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Viruses, Volume 18, Issue 8 (August 2026) – 118 articles

Cover Story (view full-size image): To determine the timing of HIV-1 protease (PR) activation and the rate of substrate cleavage, we visualized PR-mediated cleavage of a Vpr protein-based FRET substrate in single virions assembling on the plasma membrane. Substrate cleavage was manifested as a reduction in FRET signal in a small fraction of nascent viral particles, whereas most virions released from cells contained processed FRET substrate. This finding suggests that PR activation may be delayed or suppressed in virions assembled at the ventral membrane. Cleavage of the FRET substrate was completed within a few minutes, and the rate and efficiency of cleavage were modulated by PR cleavage sequences derived from domains of Gag and Gag-Pol polyproteins, providing insights into the tightly orchestrated order of Gag and Gag-Pol cleavage leading to HIV-1 maturation. View this paper
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17 pages, 988 KB  
Review
Chikungunya Virus: What a Transfusion Service Needs to Know
by Daniele Focosi, Giuseppe Sberna, Francesca Colavita, Fabrizio Maggi and Massimo Franchini
Viruses 2026, 18(8), 924; https://doi.org/10.3390/v18080924 - 21 Aug 2026
Viewed by 535
Abstract
Togaviridae represents a candidate family for emerging public health emergencies of international concern. Among them, chikungunya virus (CHKIV) has caused recurrent epidemics in the temperate zone of most continents and represents a threat to the safety of blood supplies. The global expansion of [...] Read more.
Togaviridae represents a candidate family for emerging public health emergencies of international concern. Among them, chikungunya virus (CHKIV) has caused recurrent epidemics in the temperate zone of most continents and represents a threat to the safety of blood supplies. The global expansion of vectors (i.e., Aedes mosquitoes) and increasing international travel have contributed to the growing epidemiological importance of this pathogen. In fact, CHIKV has been reported in more than 110 countries across the following four continents: Africa, Asia, Americas, and Europe. Consequently, public health authorities have emphasized the importance of surveillance, vector control programs, outbreak preparedness, and blood safety measures. The aim of this review was to summarize the current knowledge of CHIKV considering virology, molecular epidemiology, transmission mechanisms, clinical features, preventive strategies, and blood safety implications, with particular attention to issues relevant to transfusion services. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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13 pages, 1461 KB  
Article
Wastewater-Based Genomic Surveillance of SARS-CoV-2 Antiviral Resistance Determinants in Ontario: Towards a Scalable Framework for Population-Level Antiviral Resistance Monitoring
by Opeyemi U. Lawal, Valeria R. Parreira, Alyssa K. Overton, Jennifer J. Knapp, Richard Gibson, Eric J. Arts, Linkang Zhang, Fozia Rizvi, Melinda Precious, Trevor C. Charles and Lawrence Goodridge
Viruses 2026, 18(8), 923; https://doi.org/10.3390/v18080923 - 21 Aug 2026
Viewed by 386
Abstract
Background: Wastewater surveillance has emerged as an effective tool for population-level pathogen monitoring. Its application to mutations associated with resistance to antivirals remains comparatively underdeveloped. We assessed the wastewater epidemiology framework using SARS-CoV-2 as a model pathogen to evaluate spatial, temporal, and therapeutic [...] Read more.
Background: Wastewater surveillance has emerged as an effective tool for population-level pathogen monitoring. Its application to mutations associated with resistance to antivirals remains comparatively underdeveloped. We assessed the wastewater epidemiology framework using SARS-CoV-2 as a model pathogen to evaluate spatial, temporal, and therapeutic class-specific resistance dynamics. Methods: We analyzed about 10,000 SARS-CoV-2-positive wastewater samples from six Ontario public health regions collected between October 2021 and July 2024. Fifty-five mutations were screened, comprising therapeutic resistance-associated mutations and a biologically distinct group of immune-evasion mutations. Mutations detected in ≥10 samples at ≥1% frequency were retained for spatiotemporal analysis using LOESS smoothing and Kruskal–Wallis testing. Results: Twelve mutations met the inclusion thresholds. S:E340D, associated with reduced susceptibility to sotrovimab was geographically widespread but transient and low-frequency. Five remdesivir-associated polymerase mutations were sporadic with sharp localized peaks, including two mutations exceeding 99% frequency in isolated catchments. Three nirmatrelvir-associated protease mutations were detected, with ORF1a:Q3452K showing significant regional variation. FLiRT and FLuQE immune-evasion mutations were most persistent and abundant. LOESS smoothing showed distinct temporal patterns among mutations, while Kruskal–Wallis testing identified significant regional variation for ORF1a:Q3452K and the three immune-evasion mutations. Conclusions: These findings demonstrate that wastewater surveillance enables population-scale monitoring of antiviral resistance and immune escape-associated mutations and offers a scalable model for broader surveillance. Full article
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21 pages, 1273 KB  
Review
Determinants of Senecavirus A Pathogenesis: From Viral Genome to ANTXR1, Immunity, and Programmed Cell Death
by Xiaozhan Zhang, Siyu Wang, Ping Lu, Runfan Zeng, Guoyang Li, Changyao Li, Yiting Li, Xiuqing Li, Jinxing Song, Pandeng Zhao, Yunze Guo, Chuanzhou Bian, Decheng Yang and Xiaoyang Yan
Viruses 2026, 18(8), 922; https://doi.org/10.3390/v18080922 - 21 Aug 2026
Viewed by 397
Abstract
Senecavirus A (SVA), an emerging causative agent of porcine vesicular disease, belongs to the genus Senecavirus of the family Picornaviridae. The virus has been circulating in pig herds in the USA dating back to 1988, evolved into clinically significant pathogenic SVA variants [...] Read more.
Senecavirus A (SVA), an emerging causative agent of porcine vesicular disease, belongs to the genus Senecavirus of the family Picornaviridae. The virus has been circulating in pig herds in the USA dating back to 1988, evolved into clinically significant pathogenic SVA variants causing a pandemic in the USA and Canada since 2014, and thereafter gradually spread to the Americas and Asia. To date, most studies have illustrated the infection dynamics, epidemiology, diagnostic methods, and vaccine development, yet the molecular pathogenesis of SVA remains incompletely characterized. As a novel picornavirus capable of establishing persistent subclinical infections, SVA has been detected in tissues such as tonsils and testicles for up to 156 days post-infection, posing a substantial challenge to swine health and production systems. In parallel, SVA has gained attention as an oncolytic virotherapy candidate for neuroendocrine tumors due to its tumor-selective tropism. Therefore, elucidating the mechanisms underlying SVA pathogenesis will not only support the development of effective countermeasures for swine but also inform the engineering of recombinant variants with enhanced therapeutic potential for human oncology. This review comprehensively summarizes the current knowledge on viral and host determinants of SVA pathogenesis, from the viral genome, evolution, and recombination to ANTXR1 host immunity, and programmed cell death, and presents future research directions, aiming to identify key knowledge gaps to guide future studies on SVA. Full article
(This article belongs to the Special Issue Novel Insights into Porcine Viral Diseases: Recombinant Strains and Immune Responses)
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17 pages, 1082 KB  
Review
Trends in Tick-Borne Virus Ecology: Vector Incrimination, Focal Distribution, and Reservoir Associations
by Rachel E. Lange, Alan P. Dupuis II and Alexander T. Ciota
Viruses 2026, 18(8), 921; https://doi.org/10.3390/v18080921 - 21 Aug 2026
Viewed by 542
Abstract
Ticks are prominent hosts for many viruses that are pathogenic to humans on almost every continent. Despite the documented historical association of ticks with viral disease in humans, clinical case reports are low, likely due to under-recognition of these pathogens. A key feature [...] Read more.
