Search Results (1,364)

Equine sarcoid is the most common cutaneous neoplasm of equids and represents a distinctive model of virus-associated tumor persistence. Although bovine papillomaviruses, particularly BPV-1 and BPV-2, are recognized as the main etiological agents, viral infection alone does not fully explain the clinical heterogeneity, frequent recurrence, and limited spontaneous regression of these lesions. This review summarizes current evidence on the molecular and cellular mechanisms underlying equine sarcoid pathogenesis, with emphasis on the interaction between BPV infection, host signaling pathways, tumor microenvironment dynamics, and multi-omic evidence of host regulatory networks. BPV oncoproteins, especially E5, promote fibroblast transformation through PDGFβR activation, downstream PI3K/AKT, MAPK and p38 signaling, altered cell survival, and immune evasion mediated by impaired antigen presentation. However, sarcoid persistence appears to depend on broader host-driven processes, including extracellular matrix remodeling, activated fibroblastic and myofibroblastic phenotypes, chronic inflammatory signaling, and ineffective immune clearance. Recent transcriptomic and epigenomic studies further indicate that long non-coding RNAs, DNA methylation changes, circulating microRNAs, and recently identified virus–host chimeric transcripts may contribute to stabilization of the neoplastic phenotype and may represent future biomarkers. Overall, this review proposes a virus-initiated, host-sustained conceptual framework for equine sarcoid pathogenesis, in which viral oncogene activity and host tissue reprogramming cooperate to promote lesion persistence, recurrence, and therapeutic resistance. Full article

The red-spotted grouper nervous necrosis virus (RGNNV) exhibits high pathogenicity in larval C. sonnerati, yet the immune molecular mechanism remains unclear. Non-coding RNAs (ncRNAs) are vital in the host’s immune responses during viral infection. However, there has been no study on ncRNA research for this species to date. We systematically identified 105 DE microRNAs (miRNAs), 157 DE long non-coding RNAs (lncRNAs) and 31 DE circular RNAs between the infection group and control group. Functional enrichment analysis revealed that these differentially expressed genes were significantly enriched in pathways associated with innate immune defense, inflammatory, and cell death, such as JAK-STAT signaling pathway, NF-κB signaling pathway, apoptosis, and necroptosis. Furthermore, the lncRNA–miRNA–mRNA interaction network involving miR-93 was constructed, which may represent a promising candidate therapy target for future investigations. This study presents the first comprehensive ncRNA transcriptome dataset of C. sonnerati infected with RGNNV, identifies key antiviral defense and cell death-related genes and hub pathways, and thereby identifies miR-93-involved lncRNA–miRNA–mRNA network and key targeted genes (STAT1, TRIM25, UNC93B, IL12RB1, IRF8, CDKN1A, FCGR1A) as hub molecular regulators in immune response of this species. Full article

Fowl adenovirus serotype 4 (FAdV-4) is the major pathogen responsible for avian hepatitis–hydropericardium syndrome (HHS), which poses a severe threat to the global poultry industry. This study aimed to systematically explore virus–host interactions and elucidate the transcriptomic alterations and underlying molecular mechanisms in LMH cells following FAdV-4 infection. LMH cells were infected with FAdV-4 at a multiplicity of infection (MOI) of 1 for 24 h, and whole-transcriptome sequencing was subsequently performed. Differential expression analysis was conducted between the FAdV-4-infected group and the uninfected Mock group, followed by functional interaction prediction. Quantitative polymerase chain reaction (qPCR) was used to verify the expression profiles of differentially expressed genes (DEGs). The results identified a total of 8292 differentially expressed messenger RNAs (dif-mRNAs), 80 differentially expressed microRNAs (dif-miRNAs), 3263 differentially expressed long non-coding RNAs (dif-lncRNAs), and 52 differentially expressed circular RNAs (dif-circRNAs) in the infected group compared with the Mock group. The identified DEGs were further validated and subjected to Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Additionally, protein–protein interaction (PPI) analysis and regulatory network analyses of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were performed. This study provides novel insights and research perspectives into the potential mechanisms underlying FAdV-4–host interactions and further deepens the current understanding of the pathogenesis of FAdV-4 infection. Full article

