Search Results (298)

The innate immune system, particularly the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling pathway, is a major early defense barrier against influenza A virus infection. However, excessive immune responses can trigger lethal cytokine storms and severe immune-mediated pathology. In this study, we performed a genome-wide CRISPR/dCas9 gene activation screen in human lung epithelial (A549) cells by using an A/Puerto Rico/8/1934 (H1N1) reporter virus, and identified the ubiquitin-specific protease USP17L13 as a novel negative regulator of innate immunity that promotes influenza virus replication. Overexpression of USP17L13 significantly enhanced the replication of multiple subtypes of influenza viruses in A549 cells, including a human pandemic H1N1 virus, seasonal H3N2 viruses, as well as a globally circulating clade, 2.3.4.4b, of the highly pathogenic avian H5N1 virus. Transcriptomic analysis demonstrated that USP17L13 suppresses host antiviral defenses by downregulating nuclear factor kappa B (NF-κB) signaling and arachidonic acid metabolism, while upregulating pathways associated with ribosomal translation and oxidative phosphorylation to facilitate viral production. Mechanistically, USP17L13 attenuates the host interferon (IFN) response by promoting the degradation of the key viral RNA sensors, RIG-I, and melanoma differentiation-associated protein 5 (MDA5). Further analysis revealed that USP17L13 is inducible by type I and type II interferons as well as inflammatory cytokines, suggesting that it may act as a negative-feedback regulator to limit excessive inflammation. Collectively, our findings identify USP17L13 as a previously unrecognized proviral host factor and provide new insight into how host deubiquitinases shape influenza virus-host interactions, with potential implications for host-directed approaches to controlling excessive inflammation during viral infection and improving influenza vaccine production. Full article

The H5N1 subtype of highly pathogenic avian influenza (HPAI) poses a major zoonotic threat due to its high fatality rate and capacity for cross species transmission. In early 2025, Argentina detected a novel triple reassortant A(H5N1) virus in Chaco Province, combining Eurasian, North American, and South American lineage segments. Genomic analyses of subsequent outbreaks in Buenos Aires and Entre Ríos confirmed persistence of this reassortant and additional HA substitutions (T204K, P251S) potentially linked to increased mammalian receptor affinity. Although PB2 sequences lacked canonical mammalian-adaptive markers (E627K, Q591K, D701N), all contained I292M, a mutation associated with human adaptation. Phylogenetic analyses revealed distinct genotypes and increasing divergence. These findings indicate ongoing viral evolution and adaptation within Argentina, emphasizing the urgent need for sustained genomic surveillance, timely data sharing, and integrated One Health strategies to mitigate zoonotic and socioeconomic risks associated with H5N1 spread in South America. Full article

Background: Hemagglutinin (HA) is the primary surface protein of the influenza A virus, determining its subtype and antigenic properties. Traditional subtype classification methods rely on DNA or amino acid sequence analysis, which does not account for protein spatial folding. Methods: In this work, we propose EpitopeGNN—a graph neural network (GNN) that constructs a residue interaction network (RIN) from the 3D structure of HA and classifies the virus subtype. The model was trained on 249 structures from the Protein Data Bank (PDB), containing H1N1, H3N2, H5N1, and other subtypes. Results: After rigorous sequence redundancy reduction (92% identity), the model maintained 95–100% accuracy on non-redundant data, significantly outperforming sequence-only baselines (the best baseline achieved 85% for multi-class and 92.3% for binary classification). A significant correlation was found between the obtained structural embeddings and phylogenetic distances (r = 0.38, p < 0.001), confirming their biological relevance and opening opportunities for structural monitoring of virus evolution, as well as rapid analog searching for novel strains. Conclusions: We developed a new graph neural network that classifies influenza A virus subtypes directly from the 3D structure of hemagglutinin using residue interaction networks and physicochemical features, which can serve as a foundation for predicting influenza virus receptor specificity and epitope immunogenicity. Full article