Ticks are prominent hosts for many viruses that are pathogenic to humans on almost every continent. Despite the documented historical association of ticks with viral disease in humans, clinical case reports are low, likely due to under-recognition of these pathogens. A key feature of understanding tick-borne virus transmission to humans lies in the natural invertebrate and vertebrate hosts supporting ecological maintenance. As humans are often infected as incidental hosts during the tick–virus life cycle, determining relevant ticks and mammals involved in maintenance can inform prevention strategies, surveillance priorities, and diagnostic assay development. This review aims to cover common trends in tick-borne virus ecology, including the wide breadth of implicated tick species, an unclear role for definitive vertebrate reservoirs, and the focal distributions of these viruses closely linked to these host ecological features. Here we also provide examples of prominent tick-borne viruses causing human disease between the Old (Africa, Asia, Europe) and New (Americas) Worlds, highlighting parallels in initial discoveries, vectors, and vertebrates including tick-borne encephalitis, Crimean–Congo hemorrhagic fever, severe fever with thrombocytopenia syndrome, Colorado Tick fever, and Powassan, Heartland, and Bourbon viruses. Full article
(This article belongs to the Special Issue Tick-Borne Viruses 2026)
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15 pages, 1073 KB  
Review
The L-A dsRNA Virus and Its Satellites: Totiviruses and Killers in Saccharomyces cerevisiae
by Reed B. Wickner and Herman K. Edskes
Viruses 2026, 18(8), 920; https://doi.org/10.3390/v18080920 - 21 Aug 2026
Viewed by 493
Abstract
A secreted protein toxin encoded by a satellite dsRNA-enabled dissection of the genetic control of replication and expression of a single-segment dsRNA virus, the first Totivirus, L-A. Among the then-novel findings were i. “head-full replication”, ii. a supposedly forbidden “T = 2” capsid [...] Read more.
A secreted protein toxin encoded by a satellite dsRNA-enabled dissection of the genetic control of replication and expression of a single-segment dsRNA virus, the first Totivirus, L-A. Among the then-novel findings were i. “head-full replication”, ii. a supposedly forbidden “T = 2” capsid symmetry based on an asymmetric dimer, iii. a host N-acetyltransferase whose modification of the coat protein is necessary for packaging, iv. Kex1 and Kex2 pro-toxin peptidases leading to discovery of the pre-pro-insulin processing enzymes, and v. specific viral (+) strand sites/structures needed for RNA packaging and (-) strand synthesis. L-A viral (+) strands made in the particle are extruded to the cytoplasm. Those destined for translation are 5′ 7meGMP-capped by a coat protein activity that steals the cap from cellular mRNAs. (+) strands destined for encapsidation in new coats are not capped. Three host-encoded anti-viral systems were found, one based on blocking translation of the viral non-polyA mRNAs (Ski2,3,8 complex), another a 5′->3′ exoribonuclease specific for uncapped molecules (such as the viral (+) strands)(Ski1/Xrn1), and the third a mitochondrial nuclease released in cells undergoing meiosis/sporulation (Nuc1). All of these systems protect cells from virus-induced pathology and have clear animal homologs. The 3′ polyA of yeast mRNAs is dispensable for translation in ski2Δ slh1Δ cells, and such cells are healthy unless the L-A and M dsRNAs are present, suggesting that this polyA is primarily a device allowing cells to distinguish viral and cellular mRNAs. We suggest that the ribosome-associated Ski2,3,8 proteins block 60S subunit joining on polyA− mRNAs. Recent evidence of roles for other cellular components controlling viral expression and replication suggests that yeast viruses will continue to be a fertile area for study of viral pathogenesis and host anti-viral systems. Full article
(This article belongs to the Special Issue Discovery, Classification, and Early Research on the Lipid-Containing, Double-Stranded RNA Bacteriophage φ6)
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16 pages, 3802 KB  
Article
Genetic Diversity, Reassortment Patterns, and Antigenic Characterization of Two H9N2 Avian Influenza Viruses Isolated from Quails in China
by Yutao Teng, Peidong Li, Fuyou Zhang, Wanting Zhou, Xue Wang, Hao Zhu, Qingqing Song, Zhaoyang Li and Chunguo Liu
Viruses 2026, 18(8), 919; https://doi.org/10.3390/v18080919 - 21 Aug 2026
Viewed by 466
Abstract
H9N2 avian influenza viruses pose a persistent zoonotic risk owing to their broad host adaptability. Between 2024 and 2025, two H9N2 isolates (ZHY1022B2 and ZHY0417A11) were recovered from quail flocks in Hebei, China. Phylogenetic analysis clustered their HA genes within the dominant B4.7.2 [...] Read more.
H9N2 avian influenza viruses pose a persistent zoonotic risk owing to their broad host adaptability. Between 2024 and 2025, two H9N2 isolates (ZHY1022B2 and ZHY0417A11) were recovered from quail flocks in Hebei, China. Phylogenetic analysis clustered their HA genes within the dominant B4.7.2 subclade, but diverged into two subgroups (B4.7.2.2 and B4.7.2.1). Of particular interest was ZHY0417A11, which displayed a multigenic reassortment pattern—its PB1 originated from an H3N8 virus, PA and PB2 from H3N3, NS from H10N3, and the M gene was nearly identical (99.32%) to a human H3N8 isolate, whereas the remaining HA, NA and NP segments maintained the H9N2 backbone. Despite the presence of the HA mammalian-adaptive markers (H191N, A198V and Q234L), both strains showed marked antigenic drift from the vaccine strain SS (BJ/94-like; R < 0.5), while retaining reactivity with currently circulating field strains. These findings argue for heightened vigilance in quail populations, given their role as mixing vessels, and highlight the limitations of current vaccine matching in light of ongoing H9N2 evolution. Full article
(This article belongs to the Special Issue Avian Viruses and Antiviral Immunity)
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16 pages, 15463 KB  
Article
ENSO Impact on Global Chikungunya Virus Transmission, 2008–2024: A Multi-Country Distributed-Lag Time-Series Analysis
by Shi-Hui Shan, Long-Tao Chen, Wen-Qi Xie, Chen-Long Lv, Dong Jiang, Fang-Yu Ding, Gang Dong and Li-Qun Fang
Viruses 2026, 18(8), 918; https://doi.org/10.3390/v18080918 - 21 Aug 2026
Viewed by 473
Abstract
Chikungunya is undergoing global expansion, but how El Niño–Southern Oscillation (ENSO) influences its transmission remains unclear. We aim to assess the impact of ENSO phases on chikungunya incidence via temperature and precipitation teleconnections and to project future risk burden under climate change. We [...] Read more.
Chikungunya is undergoing global expansion, but how El Niño–Southern Oscillation (ENSO) influences its transmission remains unclear. We aim to assess the impact of ENSO phases on chikungunya incidence via temperature and precipitation teleconnections and to project future risk burden under climate change. We compiled annual national and subnational chikungunya case data (2008–2024), quantified ENSO–climate teleconnections using the E-index (eastern Pacific El Niño) and C-index (central Pacific La Niña), and applied distributed-lag time-series models to assess the teleconnection-mediated impact of ENSO on chikungunya incidence. We further projected future risk burden under climate change scenarios. Modelling shows that El Niño increased chikungunya risk after a 2-year lag (cumulative relative risk [CRR] = 1.40, 95% confidence interval [CI]: 1.02–1.85), while La Niña suppressed it (CRR = 0.09, 95% CI: 0.07–0.13). Temperature teleconnections were the dominant modifier of spatial heterogeneity in effects. Under all scenarios, El Niño-driven warming led to positive median excess cases, the highest under SSP2-4.5, whereas La Niña-driven changes projected smaller, highly uncertain reductions. ENSO influences chikungunya transmission through asymmetric and spatially heterogeneous teleconnection pathways. Integrating ENSO forecasts into surveillance efforts has the potential to enhance preparedness in climate-sensitive regions. Full article
(This article belongs to the Special Issue Current Trends in Arbovirus Outbreaks and Research)
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16 pages, 317 KB  
Review
Performance of Oral Rotavirus Vaccines in Low- and Middle-Income Settings: Current Evidence, Persistent Gaps and Future Directions
by Bharathikumar Sivakumar, Jason Mathiu Mwenda, Benjamin Alan Lopman, Gagandeep Kang and Tintu Varghese
Viruses 2026, 18(8), 917; https://doi.org/10.3390/v18080917 - 21 Aug 2026
Viewed by 505
Abstract
Oral, live-attenuated rotavirus vaccines (ORVs) have significantly reduced severe diarrheal disease and deaths; however, vaccine performance in low- and middle-income countries (LMICs) remains lower than in high-income countries. With increasing global use, real-world data now provide important insights into strategies to improve vaccine [...] Read more.
