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Animals such as raccoon dogs, mink and muskrats are farmed for fur and are sometimes used as food or medicinal products1,2, yet they are also potential reservoirs of emerging pathogens3. Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues. Three subtypes of influenza A virus-H1N2, H5N6 and H6N2-were detected in the lungs of guinea pig, mink and muskrat, respectively. Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus4,5, were detected in guinea pigs. Raccoon dogs and mink carried the highest number of potentially high-risk viruses, while viruses from the Coronaviridae, Paramyxoviridae and Sedoreoviridae families commonly infected multiple hosts. These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses.

Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity.

Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate gradient enables scaling of sampling-based inference, namely Bayesian inference via Hamiltonian Monte Carlo, under random-effects substitution models across large trees and state-spaces. Applied to a dataset of 583 SARS-CoV-2 sequences, an HKY model with random-effects shows strong signals of nonreversibility in the substitution process, and posterior predictive model checks clearly show that it is a more adequate model than a reversible model. When analyzing the pattern of phylogeographic spread of 1441 influenza A virus (H3N2) sequences between 14 regions, a random-effects phylogeographic substitution model infers that air travel volume adequately predicts almost all dispersal rates. A random-effects state-dependent substitution model reveals no evidence for an effect of arboreality on the swimming mode in the tree frog subfamily Hylinae. Simulations reveal that random-effects substitution models can accommodate both negligible and radical departures from the underlying base substitution model. We show that our gradient-based inference approach is over an order of magnitude more time efficient than conventional approaches.

The M2 proton channel aids in the exit of mature influenza viral particles from the host plasma membrane through its ability to stabilize regions of high negative Gaussian curvature (NGC) that occur at the neck of budding virions. The channels are homo-tetramers that contain a cytoplasm-facing amphipathic helix (AH) that is necessary and sufficient for NGC generation; however, constructs containing the transmembrane spanning helix, which facilitates tetramerization, exhibit enhanced curvature generation. Here, we used all-atom molecular dynamics (MD) simulations to explore the conformational dynamics of M2 channels in lipid bilayers revealing that the AH is dynamic, quickly breaking the fourfold symmetry observed in most structures. Next, we carried out MD simulations with the protein restrained in four- and twofold symmetric conformations to determine the impact on the membrane shape. While each pattern was distinct, all configurations induced pronounced curvature in the outer leaflet, while conversely, the inner leaflets showed minimal curvature and significant lipid tilt around the AHs. The MD-generated profiles at the protein-membrane interface were then extracted and used as boundary conditions in a continuum elastic membrane model to calculate the membrane-bending energy of each conformation embedded in different membrane surfaces characteristic of a budding virus. The calculations show that all three M2 conformations are stabilized in inward-budding, concave spherical caps and destabilized in outward-budding, convex spherical caps, the latter reminiscent of a budding virus. One of the C2-broken symmetry conformations is stabilized by 4 kT in NGC surfaces with the minimum energy conformation occurring at a curvature corresponding to 33 nm radii. In total, our work provides atomistic insight into the curvature sensing capabilities of M2 channels and how enrichment in the nascent viral particle depends on protein shape and membrane geometry.

Birth-death models play a key role in phylodynamic analysis for their interpretation in terms of key epidemiological parameters. In particular, models with piecewise-constant rates varying at different epochs in time, to which we refer as episodic birth-death-sampling (EBDS) models, are valuable for their reflection of changing transmission dynamics over time. A challenge, however, that persists with current time-varying model inference procedures is their lack of computational efficiency. This limitation hinders the full utilization of these models in large-scale phylodynamic analyses, especially when dealing with high-dimensional parameter vectors that exhibit strong correlations. We present here a linear-time algorithm to compute the gradient of the birth-death model sampling density with respect to all time-varying parameters, and we implement this algorithm within a gradient-based Hamiltonian Monte Carlo (HMC) sampler to alleviate the computational burden of conducting inference under a wide variety of structures of, as well as priors for, EBDS processes. We assess this approach using three different real world data examples, including the HIV epidemic in Odesa, Ukraine, seasonal influenza A/H3N2 virus dynamics in New York state, America, and Ebola outbreak in West Africa. HMC sampling exhibits a substantial efficiency boost, delivering a 10- to 200-fold increase in minimum effective sample size per unit-time, in comparison to a Metropolis-Hastings-based approach. Additionally, we show the robustness of our implementation in both allowing for flexible prior choices and in modeling the transmission dynamics of various pathogens by accurately capturing the changing trend of viral effective reproductive number.