The efficacy of the host antiviral response against Influenza A virus (IAV), a leading cause of global pandemics, hinges upon the rapid recognition of the pathogen and the prompt activation of immune mechanisms. Nevertheless, the epigenetic landscape that orchestrates this antiviral response remains largely elusive. Here, we identify histone demethylase JMJD2D as a critical regulator in defense against IAV infection. A significant upregulation of JMJD2D expression was observed clinically in response to IAV infection, indicating that JMJD2D may play a role in regulating IAV infection. Indeed, JMJD2D-deficient mice exhibit increased susceptibility to IAV, characterized by elevated viral loads, severe lung tissue damage, and reduced survival rates, suggesting that JMJD2D plays an essential role in defense against IAV infection. Consistently, knockdown or pharmacological inhibition of JMJD2D in lung cells suppressed IAV replication and the IAV-triggered innate immune response. Mechanistically, JMJD2D suppressed IAV infection by removing H3K9me3 at the promoter region of retinoic acid inducible gene-I (RIG-I) and cooperating with NF-κB to enhance the expression of RIG-I, a critical sensor for IAV RNA. This study identifies JMJD2D as an epigenetic rheostat that governs RIG-I-mediated antiviral signaling, highlighting its potential as a therapeutic target for mitigating severe IAV infection. Full article

Elaeocarpus sylvestris (Lour.) Poir., an evergreen tree native to East and Southeast Asia, has gained increasing scientific attention owing to its broad pharmacological properties. Traditionally used in East Asian medicine to treat inflammation, fever, and infectious diseases, modern research has revealed diverse bioactivities, including potent antioxidant, anti-inflammatory, antiviral, anticancer, antidiabetic, and immunomodulatory effects. This therapeutic potential is primarily attributed to its rich phytochemical composition, particularly polyphenols such as geraniin, 1,2,3,4,6-penta-O-galloyl-β-D-glucose and quercetin. This review particularly focuses on the chemistry of E. sylvestris, summarizing structurally elucidated compounds, including hydrolysable tannins, flavonoids, and triterpenoids, along with recent insights into the structure–activity relationships that underpin these antiviral, antioxidant, and anticancer activities. Recent studies have demonstrated substantial antiviral efficacy of E. sylvestris extracts and isolated compounds against major human pathogens, including herpesviruses, influenza A virus, and SARS-CoV-2, supported by in silico, in vitro, in vivo, and early-phase clinical evaluations. Its cosmeceutical applications, including antioxidant, skin-whitening, and blue-light protective effects, further highlight its multifunctional potential. To our knowledge, this is the first comprehensive review summarizing the phytochemistry, pharmacological activities, therapeutic potential, and cosmeceutical applications of E. sylvestris. Despite these promising findings, challenges remain in elucidating precise molecular mechanisms, pharmacokinetics, and clinical validation. This review identifies current research gaps and future directions necessary to advance E. sylvestris as a scientifically validated natural therapeutic resource. Full article

Seasonal influenza A evolves quickly through mutations in haemagglutinin (HA) and neuraminidase (NA), which can reduce vaccine match and lower protection. Many sequence-only models do not link codon-level mutations to three-dimensional (3D) protein context and long-term evolutionary signals within one scoring framework. This study presents TRIAD-Influenza (TRIAD: Token–Residue–Integrated Architecture for Drift), a multi-view transformer that combines (i) codon- and residue-level sequence representations, (ii) structure-derived residue interaction features from predicted HA/NA models, and (iii) an embedding-space phylogeny that captures cluster and drift context. The pipeline curates more than $3\times {10}^5$ paired HA/NA coding sequences from the NCBI Virus resource (2010–2024) using strict quality control and codon-aware alignment and predicts 3D structures for nearly all unique HA and NA proteins to build contact graphs and surface/stability descriptors. TRIAD-Influenza outputs a continuous, structure-aware risk score for each HA/NA pair and produces interpretable mutation hotspot maps using gradient saliency and a contact-weighted mutation risk index (CMRI). On rolling-origin temporal cross-validation and for a temporally held-out internal test window with strong class imbalance (∼3.4% high-risk), the model shows strong ranking performance (AUROC $\approx 0.89$; AUPRC $\approx 0.44$; Brier score $=0.069$) while operating at surveillance speed (median latency $\approx 1.6$ ms per HA/NA pair). External validation on independent GISAID/Nextstrain cohorts (2023–2024; 5000 isolates) preserves discrimination (AUROC $\approx 0.85$–$0.86$). Predicted risk scores correlate with experimental haemagglutination inhibition (HI) antigenic distances (Spearman $\rho$ up to ≈0.82 at the virus-aggregated level), and CMRI hotspots enrich known epitope and deep mutational scanning escape residues (odds ratios $\approx 2.7$–$3.6$). Overall, token–residue–phylogeny coupling enables rapid, structure-aware prioritisation of emerging influenza A HA/NA sequences and delivers compact hotspot maps for expert review and targeted experiments. Full article