Oral, live-attenuated rotavirus vaccines (ORVs) have significantly reduced severe diarrheal disease and deaths; however, vaccine performance in low- and middle-income countries (LMICs) remains lower than in high-income countries. With increasing global use, real-world data now provide important insights into strategies to improve vaccine impact in these settings. This review summarizes current evidence on the effectiveness and impact of ORVs in LMICs, with a focus on approaches to optimize performance, including alternative dosing schedules, booster doses in late infancy, and mixed vaccine regimens. Evidence on vaccine interchangeability offers practical solutions for countries facing supply disruptions and financial constraints. The review also highlights the growing importance of economic sustainability, particularly in the context of transitions from external funding support. Despite lower efficacy, ORVs continue to provide substantial public health benefits in LMICs. Sustained impact will depend on strengthening programme delivery, ensuring stable vaccine supply, and advancing next-generation vaccines. Continued evaluation of effectiveness, cost, and implementation strategies will be critical to maximizing long-term benefits in high-burden settings. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines: 2nd Edition)
22 pages, 6295 KB  
Review
Antibody-Dependent Enhancement in Flavivirus Infections: From Fc Receptor Signaling to Vaccine and Therapeutic Design
by Yiling Li, Zonghui Wu, Yingchao Cha, Wei Pang and Le Sun
Viruses 2026, 18(8), 916; https://doi.org/10.3390/v18080916 - 20 Aug 2026
Viewed by 552
Abstract
Infections caused by flaviviruses, including dengue virus (DENV), Zika virus (ZIKV), and West Nile virus (WNV), can lead to severe hemorrhagic or neurological disease. Antibody-dependent enhancement (ADE) remains a major obstacle to the development of safe flavivirus vaccines and antibody-based therapeutics. ADE includes [...] Read more.
Infections caused by flaviviruses, including dengue virus (DENV), Zika virus (ZIKV), and West Nile virus (WNV), can lead to severe hemorrhagic or neurological disease. Antibody-dependent enhancement (ADE) remains a major obstacle to the development of safe flavivirus vaccines and antibody-based therapeutics. ADE includes ADE of infection, in which antibodies increase in viral entry, replication, or infection load, and ADE of disease, in which antibody-dependent inflammatory and immunopathological responses exacerbate disease severity. Previous reviews have largely addressed the general virological and immunological mechanisms of ADE, but few have integrated antibody isotypes and subclasses, Fc-region modifications, Fc receptor diversity, host FcγR polymorphisms, and complement activation within a translational framework. Consequently, how these factors jointly shape ADE of infection, progression to ADE of disease, and individual risk remains incompletely understood. Here, we synthesize evidence linking antibody properties, Fc receptor expression and signaling, FcγR genetic variation, and complement regulation to both forms of ADE. We then discuss how these findings can inform antigen selection, Fc engineering, complement-informed intervention, and systems serology-based risk stratification. By connecting mechanistic evidence with vaccine and therapeutic development, this review offers a framework for designing safer flavivirus interventions and advancing individualized assessment of ADE risk. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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15 pages, 267 KB  
Review
Cardiopulmonary Failure in Hantavirus Disease: Mechanisms, Recognition, and ECMO-Based Management
by Deng Siang Lee and Aboubakr Hasan
Viruses 2026, 18(8), 915; https://doi.org/10.3390/v18080915 - 20 Aug 2026
Viewed by 525
Abstract
Background: Hantavirus pulmonary syndrome (HPS), also designated hantavirus cardiopulmonary syndrome, is caused by New World hantaviruses, principally Sin Nombre virus in North America and Andes virus in South America. The syndrome is characterized by rapidly progressive noncardiogenic pulmonary edema and myocardial depression, with [...] Read more.
Background: Hantavirus pulmonary syndrome (HPS), also designated hantavirus cardiopulmonary syndrome, is caused by New World hantaviruses, principally Sin Nombre virus in North America and Andes virus in South America. The syndrome is characterized by rapidly progressive noncardiogenic pulmonary edema and myocardial depression, with case fatality rates of 25% to 40%. A 2026 outbreak aboard an expedition cruise ship in the South Atlantic, comprising 13 cases and three deaths, confirmed that Andes virus can be transmitted between humans in a confined setting remote from the rodent reservoir. Methods: Virological, pathophysiological, clinical, and therapeutic aspects of HPS were reviewed, with particular emphasis on cardiopulmonary mechanisms. Sources were identified through PubMed, Scopus, and Google Scholar, with priority given to original research articles, clinical series, and controlled trials published through 2025. Literature published in English and Spanish was included. Results: Pathogenic hantaviruses enter endothelial cells and platelets via αvβ3 integrins, disrupting the VEGF-VEGFR2 signaling axis and rendering endothelial cells hypersensitive to physiological VEGF concentrations. Expansion of CD8+ T cells and activated macrophages releases TNF-alpha, IFN-gamma, and nitric oxide, amplifying microvascular permeability and contributing to myocardial depression. Autopsy studies demonstrate direct hantaviral myocarditis with viral antigen in cardiac endothelium and interstitial macrophages. Transpulmonary thermodilution confirms simultaneous hypovolemia, reduced global ejection fraction, and elevated extravascular lung water. Because the incubation period is long and the cardiopulmonary phase is substantially immune-mediated, seroconversion precedes rather than follows clinical deterioration, which preserves the diagnostic utility of IgM serology in a disease that can kill within 48 h. VA-ECMO initiated at the first signs of cardiopulmonary decompensation has reported survival rates approaching 80% in selected experienced centers. No antiviral has demonstrated efficacy in controlled trials during the cardiopulmonary phase, and no licensed vaccine exists. Conclusions: HPS produces a mixed shock state through increased microvascular permeability, T cell-mediated immunopathology, and direct myocarditis. Management follows a stepwise algorithm: suspected HPS triggers immediate complete blood count with peripheral blood smear and concurrent hantavirus IgM serology and RT-PCR, followed by ICU admission, conservative fluid resuscitation guided by transpulmonary thermodilution, and early contact with an ECMO-capable center at the first sign of rising lactate, falling cardiac index, refractory shock, arrhythmia, or rapid oxygenation failure. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
17 pages, 647 KB  
Article
Clinical and Analytical Performance of the AP Biotech Discovery® Dengue Virus RT-PCR Detection Kit
by Valentina Hjelt, Agustina Dronseck, Aldana Magalí Schey, María Belén Martí, Luciano Civerchia, Ana Laura Cavatorta, Eduardo Codino, Virginia Nader, Natalia Andrea Garro, Federico Manuel Aranda, Lilia Mammana, Sergio Giamperetti, Clara Theaux, Anisa Marchissio, Valeria Estefanía Burani, Erica Natalia Luczak, María Martina Bellucci, Gabriela García, Florencia Cayrol, María Belén Bouzas, Sergio Grutadauria and Lucila Brocardoadd Show full author list remove Hide full author list
Viruses 2026, 18(8), 914; https://doi.org/10.3390/v18080914 - 20 Aug 2026
Viewed by 493
Abstract
Dengue is a mosquito-transmitted viral disease caused by the positive-sense RNA dengue virus (DENV), which comprises four antigenically distinct serotypes (1–4). Although DENV circulates predominantly in tropical and subtropical regions, its global incidence continues to increase. As most patients present viremia at the [...] Read more.
Dengue is a mosquito-transmitted viral disease caused by the positive-sense RNA dengue virus (DENV), which comprises four antigenically distinct serotypes (1–4). Although DENV circulates predominantly in tropical and subtropical regions, its global incidence continues to increase. As most patients present viremia at the onset of clinical manifestations, real-time RT-PCR has become a widely adopted method for early dengue detection. The AP Biotech Discovery® Dengue Virus RT-PCR Detection Kit enables qualitative detection of DENV RNA (serotypes 1–4) by real-time RT-PCR in serum or plasma samples. The assay was recently cleared by ANMAT (National Administration of Drugs, Food and Medical Technology) as an in vitro diagnostic (IVD) assay. The Limit of Detection (LoD) was calculated for all 4 serotypes. Clinical validation was conducted among 296 serum and 221 plasma samples previously characterized as DENV-positive and -negative specimens. Among the positive samples, 56 had serotype characterization, including 25 DENV-1 and 31 DENV-2 samples. The resulting clinical sensitivity and specificity were 97.8%, 100.0% and 100.0%, 99.1% respectively. Additional validation studies demonstrated high reproducibility across three independent laboratories, absence of cross-reactivity with other febrile pathogens, and no interference from endogenous and exogenous substances at clinical levels. Collectively, these findings support the AP Biotech Discovery® Dengue Virus RT-PCR Detection Kit (AP Biotech, Lomas de Zamora, Argentina) as a sensitive, specific, and highly reproducible device for early dengue diagnosis and surveillance. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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18 pages, 5505 KB  
Article
Metabolic Signatures of Chikungunya Versus Dengue: A Comparative Study
by Yuqiu Liu, Meiyi Li, Huili Chen and Xi Liu
Viruses 2026, 18(8), 913; https://doi.org/10.3390/v18080913 - 20 Aug 2026
Viewed by 432
Abstract
Background: Chikungunya virus and dengue virus rank among the most clinically significant mosquito-borne pathogens worldwide, imposing substantial disease burdens in endemic regions. Despite their overlapping symptomatology, the diseases diverge markedly in prognosis. This disparity underscores the critical need for tools to differentiate these [...] Read more.
