus in supernatant from extended cell culture using the PERT assay. Furthermore, short-read HTS analysis did not show evidence of integration of retroviral sequences in inoculated A549 and 293 cells. The overall results showed no evidence for latent, infectious, endogenous RVLPs in CHO-K1 cells. Full article

(This article belongs to the Special Issue The Diverse Regulation of Transcription in Endogenous Retroviruses)

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15 pages, 1092 KB

Open AccessArticle

Burden and Characteristics of RSV-Associated Hospitalizations in Switzerland: A Nationwide Analysis from 2017 to 2023

by Elisa D. Bally-von Passavant, Neetha Joseph, Nike Julia Kräutler, Daphne McCarthy-Pontier, Giorgia Lüthi-Corridori, Fabienne Jaun, Jörg D. Leuppi and Maria Boesing

Viruses 2025, 17(11), 1407; https://doi.org/10.3390/v17111407 - 23 Oct 2025

Abstract

Respiratory syncytial virus (RSV) is a major cause of respiratory illness, particularly in children, yet its burden in adults—especially in older adults—remains under-recognized. We analyzed RSV-related hospitalizations in Switzerland from 2017 to 2023 using national data from the Federal Statistical Office, including cases [...] Read more.

Respiratory syncytial virus (RSV) is a major cause of respiratory illness, particularly in children, yet its burden in adults—especially in older adults—remains under-recognized. We analyzed RSV-related hospitalizations in Switzerland from 2017 to 2023 using national data from the Federal Statistical Office, including cases with RSV coded as either a primary or secondary diagnosis. Over 35,000 RSV-related hospitalizations were recorded. The highest incidence occurred in children under 10 years (390 per 100,000/year), with a second peak in adults ≥ 80 years (151 per 100,000/year). Older adults (≥60 years) accounted for more than 9700 hospitalizations overall, with an average of over 16,600 total hospital days per year. Average length of stay (LOS) was shortest in young children (4.6 days) and highest in adolescents (13.9 days), while in adults, it increased from 6.8 days (age 20–29) to 12.3 (age ≥ 80). Mechanical ventilation rates peaked at 12.6% in 60–69 year olds, and in-hospital mortality at 7.1% in those ≥80 years. In adults, RSV was more often recorded as a secondary diagnosis and commonly associated with chronic comorbidities, including chronic obstructive pulmonary disease, heart failure, kidney disease, and diabetes. Frailty-related diagnoses—such as cognitive or motor impairment, delirium, and need for nursing care—were also frequent. These findings highlight the importance of improved adult RSV surveillance and targeted prevention strategies in high-risk populations. Full article

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

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34 pages, 4931 KB

Open AccessArticle

Potential Vaccine or Antimicrobial Reagents: Simple Systems for Producing Lambda Display Particles (LDP) and Sheathed Lambda DNA Vaccine Particles (LDNAP)

by Sidney Hayes

Viruses 2025, 17(11), 1406; https://doi.org/10.3390/v17111406 - 22 Oct 2025

Abstract

The focus of this study was to explore phage display systems employing bacteriophage lambda (λ) gene fusions to its capsid decoration protein gpD as reagent tools for tackling disease. The biological activity of gpD-fusions was examined by testing for the retained antimicrobial toxicity [...] Read more.

The focus of this study was to explore phage display systems employing bacteriophage lambda (λ) gene fusions to its capsid decoration protein gpD as reagent tools for tackling disease. The biological activity of gpD-fusions was examined by testing for the retained antimicrobial toxicity of cathelicidins or defensins fused to gpD. Our previous finding that only COOH fusions of either cathelicidins or defensins to gpD were toxigenic was expanded to show that only the reduced form of fused defensin antimicrobial polypeptides was found to be toxigenic. Compared in review are gene-fusion lytic display systems (where the fusion-display gene is integrated within the viral genome) with a surrogate system, employed herein, that exogenously provides the fusion-display protein for addition to phage capsid. It is easily possible to produce fully coated lambda display particles (LDP) serving as single epitope vaccines (SEV), or antimicrobials, or to produce partially coated LDP without any complex bacteriophage genetic engineering, making the system available to all. The potential to build vaccine vector phage particles (LDNAP) comprising essentially sheathed DNA vaccines encapsulated within an environmentally protective capsid is described. LDNAP are produced by introducing a cassette into the phage genome either by phage–plasmid recombination or cloning. The cassette carries a high-level eukaryotic expression promoter driving transcription of the vaccine candidate gene and is devoid of plasmid resistance elements. Full article