Fufang Yinhua Jiedu Granules (FFYHG) is usually applied to treat influenza and the common cold. However, there is no available report concerning the effects of chemical constituents in FFYHG on antiviral activity. In our study, four new terpenoid derivatives (1–4) and seventeen known compounds were isolated from FFYHG. Their structures and absolute configurations were determined by various techniques, including high-resolution mass spectrometry analysis, 1/2-dimensional (1D/2D) nuclear magnetic resonance (NMR) analysis, comparative electronic circular dichroism (ECD) studies (experiment vs. calculation), and acid hydrolysis. In addition, the inhibitory effects of twenty-one isolated compounds against influenza A viruses (H1N1) including A/California/07/2009 (CA07) and A/WSN/1933 (WSN) strains were evaluated in vitro, and compound 4 exhibited a moderate inhibitory effect on CA07 strain, with a half maximal inhibitory concentration (IC₅₀) value of 37.10 ± 1.35 μM. This study enhanced the understanding of the active ingredients in FFYHG against influenza virus, providing a foundation for further research on the material basis and quality control of FFYHG. Full article

Background/Objectives: Influenza, RSV, and SARS-CoV-2 co-circulate and evolve under immune and therapeutic pressures, complicating decision-making for both vaccine formulation and antiviral use. Fragmented, pathogen-specific sequencing approaches limit cross-virus comparability. Methods: We applied a standardized, multiplexed, amplicon-based next-generation sequencing (NGS) workflow to 34 diagnostic specimens (Ct < 35) positive for influenza A/B, RSV-A/B, or SARS-CoV-2. Sequencing libraries were generated and run on an Illumina MiSeq platform (2 × 250 bp). Although the wet-lab workflow is standardized across pathogens, consensus generation and annotation utilized two different analysis environments: Geneious Prime for influenza and MicrobioChek for RSV and SARS-CoV-2. Quality metrics included genome breadth and depth of coverage. Results: Near-complete genomes (mean coverage ≥98%) were recovered for all samples. Influenza A(H1N1)pdm09 sequences clustered in clade 6B.1A; A(H3N2) clustered in subclade 3C.2a1b.2a.2; and influenza B belonged to the Victoria lineage V1A.3a.2. RSV sequences were assigned to Nextclade clades A.D.5.1, A.D.1.10, A.D.2.1, and A.D.3 (RSV-A) and to B.D.4.1.3 and B.D.E.1 (RSV-B), consistent with the ON1 (RSV-A) and BA (RSV-B) genotypes prevalent in recent seasons. Clinically relevant mutations included changes in the influenza HA site and neuraminidase substitutions, RSV F-protein polymorphisms, and spike protein substitutions associated with recent Omicron sublineages (L455F/S, F456L) in SARS-CoV-2. Conclusions: A unified amplicon–NGS approach yields harmonized genomic data across respiratory viruses, enabling timely detection of antigenic drift and resistance markers while supporting integrated, cross-pathogen surveillance. Full article