Background: Chikungunya virus and dengue virus rank among the most clinically significant mosquito-borne pathogens worldwide, imposing substantial disease burdens in endemic regions. Despite their overlapping symptomatology, the diseases diverge markedly in prognosis. This disparity underscores the critical need for tools to differentiate these conditions and elucidate their distinct pathogenic mechanisms. Method: We conducted liquid chromatography–tandem mass spectrometry-based comparative metabolomic analyses to systematically compare plasma profiles from infected individuals. Results: We collected plasma samples from 26 chikungunya fever (CHIKF) patients, 49 dengue fever (DF) patients and 28 healthy individuals. Clinically, CHIKF patients exhibited a higher prevalence of rash (96.3% vs. 36.7%) and involvement of small joints, while DF patients showed prolonged fever and more severe hematological abnormalities. Metabolically, significant differences were observed in specific metabolites, such as eugenol sulfate, lysophosphatidylcholine (14:0/0:0), and piperine, which were dysregulated in both groups compared to healthy controls. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted unique metabolic perturbations in CHIKF, such as peroxisome proliferator-activated receptor (PPAR) signaling and mechanistic target of rapamycin complex (mTOR) pathways, suggesting potential mechanisms underlying CHIKV-induced arthritis. Conclusions: This study identifies distinct metabolic signatures and functional pathways associated with CHIKF and DF, offering a potential mechanism for differential diagnosis and therapeutic targets. The role of eugenol sulfate in modulating CHIKV-induced arthralgia is particularly promising, supported by its known anti-inflammatory properties. Full article
(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 3rd Edition)
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24 pages, 1212 KB  
Review
Molecular Insights into High-Pathogenicity RNA Viruses
by Hana Krnjić, Adna Hrapović, Aiša Galijatović, Ajla Tipura, Maida Hajdarpašić, Selma Kozarić, Adna Berilo, Naida Odobašić, Altijana Hromić-Jahjefendić and Jasmin Šutković
Viruses 2026, 18(8), 912; https://doi.org/10.3390/v18080912 - 19 Aug 2026
Viewed by 568
Abstract
Highly pathogenic RNA viruses, such as Ebola, SARS-CoV-2, and influenza, cause severe disease in humans. High mutation rates, which enable RNA viruses to evade immunity and escape antivirals, and their ability to spread from animals to humans and cause pandemics and outbreaks, make [...] Read more.
Highly pathogenic RNA viruses, such as Ebola, SARS-CoV-2, and influenza, cause severe disease in humans. High mutation rates, which enable RNA viruses to evade immunity and escape antivirals, and their ability to spread from animals to humans and cause pandemics and outbreaks, make RNA viruses significant threats to public health. Diseases caused by Ebola, SARS-CoV-2, and influenza are prevented and treated with only a limited number of approved antiviral drugs, the effectiveness of which is limited by mutations in the viral targets. It is crucial to understand the structural determinants, molecular mechanisms, and host interactions of pathogenic RNA viruses to develop effective antiviral strategies. In this review, we discuss selected RNA viruses, focusing on the structure of their RNA polymerases and interactions with host factors during the different stages of the viral lifecycle, as well as the traditional antivirals targeting these structures and pathways. Furthermore, emerging concepts such as liquid–liquid phase separation and biomolecular condensates, and novel promising antiviral strategies are discussed. Understanding shared and distinct structures, molecular mechanisms, and host interactions across highly pathogenic RNA viruses enables the discovery of new and more effective antiviral strategies, ultimately improving clinical outcomes against evolving RNA viruses. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Structural Biology of High-Pathogenicity RNA Viruses)
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16 pages, 14237 KB  
Article
Maraviroc Inhibits SARS-CoV-2 Through Variant-Dependent Effects on Viral Entry and Mpro Activity Using Single-Round Infectious Particle and Virus-like Particle Models
by Uyen Nguyen Phuong Le, Po-Ju Chen, Li-Wei Chu, Jane Cynthia Arifin, Chih-Hao Chen, Yu-Hsuan Chen, Wen-Chi Su, Po-Ren Hsueh, Yueh-Hsin Ping and Cheng-Wen Lin
Viruses 2026, 18(8), 911; https://doi.org/10.3390/v18080911 - 19 Aug 2026
Viewed by 389
Abstract
Maraviroc (MVC), a CCR5 antagonist, has been proposed as a potential antiviral agent against SARS-CoV-2; however, its mechanism of action across viral variants remains unclear. Here, we evaluated the antiviral activity of MVC against SARS-CoV-2 wild-type (WT) and Omicron BA.1 variants using single-round [...] Read more.
Maraviroc (MVC), a CCR5 antagonist, has been proposed as a potential antiviral agent against SARS-CoV-2; however, its mechanism of action across viral variants remains unclear. Here, we evaluated the antiviral activity of MVC against SARS-CoV-2 wild-type (WT) and Omicron BA.1 variants using single-round infectious particles (SRIPs), virus-like particles (VLPs), and cell-based assays, with a focus on its impact on viral entry and Mpro function. MVC potently inhibited infection of both WT and BA.1 SRIPs in Vero E6 cells, exhibiting EC50 values of 0.0065 μM and 0.016 μM, respectively. Time-of-addition assays revealed that MVC primarily targets the early phase of infection, with the strongest inhibition observed at the viral entry stage, while moderate effects were detected during attachment and post-entry stages. Fluorescence-labeled VLP imaging demonstrated distinct entry pathways, with WT predominantly entering via plasma membrane fusion and BA.1 via endocytosis, independent of cell type. MVC altered WT-VLP trafficking by promoting internalization and lysosomal localization, whereas it had minimal impact on BA.1 internalization. In spike-mediated cell–cell fusion assays, MVC preferentially inhibited WT spike-driven syncytium formation but showed limited effects on BA.1 or BA.4 fusion, while more effectively reducing Omicron spike-mediated binding. At the post-entry stage, MVC inhibited SARS-CoV-2 main protease (Mpro) activity, with BA.1 Mpro (P132H) exhibiting greater sensitivity (IC50 = 0.496 µM) than WT (1.869 µM). Collectively, these findings demonstrate that MVC exerts variant-dependent antiviral effects by targeting viral entry, modulating trafficking pathways, and inhibiting Mpro activity. This study highlights MVC as a multi-stage inhibitor with differential efficacy against SARS-CoV-2 variants, providing insights into its potential therapeutic application. Full article
(This article belongs to the Special Issue Emerging Concepts in SARS-CoV-2 Biology and Pathology, 3rd Edition)
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19 pages, 3360 KB  
Review
AMPK-Orchestrated Metabolic Reprogramming in Some Flavivirus Infections: Mechanisms and Therapeutic Opportunities
by Kaci Craft, Imaan Muhammad, Shaokai Pei and Qiyi Tang
Viruses 2026, 18(8), 910; https://doi.org/10.3390/v18080910 - 19 Aug 2026
Viewed by 639
Abstract
5′-Adenosine monophosphate-activated protein kinase (AMPK) is the principal cellular energy sensor that coordinates metabolic adaptation by balancing anabolic and catabolic pathways in response to energic stress. Beyond its canonical role in maintaining energy homeostasis, AMPK has emerged as a central regulator of host–pathogen [...] Read more.