Enterovirus A71 (EV-A71) and enterovirus D68 (EV-D68) are recognised as causative agents of severe neurological complications, including acute flaccid myelitis (AFM). However, the molecular mechanisms underlying the neurovirulence and effects on neuromuscular integrity remain poorly understood. Here, we employed human induced pluripotent stem cell-derived neuromuscular organoids (NMOs) to investigate the cellular tropism and pathogenic effects of EV-A71 and EV-D68 in a human-relevant context. Both viruses infected neuronal populations within NMOs, with EV-A71 exhibiting higher levels of viral replication than EV-D68. Transcriptomic analysis revealed downregulation of neuronal and muscular gene networks following infection. EV-A71 preferentially suppressed neuronal pathways, while both viruses exerted comparable effects on muscle-associated gene expression. These transcriptional changes highlighted alterations in pathways governing neuronal and muscle function and communication, prompting examination of synaptic vesicle machinery components. At the protein level, both viruses were associated with sporadic cleavage of the neuronal SNARE protein synaptosomal-associated protein 25 (SNAP25). In addition, infection with either virus increased cleaved caspase-3 levels, consistent with activation of apoptotic signalling. Together, these findings indicate virus-specific downstream effects and establish NMOs as a robust platform for dissecting enterovirus–host interactions relevant to AFM. Full article

Human papillomavirus type 16 (HPV16) is a major etiological agent of cervical and other epithelial cancers, yet the mechanisms underlying host–pathogen interactions remain incompletely understood. In this study, we investigated the responses of human peripheral blood leukocytes to engineered HPV16 L1/L2 chimeric virus-like particles (VLPs), produced in suspension by HEK 293-F cells. These VLPs were designed to mimic native viral structures while incorporating chimeric features that enhance stability and immunogenicity. Through experimental assays, we characterized leukocyte engagement, primarily involving leukocyte phenotyping, VLP internalization, confocal colocalization, and endocytic pathway analyses. We demonstrated that recombinant L1/L2 proteins assembled into structured VLPs capable of interacting with mononuclear cells, including lymphocytes and monocytes, but not with polymorphonuclear cells, such as neutrophils, eosinophils and basophils. Uptake occurred via the CD71 transferrin receptor-mediated pathway, in addition to other endocytic routes analyzed, as confirmed by blockage assays using chlorpromazine, rCTB, filipin, nystatin, liquemine, and sodium azide. Confocal colocalization and endocytic pathway analyses further supported receptor-mediated uptake. These findings demonstrate that HPV16 L1/L2 chimeric VLPs interact with and are internalized by human peripheral blood mononuclear cells through CD71-associated and other endocytic pathways. The study provides new insights into HPV16 VLP–leukocyte interactions and contributes to a better understanding of the cellular mechanisms involved in VLP uptake, which may be relevant for future studies on HPV biology and VLP-based vaccine development. Full article

Human skin is a complex organ whose functions depend on coordinated interactions between the epidermal and stromal layers. Reproducing this architecture in vitro remains challenging, as existing human models reproduce a restricted subset of the structural and functional features inherent to native tissue. Here, we describe a fibrin-based, multicellular human skin equivalent (HSE) composed of primary human keratinocytes, fibroblasts, preadipocytes, and endothelial cells organized into epidermal and stromal compartments. The resulting constructs achieved mature epidermal stratification with appropriate phenotypic markers, developed robust barrier properties, underwent spontaneous endothelial network assembly, and exhibited transcriptional profiles consistent with native skin. Optimized culture conditions supported long-term structural and functional stability through 42 days, maintaining a proliferative basal cell layer and intact epidermal architecture. Non-destructive optical coherence tomography enabled longitudinal monitoring of epidermal growth, providing a practical method for real-time quality assessment. To evaluate their utility for disease modeling, HSEs were challenged with cowpox virus to model infection by a classic dermotropic virus. Infected HSEs reproduced classic epithelial pathologies of human orthopoxvirus infection and exhibited dose-dependent suppression of host interferon signaling pathways, recapitulating known viral immune-evasion mechanisms. Together, these findings establish the vascularized, adipose-integrated HSE as a platform for long-term studies of human skin biology, host–pathogen dynamics, and therapeutic development. Full article