(This article belongs to the Section Bacterial Viruses)

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27 pages, 951 KB

Open AccessReview

Mechanisms of Cell–Cell Fusion in SARS-CoV-2: An Evolving Strategy for Transmission and Immune Evasion

by Kate Chander Chiang, Cheng En Nicole Chiu, Mazharul Altaf, Mark Tsz Kin Cheng and Ravindra K. Gupta

Viruses 2025, 17(11), 1405; https://doi.org/10.3390/v17111405 - 22 Oct 2025

Abstract

Early studies on the evolution of SARS-CoV-2 revealed mutations that favored host transmission of the virus and more efficient viral entry. However, cell-free virus spread is vulnerable to host-neutralizing antibodies. As population immunity developed, mutations that confer escape from neutralization were selected. Notably, [...] Read more.

Early studies on the evolution of SARS-CoV-2 revealed mutations that favored host transmission of the virus and more efficient viral entry. However, cell-free virus spread is vulnerable to host-neutralizing antibodies. As population immunity developed, mutations that confer escape from neutralization were selected. Notably, cell syncytia formation wherein an infected cell fuses with a noninfected cell is a more efficient route of transmission that bypasses humoral immunity. Cell syncytia formation has been implicated in the pathogenicity of SARS-CoV-2 infection whilst compromising host transmission due to impaired whole virion release. Therefore, understanding the mechanisms of virus-mediated cell–cell fusion will aid in identifying and targeting more pathogenic strains of SARS-CoV-2. Whilst the general kinetics of cell–cell fusion have been known for decades, the specific mechanisms by which SARS-CoV-2 induces fusion are beginning to be elucidated. This is partially due to emergence of more reliable, high throughput methods of quantifying and comparing fusion efficiency in experimental models. Moreover, the ongoing inflammatory response and emerging health burden of long COVID may point to cell–cell fusion in the pathogenesis. In this review, we synthesize current understanding of SARS-CoV-2-mediated cell–cell fusion and its consequences on immune escape, viral persistence, and the innate immune response. Full article

(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))

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28 pages, 2421 KB

Open AccessReview

Roles of RNA Structures in the Genome Translation of (+) Sense RNA Viruses

by Guangming Lu, Bethel G. Beyene, Joshua Miguele Camacho and Deepak Koirala

Viruses 2025, 17(11), 1404; https://doi.org/10.3390/v17111404 - 22 Oct 2025

Abstract

Positive (+) sense RNA viruses include many important pathogens that exploit noncanonical translation mechanisms to express their genomes within the host cells. Unlike DNA or negative (−) sense RNA viruses, (+) sense RNA viruses can directly function as mRNAs, even though they lack [...] Read more.