Aim: Backyard production systems (BPS) represent an interface of contact between people, domestic and wild animals. Studies conducted in Chile during the last decade have provided extensive evidence of influenza A virus (IAV) circulation in backyard poultry and swine. The aim of this study was to investigate exposure practices of humans to animal‐origin IAV within backyards. Methods and Results: Backyard farmers and household members of a total of 101 BPS in the proximity of wetlands located throughout Chile were interviewed between 2021 and 2022. Data were collected on the nature of human–animal contacts through participation in productive activities conducted within backyards, which was used to estimate participants' exposure risk to animal‐origin IAV. Additionally, RT‐qPCR and serologic IAV active surveillance was carried out in backyard animals. Multilinear regression was used to identify factors associated with exposure risk. Overall, IAV prevalence was 10.1% (95% CI: 4.7%–15.5%) and seroprevalence was 43.5% (95% CI: 29.7%–54.2%), both at the BPS level. Of 180 interviewees, 86% reported participating regularly in poultry or swine exposure activities within the backyard. A greater participation of male participants was observed when evaluating swine exposure activities, while female participation was greater for some activities related to poultry handling. Handwashing was a very extended hygiene practice; however, the use of personal protective equipment was uncommon. Different factors related to participants, households and backyards were associated with an increased exposure risk of participants to animal‐origin IAV: (i) older age, (ii) less years of education, (iii) no off‐farm work, (iv) greater backyard production value and (v) greater household consumption of backyard products. Conclusion: These results indicate the circulation of IAV in BPS and the frequent human–animal contact at this interface, highlighting the need for awareness campaigns and educational programmes aimed at backyard farmers on prevention and biosecurity measures in the management of backyard animals. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) are involved in the host antiviral response, but how host lncRNAs interact with viral proteins remains unclear. The NS1 protein of avian influenza viruses can affect the interferon-dependent expression of several host lncRNAs, but the exact mechanism is unknown. To further investigate the molecular mechanism and functions of NS1 proteins and host lncRNAs, we performed RNA-immunoprecipitation sequencing assays on A549 cells transfected with the H5N1-NS1 gene. We identified multiple sets of host lncRNAs that interact with NS1. The results of the RNA pulldown assay indicated that PIK3CD-AS2 can directly interact with NS1 in vitro. Immunofluorescence confocal microscopy showed that these proteins were colocalized in the nucleus. Further studies revealed that PIK3CD-AS2 can also inhibit the transcription of NS1, which in turn affects the translation of the NS1 protein. PIK3CD-AS2 overexpression regulates NS1 protein-induced cell cycle arrest and initiates apoptosis. We hope this work will help elucidate the molecular mechanisms associated with NS1 proteins in the study of viral infections to promote the development of potential treatments for patients infected with avian influenza A viruses. [ABSTRACT FROM AUTHOR]