The intestinal barrier is a key interface maintaining host–microbial segregation and systemic homeostasis. A broad range of viruses, including enteric, respiratory, and systemic pathogens, can disrupt this barrier through effects on epithelial integrity, vesicular transport, immune responses, and microbial ecology. Whether these diverse insults converge on shared regulatory nodes or act through distinct virus-specific pathways that ultimately result in barrier failure remains unclear. Building on this premise, this review systematically delineates the molecular and cellular mechanisms underlying virus-induced disruption of the intestinal barrier. Viral infection disrupts epithelial integrity through multiple converging processes, including disassembly of tight junction architecture, activation of programmed cell death pathways, degradation of the mucus layer, impaired regeneration driven by intestinal stem cells, and dysregulation of transcellular transport. These processes are interconnected and collectively drive epithelial dysfunction and barrier breakdown. Beyond epithelial damage, we further highlight the pivotal contribution of host immune responses to barrier breakdown. Viral infection induces dysregulated cytokine production and aberrant immune activation, which amplify epithelial damage and further increase barrier permeability. In parallel, increasing evidence supports a bidirectional interaction between viral infection and gut microbiota dysbiosis, in which each process reinforces the other to accelerate barrier disruption and disease progression. We also discuss emerging therapeutic strategies aimed at restoring intestinal homeostasis, including antiviral therapies, host-targeted interventions, and microbiota modulation. Despite recent progress, key questions remain, particularly regarding mechanisms of failed barrier repair after viral clearance and the multilayered regulatory networks linking viruses, immunity, and the microbiota. Together, this review provides a framework for understanding virus-induced intestinal barrier dysfunction and identifies potential therapeutic nodes for intervention. Full article

The receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein remains a central target for antiviral drug development. Recent in silico studies have revealed an expansion of amyloidogenic regions within the RBD of the Omicron variant, raising the possibility that amyloid-prone peptide fragments could modulate Spike function or host–virus interactions. In this study, we combined experimental assays with multiscale computational modeling to systematically characterise two short RBD-derived peptides: Pep-2 (YFPLQSYGFQ) from the ancestral Wuhan strain and Pep-3 (YFPLRSYSFR) from the Omicron BA.1 variant, the latter being predicted to have higher amyloidogenic potential. Cell-based assays demonstrated that neither peptide exhibited intrinsic cytotoxic or cytostatic effects on human lung fibroblasts or A549 lung adenocarcinoma cells at physiologically relevant concentrations, whereas significant cytotoxicity was observed in Vero E6 cells. In infection models with the B.1.1.1 (Wuhan) and BA.1 (Omicron) variants, the peptides unexpectedly enhanced virus-induced cytopathic effects at lower concentrations but inhibited viral infection at higher concentrations, indicating to a dose-dependent modulatory role for these short amyloidogenic RBD fragments. Fluorescence spectroscopy measurements did not detect the formation of stable thioflavin-T-positive amyloid fibrils. Computational analyses revealed that both peptides interact with the Spike RBD via multiple energetically favorable yet spatially heterogeneous modes, mostly outside the ACE2-binding site. Moreover, their predicted binding affinities for the ACE2 receptor were comparable, suggesting an additional route of interaction via the host receptor. Collectively, our findings demonstrate that these short amyloidogenic RBD-derived peptides exert a complex antiviral profile, with their interactions with both viral and host factors potentially shaping infection outcomes. This highlights the importance of spatially targeted and conformationally constrained peptide designs to effectively harness amyloidogenic features for antiviral therapy. Full article

Orthoflaviviruses comprise genetically diverse mosquito-borne viruses responsible for a broad spectrum of human diseases. Although naturally circulating clinical isolates exhibit biological variability, the extent to which they generate distinct early epithelial innate immune responses remains incompletely understood. Here, we characterized five clinical orthoflavivirus isolates obtained in Oaxaca, Mexico, using human HaCaT keratinocytes as an in vitro model of early infection. Productive infection was assessed by immunofluorescence microscopy, immunostained focus appearance under isolate-optimized assay conditions, and infectious virus production, whereas host responses were evaluated by transcriptional profiling and quantitative whole-slide single-cell immunofluorescence. All isolates established productive infection and exhibited different viral replication profiles. Temporal transcriptional analyses revealed variable expression of antiviral (IFNβ, Mx1, OAS1, PKR, IFITM3, Viperin, and RANTES) and inflammatory (TNF-α, IL-8, and MCP-1) genes. Quantitative whole-slide analysis provided complementary evidence of variable STAT1 and NF-κB signaling activation across the analyzed isolates. Within this limited panel, viral replication was not consistently aligned with the selected transcriptional and signaling readouts, although the exploratory nature of these comparisons precludes establishing independence between these variables. Together, the virological, transcriptional, and imaging analyses revealed distinct multidimensional functional profiles across the isolate panel. Overall, these findings demonstrate functional heterogeneity among the analyzed clinical orthoflavivirus isolates and highlight integrated functional phenotyping as a useful framework for examining virus–host interactions beyond viral replication alone. Full article