5′-Adenosine monophosphate-activated protein kinase (AMPK) is the principal cellular energy sensor that coordinates metabolic adaptation by balancing anabolic and catabolic pathways in response to energic stress. Beyond its canonical role in maintaining energy homeostasis, AMPK has emerged as a central regulator of host–pathogen interactions by integrating lipid metabolism, autophagy, mitochondrial dynamics, oxidative stress, and innate immune signaling. Flaviviruses, including dengue virus, Zika virus, West Nile virus, Japanese encephalitis virus, and yellow fever virus, extensively remodel host metabolism to establish productive infection. As a master regulator of cellular metabolism, AMPK can either restrict or facilitate flavivirus replication in a context-dependent manner by regulating lipid droplet biogenesis, fatty acid synthesis and beta-oxidation, autophagy, mitochondrial homeostasis, and interferon-mediated antiviral responses. Conversely, flaviviruses actively manipulate AMPK signaling and its downstream metabolic networks to promote endoplasmic reticulum remodeling, replication organelle biogenesis, energy production, and immune evasion. In this review, we summarize recent advances in understanding the multifaceted roles of AMPK during flavivirus infection, with an emphasis on its regulation of metabolic reprogramming, organelle remodeling, and antiviral immunity. We further discuss the therapeutic potential of pharmacologically targeting AMPK and its downstream pathways as a host-directed strategy for broad-spectrum antiviral intervention against flaviviruses. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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20 pages, 4135 KB  
Review
A Review: Bovine Coronavirus Evolution, Molecular Epidemiology, and Genetic Variation
by Dong Wang, Wenzheng Zhang, Zheng Nie, Xutian Wang, Jinhui Liu, Yannan Zhang, Yabin Lu, Zhanhai Mai, Xiaodong He, Jianlong Li, Chao Gong and Qingyong Guo
Viruses 2026, 18(8), 909; https://doi.org/10.3390/v18080909 - 18 Aug 2026
Viewed by 346
Abstract
Bovine coronavirus (BCoV) is a key pathogen causing calf diarrhea and bovine respiratory diseases, bringing sustained economic losses to the cattle industry. As an RNA virus, BCoV possesses high mutation and recombination capacities, leading to prominent genomic genetic diversity. The genome contains hypervariable [...] Read more.
Bovine coronavirus (BCoV) is a key pathogen causing calf diarrhea and bovine respiratory diseases, bringing sustained economic losses to the cattle industry. As an RNA virus, BCoV possesses high mutation and recombination capacities, leading to prominent genomic genetic diversity. The genome contains hypervariable and conserved regions, with the S (especially S1), HE and Open Reading Frame (ORF4) genes serving as major variation hotspots linked to viral antigenicity, tissue tropism shift and immune evasion. Host immune pressure drives strong positive selection on S protein antigenic variation. This review discusses existing research limitations and proposes future directions including genomic surveillance, reverse genetics verification and broad-spectrum vaccine development to support BCoV prevention and control. Full article
(This article belongs to the Special Issue Epidemiology, Evolution, Pathogenicity and Antiviral Strategies of Animal Coronaviruses)
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32 pages, 3621 KB  
Review
Advances in Molecular Techniques for Detecting Sweet Potato (Ipomoea batatas (L.) Lam) Viruses: A Comprehensive Review
by Muhammad Abul Kalam Azad, Nanziba Ibnat, Saleh Shafique Chowdhury, Saaimatul Huq and Shahidul Islam
Viruses 2026, 18(8), 908; https://doi.org/10.3390/v18080908 - 18 Aug 2026
Viewed by 659
Abstract
Sweet potato (Ipomoea batatas (L.) Lam) is an important global food crop, but its production is threatened by numerous viral pathogens. More than 30 RNA and DNA viruses have been reported worldwide, making rapid and accurate detection essential for disease management, epidemiological [...] Read more.
Sweet potato (Ipomoea batatas (L.) Lam) is an important global food crop, but its production is threatened by numerous viral pathogens. More than 30 RNA and DNA viruses have been reported worldwide, making rapid and accurate detection essential for disease management, epidemiological surveillance, germplasm exchange, and resistance breeding. Although previous reviews have addressed sweet potato viruses and individual diagnostic methods, a comprehensive synthesis of emerging molecular technologies remains limited. This review addresses that gap by critically integrating recent advances from PCR-based and isothermal assays to high-throughput sequencing, CRISPR-based diagnostics, biosensors, nanotechnology, and artificial intelligence-driven detection platforms. Conventional approaches, including symptom observation, biological indexing, electron microscopy, and ELISA, have contributed to early virus identification but often lack the sensitivity, specificity, and speed needed for modern diagnostics. Molecular and isothermal techniques have substantially improved detection accuracy and enabled rapid identification and field-deployable diagnostics of diverse and mixed infections, while sequencing, CRISPR, biosensors, and AI-based platforms offer greater capacity for detecting novel and emerging viruses. This review discusses the comparative evaluation of molecular technologies for sweet potato virus detection in terms of diagnostic performance, cost-effectiveness, speed, and suitability for both laboratory and field applications, while highlighting future priorities for next-generation virus diagnostics. Integrating portable and high-throughput diagnostic platforms will strengthen virus surveillance, support virus-free planting material production, and promote sustainable sweet potato production worldwide. Full article
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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30 pages, 3276 KB  
Review
Bacteriophages as Phagobiotics: Scientific Rationale and Translational Boundaries for Gut Microbiome Modulation
by Fedor Zurabov
Viruses 2026, 18(8), 907; https://doi.org/10.3390/v18080907 - 18 Aug 2026
Viewed by 542
Abstract
Most translational work on bacteriophages has focused on antibacterial therapy or food biocontrol. A third use case is scientifically plausible but remains insufficiently defined: the intentional use of characterized phages to modulate gut microbial communities without infection-treatment claims. In this review, the term [...] Read more.
Most translational work on bacteriophages has focused on antibacterial therapy or food biocontrol. A third use case is scientifically plausible but remains insufficiently defined: the intentional use of characterized phages to modulate gut microbial communities without infection-treatment claims. In this review, the term “phagobiotics” is used for defined, purified and process-controlled bacteriophages or phage cocktails intended for selective gut microbiota modulation. The concept is evaluated across natural human phage exposure, the gut phageome, mechanisms of phage-mediated community modulation, human intervention studies, preclinical models, manufacturing quality and regulatory boundaries. Current evidence supports biological plausibility and indicates that oral phage exposure can be well tolerated and, in some contexts, can selectively affect target bacterial groups without broad microbiota disruption. Generalized clinical efficacy and broad microbiome-support claims, however, remain insufficiently established. Microbiological-modulation claims require target-linked evidence, whereas claims to treat, prevent or cure disease or replace antibiotics fall outside the proposed non-therapeutic category. A proportionate framework is proposed in which natural exposure and food-use precedents inform, but do not determine, the safety rationale; product-specific controls focus on identity, purity, production-host control, manufacturing consistency, stability, genomic characterization and claim-linked evidence. Regulatory classification remains case-specific and depends on intended use, product format, target population and claims. Full article
(This article belongs to the Special Issue Bacteriophages as Precision Tools for Microbiome Modulation)
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26 pages, 4110 KB  
Article
Distinct Activation of Defense-Related Gene Networks in Rosetted Versus Symptomless Shoots in Rose Rosette Virus-Infected Roses
by Shakil Hosain, Venura Herath, Reghan Mutethia, Michael V. Kolomiets, Kevin Ong, Oscar Riera-Lizarazu and Jeanmarie Verchot
Viruses 2026, 18(8), 906; https://doi.org/10.3390/v18080906 - 18 Aug 2026
Viewed by 654
Abstract
Rose rosette virus (RRV) causes witches’ broom disease in roses. This study examined whether differences in disease in these spatially distinct domains are associated with local changes in defense-related hormones and transcriptional reprogramming. The levels of defense-related phytohormones salicylic acid (SA), jasmonic acid [...] Read more.
Rose rosette virus (RRV) causes witches’ broom disease in roses. This study examined whether differences in disease in these spatially distinct domains are associated with local changes in defense-related hormones and transcriptional reprogramming. The levels of defense-related phytohormones salicylic acid (SA), jasmonic acid (JA), 9-lipoxygenase (9-LOX), 13-lipoxygenase (13-LOX), and derived oxylipins were different in these distinct tissues. We curated differentially expressed genes involved in the biosynthesis, storage, and signaling of SA, JA, and oxylipins to reveal how specific defense pathways correlate with these distinct disease states. Gene ontology (GO) analysis and the Disease Resistance Analysis and Gene Orthology 3 (DRAGO3) pipeline revealed stress-associated genes and classical resistance (R) gene families that were differently expressed in these distinct tissue domains. Promoter analysis of defense-associated transcription factors and histone modifiers revealed hormone responsive elements, suggesting complex hormone crosstalk is involved in defense-related gene expression. We confirmed by RT-qPCR, a notable subset of defense genes in the chromosome 5 hotspot, specifically in the linkage group 5 (LG5) quantitative trait loci, linked to reduced RRV susceptibility, was altered in both field-infected and greenhouse-inoculated plants. The association of high versus low disease states with distinct defense hormone signatures and gene expression patterns suggests that local immune states, rather than whole-plant defenses, determine whether a cane becomes rosetted or remains asymptomatic. Full article
(This article belongs to the Special Issue Common Pathogenic Mechanisms of Plant Viruses)
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16 pages, 1256 KB  
Article
Virological Failure and Mortality Among People Living with HIV Transitioned to Second- or Third-Line Antiretroviral Therapy in Rwanda: A Competing-Risks Survival Analysis of National Case-Based Surveillance Data, 2019–2025
by Gallican N. Rwibasira, Jean Claude Kwizera, Tafadzwa Dzinamarira, Steven Karera, Gatete Gaetan, Albert Tuyishime, Eric Remera, Daniel Henry Paris and Tracy R. Glass
Viruses 2026, 18(8), 905; https://doi.org/10.3390/v18080905 - 17 Aug 2026
Viewed by 459
Abstract
Background: Despite Rwanda’s achievement of the UNAIDS 95–95–95 targets, national evidence on virological failure (VF) and mortality after transition to second- or third-line antiretroviral therapy (ART) remains limited. We estimated the incidence of these outcomes and examined associated factors among people living with [...] Read more.