Infection with Influenza A virus (IAV) induces severe inflammatory responses and lung injury, contributing significantly to mortality and morbidity rates. Alterations in the microbial composition of the lungs and intestinal tract resulting from infection could influence disease progression and treatment outcomes. Xiyanping (XYP) injection has demonstrated efficacy in clinical treatment across various viral infections. However, its specific effects and mechanisms against IAV remain unclear. In this study, we established an IAV infection mice model, and utilized 16 S rRNA sequencing, RNA sequencing, protein chips, and molecular docking, to investigate the mechanisms of XYP injection on altering pulmonary and gut microbiota, and identifying its target sites. We revealed that XYP injection significantly reduced mortality, weight loss, lung viral titers, and lung pathology in IAV-infected mice. XYP injection down-regulated the activity of malondialdehyde, and the levels of interleukin (IL)-1β, IL-5, IL-6, tumor necrosis factor-α, IL-18, IL-15, granulocyte colony-stimulating factor, IL-9, chemokine (C-C motif) ligand-5, and C-X-C motif chemokine ligand 5, while up-regulated the activities of glutathione peroxidase reactive and superoxide dismutase, and the level of interferon-γ. The diversity of the pulmonary and gut microbiota was altered slightly after XYP injection. The linear discriminant analysis of the gut microbes revealed a higher proportion of potentially beneficial bacteria, including Akkermansia, Parabacteroides goldsteinii, Defluviitaleaceae, Oscillospirales, and Eubacterium_coprostanoligenes_group characterized the XYP group. Peritoneal macrophage RNA sequencing highlighted Serpinb2 as the most significantly regulated gene by XYP injection, along with consistent changes in multiple downstream Th2 structure genes. KEGG pathway analysis indicated significant modifications in genes associated with influenza A, mitogen-activated protein kinase signaling, nuclear factor kappa-B signaling, and apoptosis following XYP injection. Finally, human protein chips and molecular docking were carried out to confirm the binding of the main component of XYP injection, andrographolide, with SERPINB2/PAI-2 protein. Overall, our study provides valuable insights into the therapeutic potential of XYP injection in treating influenza, highlighting its multifaceted effects on host microbiota and immune responses, and pinpointing SerpinB2/PAI-2 as the target for XYP injection in exerting anti-inflammatory and antiviral therapeutic mechanisms. [ABSTRACT FROM AUTHOR]

Background : Numerous studies have confirmed a close relationship between the pathogenicity of influenza and respiratory microbiota, but the mechanistic basis for this is poorly defined. Also, the majority of these studies have been conducted on murine models, and it remains unclear how far these findings can be extrapolated from murine models to other animals. Considering that influenza A virus is increasingly recognized as an important canine respiratory pathogen, this study investigated the cross-talk between nasal and lung tissues mediated by microbes and its association with influenza susceptibility in a beagle dog model. Results: Using 16S rRNA gene sequencing, combined with comparative transcriptomic, anatomical, and histological examinations, we investigated viral presence, gene expression profiles, and microbiota in the nasal cavity and lung after influenza infection in the beagles with antibiotic-induced nasal dysbiosis. Our data showed that dysbiosis of the nasal microbiome exacerbates influenza-induced respiratory disease and the epithelial barrier disruption, and impairs host antiviral responses in the nasal cavity and lung. Moreover, dysregulation of nasal microbiota exacerbates the influenza-induced disturbance in lung microbiota. Further, we also identified a strain of Lactobacillus plantarum isolated from canine nasal cavity with a significant antiviral effect in vitro, and found that its antiviral activity might be associated with the activation of the interferon (IFN) pathway and modulation of the impaired autophagy flux induced by influenza infection. Conclusions: Our investigation reveals that nasal microbiota dysbiosis exerts a prominent impact on host antiviral responses, inflammation thresholds, and mucosal barrier integrity during influenza infection. Lactobacilli, as part of the nasal microbiota, may contribute to host antiviral defenses by modulating the IFN and autophagy pathways. Collectively, this study underscores the importance of nasal microbiota homeostasis in maintaining respiratory health. ELb-wCzpDVSzGHyDeap6A8 Video Abstract [ABSTRACT FROM AUTHOR]