Enterovirus alphacoxsackie (EV-A) is a highly diverse viral species containing at least 25 serotypes with diverse biological and clinical characteristics. EV-A can cause diseases ranging from asymptomatic infections to severe neurological disorders, as well as mucocutaneous diseases such as hand, foot, and mouth disease. 2A, a cysteine protease expressed by EV-A, plays critical roles in virus–host interactions. Although 2A orthologs of different EV-A serotypes share consistent protease-catalytic motifs and cleavage patterns, they show functional diversity in interacting with cellular proteins, probably due to distinct protease-independent activities determined by the single amino acid polymorphisms (SAPs) among different 2A orthologs. However, routine sequence alignment and phylogenetic analysis can hardly identify the key SAP sites (kSAPs) contributing to the functional variance, mainly due to the high conservation of the proteins and the unequal weight of SAPs in determining protein function. Herein, we developed Single Amino Acid Polymorphism Statistics (SAAPS), an information-entropy (IE)-based algorithmic pipeline, to identify the functional kSAPs of EV-A 2A. The core principle of the algorithm is that the IE of the kSAPs can be neither too low (highly conserved sites not leading to variance) nor too high (random neutral mutations). Using SAAPS, we identified 56 kSAPs from 2A of 25 EV-A serotypes. Based on the kSAPs, the 2As can be clustered into three major groups with a few outliers, which was distinct from the clustering generated by phylogenetic analysis using the whole amino acid sequences. Functional verification with transcriptomic profiles of HEK-293T cells expressing different 2A variants revealed closer alignment of kSAP clustering than phylogenetic clustering. Notably, EV-A89, an outlier identified by kSAP clustering but not phylogenetic clustering, showed a unique expression pattern with an altered shift in the molecular weight, which suggested that it was related to three SAPs identified by SAAPS. This study presents SAAPS as a useful tool for prioritizing functionally relevant SAPs to guide mechanistic discovery and can be applied to highly conserved proteins like EV-A 2A. Full article

Nipah virus (NiV) is a highly lethal zoonotic pathogen with significant pandemic potential, for which no approved antiviral therapies are currently available. Viral entry is mediated by the interaction between the NiV attachment glycoprotein (NiV-G) and host ephrin receptors, particularly ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3), making this interface an attractive therapeutic target. In this study, we evaluated a set of structurally related flavonoids, apigenin, cynaroside, and lonicerin, as potential modulators of the EFNB2–NiV-G and EFNB3–NiV-G interactions. These compounds were selected based on their structural similarity, reported antiviral activity, chemical diversity, and favorable drug-like properties. Apigenin was employed as a reference scaffold due to its well-characterized pharmacological profile and its suitability for guiding analog-based compound selection. Apigenin served as a reference scaffold for selecting structurally related flavonoids, which were analyzed through density functional theory optimization, molecular docking, pharmacokinetic and toxicity predictions, molecular dynamics simulations, and binding free energy calculations. These flavonoids demonstrated high predicted affinity for both the EFNB2–NiV-G and EFNB3–NiV-G interfaces. According to results, these compounds consistently interacted with residues known to play a critical role in receptor recognition, with special emphasis on leucine and tryptophan residues within the G–H loop. These residues are well established as key determinants in the entry process of Nipah virus (NiV) into host cells, highlighting the potential relevance of these flavonoid–protein interactions. Molecular dynamics analyses indicated that flavonoid binding reduced the affinity and the conformational flexibility at the receptor–glycoprotein interfaces and decreased the stability of the complexes. Pharmacokinetic and toxicity predictions suggested favorable drug-like properties for the flavonoids, with apigenin displaying the most balanced profile. Collectively, these results support the potential of selected flavonoids as modulators of EFNB2–NiV-G and EFNB3–NiV-G interactions and provide a rationale for their prioritization in experimental studies aimed at developing scaffolds for the modulation of viral entry against Nipah virus. Full article

Ubiquitination is a post-translational modification that governs various facets of eukaryotic biology, including protein stability, signaling, and immune regulation. The modification process is mediated by a coordinated enzymatic cascade, in which E3 ubiquitin ligases confer substrate specificity and determine the functional outcome of ubiquitin attachment. In the case of a virus infection, host cellular signaling networks undergo major ubiquitin-dependent changes to protect the host cell, including remodeling of cellular organelles, coordination of innate immunity, and reprogramming of metabolic pathways to prevent virus replication. African swine fever virus (ASFV) has evolved numerous strategies to counteract or evade these responses, thereby manipulating host defenses and promoting its replication. By modulating ubiquitination-dependent host cellular functions, the virus can regulate key immune signaling factors, suppress interferon production, and interfere with inflammatory pathways. These actions not only antagonize antiviral defenses but also remodel cellular homeostasis to favor infection. The important interplay between host defense and viral manipulation underscores the versatility of the ubiquitin system as a battleground in ASFV infection. In this review, we discussed mechanistic insights into how ASFV subverts ubiquitin pathways during host–virus interactions. This comprehensive knowledge might be beneficial for pharmaceutical exploration of host E3 ligase-dependent anti-ASFV treatment. Full article