Background: Despite Rwanda’s achievement of the UNAIDS 95–95–95 targets, national evidence on virological failure (VF) and mortality after transition to second- or third-line antiretroviral therapy (ART) remains limited. We estimated the incidence of these outcomes and examined associated factors among people living with HIV (PLWH) transitioned to second- or third-line ART in Rwanda between 2019 and 2025. Methods: We conducted a retrospective cohort study using Rwanda’s national HIV case-based surveillance (CBS) system. PLWH aged ≥15 years who transitioned to second- or third-line ART between 1 January 2019 and 31 December 2025 were followed from transition until the first recorded outcome, last clinical contact, or administrative censoring. The primary operational VF endpoint was the first viral load >1000 copies/mL recorded ≥180 days after transition; a prespecified sensitivity analysis required two consecutive measurements >1000 copies/mL. We used Kaplan–Meier estimation and facility-clustered Cox regression for the composite outcome of VF or death, and Aalen–Johansen cumulative incidence functions and Fine–Gray regression for VF with death treated as a competing event. Results: Among 778 PLWH followed for 3564 person-years (median follow-up, 60.0 months), 81 (10.4%) met the primary operational VF endpoint, and 13 (1.7%) had death recorded as the first event. The composite incidence rate was 2.64 per 100 person-years (95% CI 2.10–3.17). In adjusted Cox regression, a PI-based regimen (adjusted hazard ratio [aHR] 2.14, 95% CI 1.37–3.36), WHO stage III (aHR 1.92, 95% CI 1.10–3.34), and WHO stage IV (aHR 3.59, 95% CI 1.61–8.02) were associated with the composite outcome. In Fine–Gray analysis, a PI-based regimen (subdistribution hazard ratio [sHR] 3.37, 95% CI 1.96–5.78) and WHO stage IV (sHR 4.44, 95% CI 1.91–10.4) were associated with VF. Conclusions: PI-based regimen use and advanced WHO clinical stage were associated with poorer outcomes after ART line transition. These findings support intensified viral load monitoring, adherence and resistance assessment, and individualized regimen review for patients receiving PI-based therapy, together with systematic implementation of the WHO advanced HIV disease package for patients with stage III or IV disease. Full article
(This article belongs to the Special Issue HIV Infection, Latency, Pathogenesis and Associated Comorbidities, Including Cancer and Inflammation in the Context of Drugs of Abuse and ART)
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15 pages, 959 KB  
Article
Deep Sequencing of Hepatitis B Virus Reveals Clinically Relevant Low-Frequency Variants Among People Living with HIV in Botswana
by Tsholofelo Sethibe, Wonderful Tatenda Choga, Florence G. Gaongalelwe, Bonolo B. Phinius, Gorata G. A. Mpebe, Kabo Baruti, Chanana Dorcus Tsayang, Goabaone Mbae, Basetsana Katlo S. Phakedi, Patience Motshosi, Linda Mpofu-Dobo, Mosimanegape Jongman, Sikhulile Moyo, Motswedi Anderson and Simani Gaseitsiwe
Viruses 2026, 18(8), 904; https://doi.org/10.3390/v18080904 - 17 Aug 2026
Viewed by 388
Abstract
(1) Background: The Hepatitis B virus (HBV) is characterized by extensive genetic diversity, including low-frequency variants that contribute to disease progression. We aimed to characterize low-frequency variants and evaluate their potential clinical impact. (2) Methods: We utilized 104 HBV near-full-length sequences generated using [...] Read more.
(1) Background: The Hepatitis B virus (HBV) is characterized by extensive genetic diversity, including low-frequency variants that contribute to disease progression. We aimed to characterize low-frequency variants and evaluate their potential clinical impact. (2) Methods: We utilized 104 HBV near-full-length sequences generated using next-generation sequencing (NGS) from people living with HIV (PLHIV). We used an in-house bioinformatics suite (HBVgenomeR v5.9.7) to filter for low-frequency variants (5–50%), which were compared to escape and drug resistance mutations (DRMs) and hepatocellular carcinoma (HCC)-associated mutations reported at the consensus level. Unclassified variants were characterized by HBV open reading frames (ORFs) to determine mutation frequency per genomic region. (3) Results: A total of six escape mutations were detected in 8/104 (7.7%) sequences, with surfaceN131T being the most prevalent (5/8). We also observed six DRMs in 30/104 (28.8%), with rtV173L being the most prevalent (21/30). Truncation mutations were also observed with rtA181T/sW172* and rtM204I/sW196L being the most prevalent. A total of 8/104 (7.7%) sequences had four variants associated with HCC. The xP46S was the highest observed HCC-associated mutation at 5/8. We report 1152 unique uncharacterized variants across all ORFs, and these were found in 94/104 (90.4%) sequences. The RNaseH domain had the highest burden (330/1152, 28.6%). (4) Conclusions: Deep sequencing results identified clinically significant mutations, including those below the 20% detection limit of traditional sequencing, that would go unreported. This highlights the possible underreporting of mutational burden in people living with HBV/HIV, indicating the importance of deep sequencing to aid in HBV/HIV understanding and management. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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15 pages, 924 KB  
Article
Seroepidemiology of Enterovirus D68 in Xiamen Children: A Cross-Sectional Study in 2022
by Liting Wang, Qiguo Zhu, Yi Lu, Yuanyuan Wu, Zhifeng Ke, Qingbing Zheng, Longfa Xu, Tong Cheng, Rui Zhu and Jun Shen
Viruses 2026, 18(8), 903; https://doi.org/10.3390/v18080903 - 17 Aug 2026
Viewed by 407
Abstract
Enterovirus D68 (EV-D68) is a re-emerging pathogen associated with severe acute flaccid myelitis (AFM) and pneumonia, predominantly in children but also capable of causing severe disease in immunocompromised adults. Seroprevalence data are essential for understanding population immunity, age-specific susceptibility, and viral transmission dynamics; [...] Read more.
Enterovirus D68 (EV-D68) is a re-emerging pathogen associated with severe acute flaccid myelitis (AFM) and pneumonia, predominantly in children but also capable of causing severe disease in immunocompromised adults. Seroprevalence data are essential for understanding population immunity, age-specific susceptibility, and viral transmission dynamics; yet, such data for the period after the COVID-19 pandemic are scarce. We conducted a cross-sectional serological survey to characterize the neutralizing antibody profile of EV-D68 among children in Xiamen, China, in 2022. A total of 453 children aged 0–16 years (217 with acute respiratory tract infection [ARTI] and 236 without) were enrolled. Neutralizing antibody (NtAb) titers against the EV-D68 STL strain were measured using a microneutralization assay, seropositivity was defined as a titer ≥1:16. Multivariable regression and analysis of covariance were used to adjust for age and sex. Overall seroprevalence was 96.0% (435/453), exceeding 90.0% in every age subgroup (0–1 y: 100%; 1–3 y: 97.6%; 3–5 y: 92.6%; ≥5 y: 96.2%). The geometric mean titer (GMT) was 76.78 (95% CI: 68.32–85.24). After adjustment, ARTI status was not significantly associated with seropositivity (adjusted OR = 1.42, 95% CI: 0.46–4.41, p = 0.542). In an exploratory comparison, children with ARTI showed nominally higher antibody titers than those without (Mann–Whitney U test, p = 0.003), although the absence of EV-D68-specific PCR testing precludes etiologic attribution of respiratory symptoms to EV-D68 infection. Infants < 1 year showed the highest GMT (86.31), while children aged 1–3 years had the lowest GMT (63.52) and the largest low-titer fraction, indicating a susceptibility gap. Our study revealed EV-D68 circulated endemically in this pediatric population, establishing a high population immune baseline (>90.0%) with distinct age-dependent patterns. These findings provide key reference data for ongoing serosurveillance, outbreak risk assessment, and the evaluation of future vaccines or immunoprophylactic strategies should they become available. Full article
(This article belongs to the Special Issue Enteric Viruses in Environment and Humans: Identification, Surveillance and Control)
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14 pages, 2509 KB  
Article
Possible Volumetric Changes in the Hippocampus and Olfactory Bulbs After COVID-19: A Stereological MRI Study
by Gamze Altun, Aynur Atilla, Kerim Aslan, Kıymet Kübra Tüfekci, Barış Genç, Arife Ahsen Kaplan, Özgür Kemal, Murat Terzi, Hüseyin Akan and Süleyman Kaplan
Viruses 2026, 18(8), 902; https://doi.org/10.3390/v18080902 - 16 Aug 2026
Viewed by 503
Abstract
COVID-19 affects the olfactory system and the hippocampus, leading to severe olfactory and cognitive impairments. This study aimed to quantify volumetric changes in the olfactory bulbs and hippocampus in patients with COVID-19, and to investigate these differences in relation to loss of smell [...] Read more.