Influenza-related acute lung injury is a life-threatening condition primarily caused by uncontrolled replication of the influenza virus and intense proinflammatory responses. Cereblon (CRBN) is a protein known for its role in the ubiquitin-proteasome system and as a target of the drug thalidomide. However, the function of CRBN in influenza virus infection remains poorly understood. In this study, we investigated the impact of CRBN on A/Puerto Rico/8/34 (PR8) influenza virus-induced lung injury and its potential as a therapeutic target. Knocking down CRBN in vitro significantly reduces PR8-induced cell death. Using Sftpc-Cre; Crbnflox/flox lung-specific Crbn knockout mice, we demonstrated that Crbn deficiency significantly decreased mortality, weight loss, lung pathology, edema, and viral load in PR8-infected mice. PR8-infected Sftpc-Cre; Crbnflox/flox mice exhibited a marked reduction in lung inflammatory cell infiltration and suppression of MAPK pathway activation, highlighted by a significant downregulation of the MKK4-JNK-c-JUN signaling cascade. Collectively, these findings indicate that CRBN plays a pivotal role in the pathogenesis of influenza-induced lung injury by modulating MAPK pathway signaling, underscoring its therapeutic potential as a target for intervention. [ABSTRACT FROM AUTHOR]

One approach for developing a more universal influenza vaccine is to elicit strong immune responses against canonically immunosubdominant epitopes in the surface exposed viral glycoproteins. While standard vaccines typically induce responses directed primarily against mutable epitopes in the hemagglutinin (HA) head domain, there are generally limited or variable responses directed against epitopes in the relatively more conserved HA stalk domain and neuraminidase (NA) proteins. Here we describe a vaccine approach that utilizes a combination of wildtype (WT) influenza virus particles along with virus particles engineered to display a trimerized HA stalk in place of the full-length HA protein to elicit both responses simultaneously. After initially generating the "headless" HA-containing viral particles in the A/Hawaii/70/2019 (HI/19) genetic background and demonstrating the ability to elicit protective immune responses directed against the HA-stalk and NA, we co-formulated those virions with unmodified WT viral particles. The combination vaccine elicited "hybrid" and protective responses directed against the HA-head, HA-stalk, and NA proteins in both naïve and pre-immune mice and ferrets. Collectively, our results highlight a potentially generalizable method combining viral particles with differential antigenic compositions to elicit broader immune responses that may lead to more durable protection from influenza disease post-vaccination. Author summary: Influenza A virus infections remain a significant and persistent global challenge, as the viruses cause seasonal outbreaks and have pandemic-causing potential. Thus, improving the protection afforded by influenza vaccines is of high importance for human health. In this study we produced influenza viral particles that lack the classical immunodominant epitopes typically present in the head domain of the hemagglutinin (HA) protein. Vaccination with these modified virions allowed strong immune responses to develop against other protective viral epitopes, particularly within the relatively conserved HA stalk domain. We then showed that co-formulation of our engineered viral particles with unmodified virions allowed a "hybrid" vaccine response directed against all major viral epitopes of interest and provided protection from virally-induced disease. In ferrets with pre-existing influenza immunity, the experimental vaccine regimen also effectively elicited differential antibody profiles and allowed better control of infection in a heterologous viral challenge model. These data together suggest this approach has potential to serve as an improved, next-generation, influenza virus vaccine. [ABSTRACT FROM AUTHOR]

Influenza A virus (IAV) continuously threatens animal and public health globally, with swine serving as a crucial reservoir for viral reassortment and evolution. In Chile, H1N2 and H3N2 subtypes were introduced in the swine population before the H1N1 2009 pandemic, and the H1N1 was introduced from the H1N1pdm09 by successive reverse zoonotic events. Here, we report two novel introductions of IAV H3N2 human-origin in Chilean swine during 2023. Our study reveals a closer relationship between recent human seasonal H3N2 and novel swine strains. Interestingly, one strain maintains all the genes from the original human virus, but the other strain is already a reassortment of human H3N2 and an H1N2 previously observed on the farm. Observing global IAV sequences, a similar pattern was identified in the USA confirming the reverse zoonotic potential of current seasonal human H3N2 strains. These results highlight the importance of ongoing surveillance and reinforcing biosecurity in swine farms. These findings raise questions about their potential impact on viral dynamics in the swine population and public health, underscoring the need for further investigation into the origin and evolutionary dynamics of this emerging swine H3N2 reassortant virus. [ABSTRACT FROM AUTHOR]