The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. Coronaviruses are a diverse group of RNA viruses classified into alpha, beta, gamma, and delta genera, with SARS-CoV-2 belonging to the beta-coronavirus family. The virus exhibits high transmissibility and causes a wide spectrum of clinical manifestations ranging from mild respiratory symptoms to severe complications such as acute respiratory distress syndrome, multi-organ failure, and death, particularly among elderly and immunocompromised individuals. Structurally, SARS-CoV-2 possesses a large single-stranded RNA genome encoding major structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, which play critical roles in host-cell recognition and viral infection. Understanding the molecular mechanisms of virus–host interactions, especially protein–protein interactions (PPIs), is essential for uncovering viral pathogenesis and identifying potential therapeutic targets. Traditional experimental techniques for PPI detection, such as yeast two-hybrid and affinity purification methods, are often expensive, labor-intensive, and prone to inaccuracies. Consequently, computational approaches based on machine learning (ML) and deep learning (DL) have gained significant attention for efficient and scalable PPI prediction. These methods use diverse biological information, including protein sequences, structural features, genomic data, Gene Ontology annotations, and interaction networks, to model complex biological relationships. This survey reviews computational approaches to PPI prediction, highlighting ML- and DL-based techniques, methodological advances, performance evaluation practices, and limitations that affect benchmark comparability. It also discusses biological databases and data sources commonly used in PPI studies and explicitly considers how models trained in coronavirus-centered settings may generalize to other viral families with different mechanisms of host interaction. Full article

Bats are important reservoirs of zoonotic pathogens and valuable models for studying antiviral tolerance and neuroinflammation within a One Health framework. However, chiropteran neural 2D-in vitro models remain limited. Here, we established and characterized the first chiropteran primary (CpBCs) and immortalized (CiBCs) cell lines from Hypsugo savii species. To overcome the limited lifespan of CpBCs, immortalization strategies based on human telomerase reverse transcriptase (hTERT) and Simian virus 40 large T antigen (SV40) were evaluated. Electroporation-mediated transfection with SV40 successfully generated CiBCs, whereas liposome-mediated and hTERT-based approaches were unsuccessful. RNA sequencing revealed marked transcriptional changes comparing CiBCs with CpCBs, such as the upregulation of pathways related to cell cycle progression, DNA replication, and proliferation in CiBCs, together with the downregulation of apoptosis, inflammatory signaling, and immune-related pathways. Immortalized cells also exhibited enrichment of neural stem cell-like and cancer-associated signatures, suggesting partial dedifferentiation induced by SV40-mediated immortalization. Overall, this study provides a novel chiropteran brain-derived 2D-in vitro platform for investigating bat neurobiology, host–pathogen interactions, viral tolerance, and neurotropic infectious diseases relevant to emerging zoonoses. Full article

The COVID-19 pandemic highlighted the urgent need to develop effective and broad-spectrum antiviral therapies against coronaviruses. One strategy to address this concern is a combination therapy using repurposed drugs against zoonotic viruses with pandemic potential. We previously demonstrated that the combination of Remdesivir and Ivermectin is highly potent and synergistic in inhibiting the replication of murine hepatitis virus (MHV) in RAW264.7 macrophages. This study investigated the interactions between the drug combination, coronavirus and host by proteomics and RNA sequencing of MHV-infected H2.35 murine liver epithelial cells. Time-of-addition and time-of-removal assays suggested that the drug combination likely affected the synthesis of viral RNA and viral protein. This combination drastically diminished the live virus titer greater than the respective monotherapies in MHV-infected H2.35 cells (by ~4 log₁₀), as well as in SARS-CoV-2-infected VeroE6 cells and human nasal epithelial cells. Proteomic and transcriptomic analyses revealed that viral protein and RNA levels were significantly depressed upon combination treatment. The drug combination exhibited considerable negative effects upon host RNA processes and resulted in the upregulation of host protein processes (e.g., response to unfolded protein; protein insertion into ER membrane). Molecular pathways affected by the combination treatment were markedly distinct from the monotherapies and indicated that Ivermectin enhances Remdesivir by modulating critical host processes to synergistically exert its inhibitory effect on the coronavirus replication cycle. Full article