COVID-19 affects the olfactory system and the hippocampus, leading to severe olfactory and cognitive impairments. This study aimed to quantify volumetric changes in the olfactory bulbs and hippocampus in patients with COVID-19, and to investigate these differences in relation to loss of smell and taste. This stereological MRI study included 60 COVID-19 (+) participants and 54 non-COVID-19 participants. Using OsiriX software, the volumes of the olfactory bulb and hippocampus were manually measured from 3T MRI images. Compared with controls, participants with loss of smell and taste had smaller olfactory bulb volumes. This decrease was especially noticeable in the left olfactory bulb of female patients. Furthermore, the right hippocampal volume in male patients with loss of smell and taste was significantly decreased. These findings suggest that atrophy of the olfactory bulb and hippocampus may be specific to certain regions and sexes following SARS-CoV-2 infection. Stereological MRI assessments can effectively identify these changes. Prospective longitudinal studies are needed to determine the clinical significance of these changes and their impact on patient management. Full article
(This article belongs to the Section Coronaviruses)
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15 pages, 5164 KB  
Article
Whole-Genome Sequencing of RSV and Phylogeographic Assessment of Viral Importations into Russia
by German V. Roev, Ekaterina V. Pimkina, Dmitry V. Svetlichnyy, Arina V. Peresadina, Maksim I. Nadtoka, Kamil F. Khafizov and Vasiliy G. Akimkin
Viruses 2026, 18(8), 901; https://doi.org/10.3390/v18080901 - 15 Aug 2026
Viewed by 508
Abstract
Lower respiratory tract infections caused by the respiratory syncytial virus (RSV) pose a major global public health challenge. The use of next-generation sequencing technologies enables detailed monitoring of viral genetic variability, which is crucial for evaluating the efficacy of immunoprophylactic measures. In this [...] Read more.
Lower respiratory tract infections caused by the respiratory syncytial virus (RSV) pose a major global public health challenge. The use of next-generation sequencing technologies enables detailed monitoring of viral genetic variability, which is crucial for evaluating the efficacy of immunoprophylactic measures. In this study, whole-genome sequencing of RSV was performed on 106 samples collected in the Russian Federation between September 2021 and April 2025. Three NGS platforms were employed: Illumina MiSeq, Oxford Nanopore Technologies MinION, and Qitan Tech QNome-3841. Using discrete phylogeographic methods, we estimated a minimum of 45 introduction events into Russia for RSV-A and 39 for RSV-B among the genomes included in the analysis. Most events were represented by a single Russian genome. These results indicate recurrent introductions of RSV into Russia from abroad. Given the limited genomic sampling available, most of these introductions were not associated with detectable transmission within the country. Full article
(This article belongs to the Special Issue RSV Epidemiological Surveillance: 3rd Edition)
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14 pages, 15849 KB  
Article
Innate Immune Responses Induced by H9N2 Influenza A Virus and Klebsiella pneumoniae Co-Infection
by Yong-Jie Zhu, Rui-Rui Du, Feng Xiao, Ling-Yi Shao, Jia-Xin Sun, Yu-Jun Zhou, Yu-Xin Shi, Ya-Wen Jin and Zhi-Jing Xie
Viruses 2026, 18(8), 900; https://doi.org/10.3390/v18080900 - 14 Aug 2026
Viewed by 469
Abstract
Klebsiella pneumoniae infection following H9N2 Influenza A virus (IAV) infection causes severe pneumonia. But the underlying pathogenic mechanisms of H9N2 IAV and K. pneumoniae co-infection are complex and need to be further explored. In this study, the lung transcriptomes of mice with H9N2 [...] Read more.
Klebsiella pneumoniae infection following H9N2 Influenza A virus (IAV) infection causes severe pneumonia. But the underlying pathogenic mechanisms of H9N2 IAV and K. pneumoniae co-infection are complex and need to be further explored. In this study, the lung transcriptomes of mice with H9N2 IAV and K. pneumoniae co-infection were characterized by transcriptomic profiling. As a result, GO enrichment analysis revealed that the differential genes were primarily involved in the activation of immune responses, cellular components of membranes and extracellular spaces, and defense responses against pathogen infections. According to KEGG enrichment, the differentially expressed genes (DEGs) were concentrated in TLR signaling pathways, RLR signaling pathways, TNF signaling pathways and NLRP3 signaling pathways. Furthermore, in vitro cell models were established to investigate the innate immune responses induced by H9N2 IAV and K. pneumoniae CPS co-stimulation. K. pneumoniae CPS stimulation influenced the cytokine profiles of mink lung epithelial cells infected with H9N2 IAV, worsened cell viability, and aggravated apoptosis, indirectly inhibiting H9N2 IAV replication. The findings demonstrated that K. pneumoniae superinfection modulated the innate immune responses induced by H9N2 IAV infection, contributing to its pathogenesis. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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16 pages, 554 KB  
Article
Hepatitis B in Isolated Anti-HBc Carriers: Predictors of Detectable HBV DNA and Implications for Risk-Stratified Screening
by Hasan Zeybek
Viruses 2026, 18(8), 899; https://doi.org/10.3390/v18080899 - 14 Aug 2026
Viewed by 448
Abstract
Background/Objectives: Isolated anti-HBc (IAHBc)—anti-HBc reactivity without HBsAg or anti-HBs—may indicate occult HBV infection (OBI) and confers reactivation risk under immunosuppression, yet most evidence derives from single specialties. We assessed the frequency, predictors, and diagnostic yield of detectable HBV DNA across multiple clinical specialties [...] Read more.
Background/Objectives: Isolated anti-HBc (IAHBc)—anti-HBc reactivity without HBsAg or anti-HBs—may indicate occult HBV infection (OBI) and confers reactivation risk under immunosuppression, yet most evidence derives from single specialties. We assessed the frequency, predictors, and diagnostic yield of detectable HBV DNA across multiple clinical specialties in a large real-world cohort to inform risk-based testing. Methods: In this 8-year, single-center retrospective study from an intermediate-endemic setting, 36,506 patients were screened for HBsAg, anti-HBs, and anti-HBc IgG. Patients with the IAHBc pattern who underwent HBV DNA testing formed the analytic cohort. Predictors of HBV DNA positivity were identified by multivariable logistic regression, and the number needed to screen (NNS) was calculated per specialty. Results: IAHBc prevalence was 4.16% (1517/36,506); 1412 patients comprised the analytic cohort (median age 60 years; 55.2% male). HBV DNA was detectable in 117 patients (8.3% of the cohort; 0.32% of all screened). Positivity varied more than fifteen-fold across specialties, with NNS ranging from 4.3 in gastroenterology to 66 in other clinics. High-intensity immunosuppression was the strongest independent predictor (adjusted OR 14.5), alongside younger age and gastroenterology or infectious diseases referral; the model showed good discrimination (AUC 0.810), while male sex was not an independent predictor. Among positive patients, 47% had HBV DNA below 200 IU/mL, consistent with low-level occult infection. Conclusions: These findings support guideline-recommended HBV DNA testing in all anti-HBc-positive patients before immunosuppression and, where universal testing is not feasible, provide local denominators for prioritizing it as an exercise in diagnostic stewardship. The proposed algorithm is institution-level rather than generalizable. Full article
(This article belongs to the Special Issue Hepatitis Viruses: Detection, Diagnosis and Treatment)
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27 pages, 4266 KB  
Review
Unraveling HBV Life Cycle by Fluorescent Microscopy Imaging
by Vanessa Sarabia Vega, Virgile Rat, Florian Seigneuret, Sébastien Eymieux, Philippe Chouteau and Hugues de Rocquigny
Viruses 2026, 18(8), 898; https://doi.org/10.3390/v18080898 - 14 Aug 2026
Viewed by 443
Abstract
The hepatitis B virus (HBV) is a worldwide hepatotropic virus despite the availability of a highly effective vaccine. Currently, the most efficacious treatment against HBV infection is the use of interferon and nucleos(t)ide analogs, which effectively suppress viral replication but do not eradicate [...] Read more.