CASK, a MAGUK family scaffold protein, regulates gene expression as a transcription co-activator in neurons. However, the mechanism of CASK nucleus translocation and the regulatory function of CASK in myeloid cells remains unclear. Here, we investigated its role in H5N1-infected macrophages. We found that H5N1 triggers CASK nuclear translocation via PKR and SRC signaling. HCK, a SRC family kinase, enhances CASK phosphorylation at S395 via CDK5, facilitating CASK's nuclear entry. Knocking out CASK in myeloid cells specifically reduces interferon-alpha (IFNA) production by hindering the nuclear export of Ifna mRNA, while leaving its mRNA levels unchanged. Myeloid-specific CASK knockout (KO) mice display exacerbated lung inflammation, which correlates with reduced IFNA levels during H5N1 infection. Interactome studies show that H5N1 triggers associations between CASK and CCT4, STIP1, and TNK1. These associations recruit IRF7, POLR2C, TAF15, HNRNPs, and CRM1, enabling the CASK complex to bind to the Ifna promoter, bind co-transcriptionally to Ifna mRNA, and facilitate CRM1-dependent Ifna mRNA export. This underscores CASK's critical role in the antiviral response. [ABSTRACT FROM AUTHOR]

Influenza A viruses have been a threat to human health for the past 100 years. Understanding the dynamics and pathogenicity of the influenza viruses in vivo is of great value in controlling the influenza pandemic. Fluorescent protein-carrying recombinant influenza virus is a substantially useful tool for studying viral characteristics in vivo and high-throughput screening in vitro. In this study, we generated a recombinant pdmH1N1 CA04 influenza virus carrying a Venus reporter gene in the non-structural (NS) segment using reverse genetics. After passaging the recombinant influenza virus carrying Venus from lung to lung in mice, we found that virulence of the passaged pdmH1N1 CA04-Venus significantly increased and was lethal to the mice. We finally isolated one mouse-adapted pdmH1N1 CA04-Venus with bigger plaques expressing the amount of Venus proteins by using the ninth passage lung homogenate with plague purification. We found three different amino acids (PB2 T340K, PA I21M, and F175L) between WT-CA04-Venus and MA-CA04-Venus using whole-genome sequencing. Interestingly, the polymerase activity of MA-CA04-Venus was significantly lower than that of WT-CA04-Venus in a minigenome assay. Further investigation demonstrates that PA I21M and PA I21M + PB2 T340K significantly enhanced the polymerase activity of WT-CA04-Venus; however, PA F175L + PB2 T340K significantly decreased the polymerase activity of MA-CA04-Venus. Therefore, PA I21M mutation may determine the increased virulence in mice, and PA F175L + PB2 T340K may be involved in the stability of Venus insertion. Above all, we generated a mouse-adapted pdmH1N1 CA04-Venus virus with high virulence and stable green fluorescent Venus protein. It is a useful tool for high-throughput screening of antiviral drugs and for investigating the interaction between the influenza virus and host in vivo. [ABSTRACT FROM AUTHOR]