Positive (+) sense RNA viruses include many important pathogens that exploit noncanonical translation mechanisms to express their genomes within the host cells. Unlike DNA or negative (−) sense RNA viruses, (+) sense RNA viruses can directly function as mRNAs, even though they lack typical features of host mRNAs, such as the 5′ cap structure required for canonical translation initiation. Instead, they exploit structured RNA elements to recruit host translational machinery without the 5′ cap, bypassing the canonical translation initiation mechanism. Prominent examples include internal ribosome entry sites (IRESs) and 3′ cap-independent translation enhancers (3′ CITEs). These RNA modules facilitate translation initiation by recruiting the ribosomal subunits, either directly or through initiation factors, and mediating long-range RNA-RNA interactions. Other regulatory motifs, such as frameshifting signals, allow the ribosome to shift reading frames to regulate protein output. All these RNA elements function through RNA-protein interactions and often utilize host and virus-encoded proteins to hijack the host’s translational apparatus. Over the past several years, various structural biology approaches, including biochemical and enzymatic probing, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryogenic electron microscopy (cryo-EM), have revealed the unique structural roles of these viral RNA elements and their protein complexes. Although a few structures of IRES and CITE domains have been solved through these methods, the structures of these RNA elements and their structure-function relationship have remained largely unknown. This review discusses the current understanding of translation-related RNA structures in (+) sense RNA viruses, the critical RNA-protein interactions they mediate, and various structural biology approaches used to study them. Since the genome of these viruses serves as a template for two mutually exclusive virological processes, namely genome translation and replication, the review also discusses how viruses can utilize RNA structure-based strategies to regulate the switch between genome translation and replication, highlighting future directions for exploring these fundamental virological processes to develop antiviral therapeutics able to combat diseases caused by these pathogens. Full article

(This article belongs to the Special Issue Viral Strategies and Cellular Countermeasures That Regulate mRNA Access to the Translation Apparatus: 2nd Edition)

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11 pages, 210 KB

Open AccessArticle

Clinical Characteristics of Paediatric RSV, Influenza, and SARS-CoV-2 Infections: Insights from Three Consecutive Seasons

by Weronika Balas, Katarzyna Balas, Maria Gancarczyk, Joanna Kośka, Martyna Radelczuk, Agata Rosińska and Adam Sybilski

Viruses 2025, 17(11), 1403; https://doi.org/10.3390/v17111403 - 22 Oct 2025

Abstract

Background: The purpose of this study was to retrospectively analyse the clinical presentation of RSV, Influenza, and SARS-CoV-2 infections in children across three consecutive seasons (2022/2023; 2023/2024; and 2024/2025). Methods: Of the 321 hospitalised patients, 129 (36%) tested positive for RSV, 110 (38%) [...] Read more.

Background: The purpose of this study was to retrospectively analyse the clinical presentation of RSV, Influenza, and SARS-CoV-2 infections in children across three consecutive seasons (2022/2023; 2023/2024; and 2024/2025). Methods: Of the 321 hospitalised patients, 129 (36%) tested positive for RSV, 110 (38%) for Influenza, and 82 (26%) for SARS-CoV-2. Children were aged ≤ 17 years (median: 15 months). The data were statistically analysed using the χ² test, multinomial multivariable logistic regression, OR (odds ratio), and 95% CI (confidence interval). Results: Significant independent predictors of RSV infection were auscultatory abnormalities (OR: 15.9 [1.49–169]) and hospital admission ≥ 4 days after symptom onset (OR: 32.5 [1.19–907]). Among RSV-positive patients, compared with those aged < 6 months, those aged 7–24 months were more likely to present with higher CRP levels (OR 1.06 [1.003–1.13]), reduced appetite (OR 6.7 [1.62–27.67]), and longer duration of fever (OR 7.22 [1.47–35.59]), while in children > 24 months, only a longer duration of fever remained significant (OR 16.82 [2.14–162.4]). In Influenza, reduced appetite was the only characteristic feature in the 7–24-month age group (OR 13.55 [1.79–102.81]). In COVID-19, children aged 7–24 months more frequently had higher CRP levels (OR 1.108 [1.001–1.226]) and chronic diseases (OR 7.59 [1.115–51.64]), whereas in those >24 months, only CRP was significant (OR 1.16 [1.047–1.31]). Conclusions: RSV was associated with severe respiratory manifestations and later hospital admission, whereas Influenza and SARS-CoV-2 were characterised by milder courses with predominant upper respiratory symptoms. Observed age- and virus-specific patterns highlight the importance of continued surveillance and comparative research on major respiratory viruses in children. Full article

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

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