The hepatitis B virus (HBV) is a worldwide hepatotropic virus despite the availability of a highly effective vaccine. Currently, the most efficacious treatment against HBV infection is the use of interferon and nucleos(t)ide analogs, which effectively suppress viral replication but do not eradicate infection. Consequently, studies are still ongoing to identify novel molecules with antiviral properties. Interfering with HBV trafficking in infected cells is an approach that would greatly benefit from the diverse techniques of microscopy. However, several challenges arise in employing such techniques for HBV, given the unique characteristics of this virus. Notably, HBV predominantly produces non-infectious subviral particles in addition to infectious virions. Moreover, both virions and SVPs are small objects, measuring only 20 to 40 nm, which challenges their observation using conventional optical microscopy. Additional obstacles include the small size of the HBV genome and its high compaction, which restrict reverse genetics and the introduction of DNA sequences coding for fluorescent polypeptides. In this review, we will provide an overview of ongoing research efforts aimed at visualizing the different stages of the HBV life cycle within infected cells. Furthermore, we will explore solutions successfully applied to the visualization of other viruses that could potentially be adapted to HBV. Full article
(This article belongs to the Special Issue Microscopy Methods for Virus Research, 2nd Edition)
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42 pages, 15278 KB  
Article
Phylogenetic Evidence of Local HIV-1 Transmission and Antiretroviral Drug Resistance in the Middle East and North Africa
by Esraa Al-Fraihat, Amal Irshaid, Mohammed Sallam, Johan Snygg, Rasha Awawdeh, Hasanain Al-Shakerchi, Sama Al-Baidhani and Malik Sallam
Viruses 2026, 18(8), 897; https://doi.org/10.3390/v18080897 - 14 Aug 2026
Viewed by 613
Abstract
The molecular epidemiology and antiretroviral (ARV) drug resistance of human immunodeficiency virus type 1 (HIV-1) remain incompletely outlined in the Middle East and North Africa (MENA). The aim of this retrospective molecular epidemiology study was to analyze MENA HIV-1 sequences for phylogenetic clustering [...] Read more.
The molecular epidemiology and antiretroviral (ARV) drug resistance of human immunodeficiency virus type 1 (HIV-1) remain incompletely outlined in the Middle East and North Africa (MENA). The aim of this retrospective molecular epidemiology study was to analyze MENA HIV-1 sequences for phylogenetic clustering and to delineate surveillance drug-resistance mutations (SDRMs) for nucleoside reverse-transcriptase inhibitors (NRTIs), non-nucleoside reverse-transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs) across various periods, locations, and subtypes/circulating recombinant forms (CRFs). Viral sequences were retrieved from the Los Alamos HIV Sequence Database as of 15 April 2026. Analyses were done using multiple sub-gene regions (two env regions (n = 224 and n = 60) and PR (n = 2413) and RT (n = 2103) of the pol gene). Phylogeny construction was conducted using maximum-likelihood estimation, while ARV drug resistance analysis was conducted using the Stanford HIVdb algorithm. The HIV-1 MENA sequences showed a remarkable genetic diversity, with co-circulation of multiple subtypes/CRFs, including subtype B in the Maghreb, Levant, and Egypt sub-regions, subtypes A1, G, CRF01_AE, and CRF02_AG in the Gulf Cooperation Council (GCC) and Yemen sub-region, and subtypes C and D in the Horn of Africa and Sudan sub-region. The percentage of MENA HIV-1 sequences in clusters was 10.3% for env1, 8.3% for env2, 22.0% for PR and 37.2% for RT. Phylogenetic reconstruction hinted at a structured epidemic dominated by small transmission units, with most clusters comprising dyads (n = 260) or networks (n = 142) and a limited number of large clusters (n = 8) that were largely confined within national boundaries, with only occasional cross-border linkages (n = 8). Overall SDRM prevalence was 3.2% in the PR region and 14.9% in the RT region, with a higher percentage of NNRTI-associated mutations (10.0%) than NRTI-associated mutations (9.1%) and dual-class resistance observed in 4.1% of sequences. Phylogenetic clustering was not associated with the probability of harboring SDRMs; however, negative binomial models showed that non-clustered sequences had a greater burden of NRTI-associated mutations, whereas no such association was observed for NNRTI- or PI-associated mutations. The findings showed predominantly localized and fragmented MENA HIV-1 transmission dynamics. Heterogeneous ARV drug resistance dynamics indicated that resistance emergence might be shaped by broader epidemiologic and treatment-related factors rather than ongoing clustered transmission. There is a need for coordinated molecular surveillance and optimized ART strategies across the MENA countries. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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12 pages, 1086 KB  
Article
Weight Gain Is Associated with Short-Term FIB-4 Increase and Concurrent Metabolic Change in People with HIV and Metabolic Dysfunction-Associated Steatotic Liver Disease
by Wei Xu, Li Liu, Meiyan Sun, Renfang Zhang, Jun Chen and Yinzhong Shen
Viruses 2026, 18(8), 896; https://doi.org/10.3390/v18080896 - 14 Aug 2026
Viewed by 407
Abstract
Background: Short-term variation in the Fibrosis-4 index (FIB-4) may identify people who warrant further liver assessment. We evaluated longitudinal FIB-4 changes and associated metabolic factors in people with HIV (PWH) and metabolic dysfunction-associated steatotic liver disease (MASLD). Methods: This retrospective cohort included 683 [...] Read more.
Background: Short-term variation in the Fibrosis-4 index (FIB-4) may identify people who warrant further liver assessment. We evaluated longitudinal FIB-4 changes and associated metabolic factors in people with HIV (PWH) and metabolic dysfunction-associated steatotic liver disease (MASLD). Methods: This retrospective cohort included 683 PWH with ultrasound-defined MASLD who underwent routine clinical and laboratory assessments approximately every three months. A prespecified FIB-4 increase required both a ≥20% rise and crossing to ≥1.3 among participants with baseline FIB-4 < 1.3, or a ≥20% rise among those with baseline FIB-4 ≥ 1.3. Results: Of 683 enrolled participants, 655 were analyzed longitudinally. Over a median follow-up of 12.0 months, 59 (9.0%) met the FIB-4 increase definition, corresponding to 8.8 events per 100 person-years. Weight gain was associated with this outcome (adjusted hazard ratio 1.19 per 1% increase, 95% CI 1.14–1.24), whereas HIV- and antiretroviral therapy-related variables were not. Transition from non-obesity to obesity was associated with the outcome (odds ratio 8.45, 95% CI 3.57–20.02). Weight change also correlated with concurrent changes in total cholesterol, triglycerides, fasting glucose, and liver enzymes (all p < 0.01). Conclusions: Weight gain was associated with short-term FIB-4 increase and with concurrent metabolic change in PWH with MASLD. Full article
(This article belongs to the Special Issue HIV in the Context of Chronic Disorders and Aging)
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20 pages, 2611 KB  
Review
LINE-1 Epigenetic Repression and Regulation of Immunity
by Holly Jefferson and Helen M. Rowe
Viruses 2026, 18(8), 895; https://doi.org/10.3390/v18080895 - 14 Aug 2026
Viewed by 730
Abstract
The long interspersed element-1 (LINE-1) family is the sole remaining transposable element family that is capable of autonomous retrotransposition in humans. LINE-1 expression, tightly controlled through epigenetic mechanisms, has complex effects on gene regulation. Due to their similarity to retroviruses, once activated, LINE-1s [...] Read more.
The long interspersed element-1 (LINE-1) family is the sole remaining transposable element family that is capable of autonomous retrotransposition in humans. LINE-1 expression, tightly controlled through epigenetic mechanisms, has complex effects on gene regulation. Due to their similarity to retroviruses, once activated, LINE-1s have the ability to trigger pathways involved in innate and adaptive immunity with both beneficial and detrimental effects. This review will explore the mechanisms and importance of LINE-1 epigenetic repression and the potential outcomes of LINE-1 expression, with a focus on their immunogenic roles in innate and adaptive immunity. Full article
(This article belongs to the Special Issue Control and Contributions of Transposable Elements: Implications for Development and Disease)
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