Background: Influenza B virus (IBV) undergoes continuous genetic mutations that can affect vaccine effectiveness and immune evasion. Although considerable research on IBV epidemiology exists globally, understanding of its genetic behavior in Saudi Arabia remains limited. This study characterized the molecular epidemiology of IBV in Riyadh, Saudi Arabia, during the 2024–2025 influenza season and evaluated compatibility with the current vaccine strain. Methods: Nasopharyngeal samples (n = 363) were collected from individuals presenting with influenza-like illness at King Khalid University Hospital in Riyadh. Detection and subtyping of IBV were performed using RT-PCR. Complete sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes was conducted on confirmed IBV isolates (n = 7), followed by phylogenetic analysis, amino acid substitution mapping, and glycosylation site prediction. Results: Of the 363 samples analyzed, 68 (18.7%) tested positive for IBV, with the majority occurring in adult females aged 15–64 years. Phylogenetic analysis revealed that all seven IBV isolates belonged to the Victoria lineage under subclade V1A.3a.2, corresponding to the current vaccine strain and strains from the 2022–2023 epidemic season. However, molecular analysis identified two substitutions (D129N and D197E) located in antigenic loop-150 and 190-helix, respectively, in the HA polypeptide that distinguished our strains from vaccine strain B/Austria/1359417/2021. Importantly, the N-glycosylation site at position 169 (NKT), which was present in B/Riyadh/1/2010, has been lost in the IBV strains circulating during 2020–2025. Conclusions: While phylogenetic clade compatibility indicates potential vaccine efficacy, the identified amino acid variations and loss of the glycosylation site underscore the necessity for ongoing molecular surveillance to monitor antigenic changes and evaluate vaccine effectiveness within the Saudi Arabian population. Full article

Zoonotic diseases account for approximately one billion cases of illness and millions of deaths globally each year. Increasing contact between humans and competent wildlife hosts elevates the risk of zoonotic spillover. Synanthropic bird species are key players in the transmission of zoonotic pathogens, including flaviviruses such as West Nile virus (WNV) and influenza A viruses like Avian Influenza Virus (AIV). Active surveillance of sentinel birds inhabiting urban areas allows for early detection of emerging pathogens before they cause zoonotic outbreaks. Despite nesting in close proximity to humans, the role of the house martin (Delichon urbicum) in the circulation of flaviviruses and AIV remains poorly understood. Here, we analyzed the presence of antibodies against flaviviruses and AIV in a colony of house martins from southwestern Spain. In addition, we aimed to detect amplicons of the matrix and nucleoprotein genes of AIV using RT-qPCR. While none of the samples tested positive for AIV by RT-qPCR, we observed an AIV seroprevalence of 2.13% based on non-subtyped ELISA. Notably, this is the first report of AIV-seropositive D. urbicum individuals captured in Spain. Moreover, we detected a flavivirus-group seroprevalence of 24.34%, similar to rates reported in the same house martin population between 2018 and 2020, suggesting widespread circulation of flaviviruses within this synanthropic species. These results support the hypothesis that house martins may participate in the transmission of these viruses between wild bird populations and humans in urban environments. Full article

Influenza A virus (IAV) infection constitutes a major public health threat. Severe influenza virus infection can induce intense inflammatory responses and lung injury, leading to serious clinical symptoms or even death. The utility of current anti-influenza drugs is often limited by side effects and the emergence of drug-resistant strains. Based on the critical role of L-type voltage-gated calcium channels (L-VGCCs) in influenza virus replication, this study investigates the antiviral activity and mechanism of verapamil, a classic L-type calcium channel antagonist, against H1N1-UI182 virus. Verapamil, an L-type calcium channel blocker, is widely used in the treatment of cardiovascular diseases and has a well-established safety profile. Through molecular dynamics (MD) simulation and network pharmacology analysis, we predicted the stable binding mode of verapamil to the target protein (PDB id: 6JPA) and its potential multi-target network. In vitro, verapamil exhibited antiviral activity against H1N1-UI182 in MDCK cells, enhancing the survival rate of infected cells and reducing viral nucleoprotein (NP) expression. In a lethal H1N1-UI182 infection mouse model, verapamil treatment markedly improved survival rates, alleviated weight loss and lung pathological damage, exhibiting a dose-dependent protective effect. Lung tissue analysis showed that verapamil effectively reduced the lung index and viral load, suppressed the activation of the Nuclear factor kappa B (NF-κB) signaling pathway, and decreased the expression of key inflammatory factors, thereby mitigating the cytokine storm. A comparison of administration regimens indicated that pre-treatment yielded optimal efficacy, suggesting verapamil acts primarily during the early stage of the viral life cycle. This study systematically elucidates that verapamil exerts antiviral and immunomodulatory effects by regulating the NF-κB pathway. Network pharmacology analysis suggested the potential involvement of multiple targets and pathways, including EGFR, SRC, and phospholipase D signaling, providing hypotheses for future mechanistic investigation. This paper supports a drug repurposing strategy against drug-resistant influenza viruses and highlights its significant potential for clinical translation. Full article

Background: Influenza A virus is an acute respiratory virus that spreads quickly, affects a broad range of populations, and can lead to many complications and mortality. Artemisia L. species are widely used in traditional medicine, but their antiviral potential against H1N1 remains uncertain. Methodology: Network pharmacology and molecular docking were used to computationally explore their potential function in this domain, and to investigate how their invasion mechanisms and adsorption occur. UPLC-MS/MS analysis identified the main components of the extracts. The anti-H1N1 mechanism of Artemisia L. extracts was studied in vitro. Results: Network pharmacology identified 95 key targets between Artemisia L. and IAV, with quercetin and luteolin as core active compounds. Molecular docking predicted strong binding affinities between these compounds and influenza virus proteins. UPLC-MS/MS analysis identified 75, 100, and 64 chemical components in ACBE, AALE, and ACTE, respectively, mainly flavonoids and terpenoids. Artemisia L. extracts exhibited both preventive and therapeutic effects against H1N1, reducing progeny virus NP mRNA and protein levels. In vitro experiments showed that higher concentrations of the extracts prevent virus attachment to MDCK cells by denaturing the HA protein. NA plays an essential role in progeny virus release. We found that a high concentration of ACTE can inhibit NA up to 85%, and ACBE showed a low inhibitory effect on NA. Conclusions: In terms of therapeutic effects, Artemisia L. extracts can regulate intracellular inflammatory factors via the TLR4/NF-κB/MyD88 signaling pathways and reduce the expression of IL-1β, IL-6, TNF-α, TLR4, NF-κB, p65, and MyD88 at the mRNA level, thereby inhibiting H1N1 virus replication. These results suggest that bioactive components in Artemisia L. extracts may inhibit H1N1, potentially leading to the development of natural-product-based anti-influenza agents. Full article

Influenza D virus (IDV) and co-circulating respiratory pathogens were investigated using RT-qPCR in 316 samples collected from 210 Spanish cattle farms with bovine respiratory disease (BRD) outbreaks between July 2023 and September 2024. Thirty-eight IDV-positive samples, from 30 farms across 15 provinces throughout Spain, were identified. IDV was significantly more frequent in bronchoalveolar lavage samples (22.1%) and nasal swabs (13.5%) compared to lung tissues (5%) and other sample mixtures (5%). All IDV-positive specimens exhibited co-infections, with most (94.7%) harboring three to seven viral and/or bacterial pathogens, highlighting the complexity of BRD outbreaks. Cramer’s V analysis revealed moderate IDV association with Mycoplasma bovis (V = 0.255) and Pasteurella multocida (V = 0.223), and a weaker IDV-bovine coronavirus association (V = 0.202), while IDV association with Histophilus somni (V = 0.025) and bovine herpesvirus 1 (V = 0.000) was negligible. Partial sequences of the hemagglutinin-esterase (HEF) gene from a subset of 13 IDV-positive samples (Ct < 32) were obtained. This confirmed the presence of the two major genetic lineages detected among cattle in Europe, D/OK and D/660, with D/660 exhibiting higher genetic diversity, as determined by DNAsp 6.12 software. This is the first report of IDV infection in Spanish cattle, confirming the circulation of the D/OK and D/660 lineages within the cattle population. Full article

Background: Adipose tissue surrounds organs and tissues in the body and can alter their function. It could secrete diverse biological molecules, including lipids, cytokines, hormones, and metabolites. In light of all this information, obesity can influence many tissues and organs in the body, and this situation makes obesity a central contributor to multiple disorders. It is very important to investigate the crosstalk between tissues and organs in the body to clarify the key mechanisms of obesity. Methods: In this study, we analyzed the gene expression profiles of the liver, skeletal muscle, blood, visceral, and subcutaneous adipose tissue. Differentially expressed genes (DEGs) were identified for each tissue, and functional enrichment and protein–protein interaction network analyses were performed on genes commonly identified across tissues. Priority candidate genes were identified using network-based centrality measures, and potential molecular intersection points were explored through host-pathogen interaction network analysis. This study provides an integrative framework for characterizing inter-tissue molecular patterns associated with obesity at the network level. Results: The muscle, subcutaneous adipose tissue, and blood have the highest number of DEGs. The subcutaneous adipose tissue and blood stand out due to the number of DEGs they possess, although liver and visceral adipose tissue have lower amounts. Cancer ranks first in terms of diseases associated with obesity, and this association is accompanied by leukemia, lymphoma, and gastric cancer. RPL15 and RBM39 are the top genes in both degree and betweenness metrics. The host–pathogen interaction network consists of 13 unique-host proteins, 54 unique-pathogen proteins, and 27 unique-pathogen organisms, and the Influenza A virus had the highest interaction. There were a small number of common metabolites in all tissues: 2-Oxoglutarate, Adenosine, Succinate, and D-mannose. Conclusions: In this study, we aimed to identify candidate molecules for obesity using an integrative approach, examining the gene profiles of different organs and tissues. The findings of this study suggest a possible link between obesity and immune-related biological processes. The network obtained from the host-pathogen interaction analysis, and especially the pathways associated with viral infections that stand out in the functional enrichment analysis, may overlap with molecular signatures linked to obesity. Furthermore, the co-occurrence of cytokine signaling, insulin, and glucose metabolism pathways in the enrichment results indicates that the response of cells to insulin may be affected in obese individuals, suggesting a potential interaction between immune and metabolic processes; however, further experimental validation is needed to reveal the direct functional effects of these relationships. Full article

Human adenoviruses (HAdVs) are globally distributed pathogens capable of causing a wide range of clinical manifestations, particularly acute respiratory infections. However, their genomic diversity remains insufficiently characterized, with substantial geographic gaps in available sequence data, including for Russia, where only a few complete genomes have been deposited prior to this work. In this study, we analyzed more than 1200 PCR-positive respiratory specimens collected from hospitalized patients within routine surveillance projects and the Global Influenza Hospital Surveillance Network (GIHSN) across plenty of Russian regions during 2023–2024. Virus isolation followed by next-generation sequencing yielded 128 complete HAdV genomes representing species B, C, and D. The dataset included 27 B3, 9 B7, 44 B55, 12 C1, 16 C2, 4 C5, 7 C89, 5 C108, and one D109 genome, as well as three unassigned recombinant viruses with p89h5f5, p5h6f6 and p5h57f6 genomic structures (p, penton base; h, hexon; f, fiber). Phylogenetic analyses of whole genomes and capsid genes revealed extensive variability in immunogenic regions, particularly in species C, and identified clusters within B3 viruses. Notably, HAdV-D109 was identified in Russia, marking only the second reported detection of this genotype worldwide. Together, these findings substantially expand the currently available genomic landscape of HAdVs, highlighting the circulation of diverse and recombinant strains in Russia. Full article