Influenza A virus (IAV) is a significant public health concern, causing seasonal outbreaks and occasional pandemics. These outbreaks result from changes in the virus's surface proteins which include hemagglutinin and neuraminidase. Influenza A virus has a vast reservoir, including wild birds, pigs, horses, domestic and marine animals. It has over 130 subtypes based on differences in hemagglutinin and neuraminidase protein. IAV affects all age groups but impacts young children more especially during the colder season. Despite the development of vaccines and antiviral drugs, IAV is still a major cause of respiratory illnesses and deaths. Surveillance of IAV is crucial to detect new strains and assess vaccine effectiveness. Detection of IAV relies on methods like hemagglutination assay, PCR, cell culturing, and immunochromatography-based tests. Precise and early detection of IAV strain is crucial for quick treatment using antiviral drugs and unraveling epidemiological patterns to curb epidemics and pandemics on time. Advancements in diagnostic methodologies have enabled us to detect the IAV at early stages by overcoming the limitations of previously used diagnostic tests, further preparing us to combat future epidemics more effectively. This review article discusses the traditional and advanced diagnosis methods for detecting IAV. [ABSTRACT FROM AUTHOR]

Long non-coding RNAs (lncRNAs) are essential components of innate immunity, maintaining the functionality of immune systems that control virus infection. However, how lncRNAs engage immune responses during influenza A virus (IAV) infection remains unclear. Here, we show that lncRNA USP30-AS1 is up-regulated by infection of multiple different IAV subtypes and is required for tuning inflammatory and antiviral response in IAV infection. Genetically inactivation of USP30-AS1 enhances viral protein synthesis and viral growth. USP30-AS1 is an interferon-stimulated gene, and the induction of USP30-AS1 can be achieved by JAK-STAT mediated signaling activation. The immune regulation of USP30-AS1 is independent of its proximal protein-coding gene USP30. In IAV infection, deletion of USP30-AS1 unleashes high systemic inflammatory responses involving a broad range of pro-inflammatory factors, suggesting USP30-AS1 as a critical modulator of immune responses in IAV infection. Furthermore, we established a database providing well-annotated host gene expression profiles IAV infection or immune stimulation. Author summary: Influenza A virus (IAV) infection can induce differential expression of long non-coding RNAs (lncRNAs). However, the understanding of IAV induced lncRNAs that involve in host immune responses is limited. Here we identified that lncRNA USP30-AS1 was induced by multiple subtypes of IAV infection, serving as a critical regulator regarding IAV induced immune responses. Deletion of USP30-AS1 led to enhanced viral protein synthesis and elevated viral growth in IAV infection. JAK-STAT signaling activation can drive the transcription of USP30-AS1. USP30-AS1 does not exert function through the nearby partner protein-coding gene USP30. Deficiency of USP30-AS1 triggers unbalanced, elevated pro-inflammatory responses in IAV infected cells, indicating the role of USP30-AS1 as a modulator regarding immune response during IAV infection. We also provide a user-friendly database that allows access to well-annotated host gene expression profiles in influenza virus infection or interferon stimulation. [ABSTRACT FROM AUTHOR]

Respiratory viral infections continue to cause pandemic and epidemic outbreaks in humans and animals. Under steady-state conditions, alveolar macrophages (AlvMϕ) fulfill a multitude of tasks in order to maintain tissue homeostasis. Due to their anatomic localization within the deep lung, AlvMϕ are prone to detect and react to inhaled viruses and thus play a role in the early pathogenesis of several respiratory viral infections. Here, detection of viral pathogens causes diverse antiviral and proinflammatory reactions. This fact not only makes them promising research targets, but also suggests them as potential targets for therapeutic and prophylactic approaches. This review aims to give a comprehensive overview of the current knowledge about the role of AlvMϕ in respiratory viral infections of humans and animals. [ABSTRACT FROM AUTHOR]

Small nucleolar RNAs (snoRNAs) are non-coding RNAs (ncRNAs) that regulate many cellular processes. Changes in the profiles of cellular ncRNAs and those secreted in exosomes are observed during viral infection. In our study, we analysed differences in expression profiles of snoRNAs isolated from exosomes of influenza (IAV)-infected and non-infected MDCK cells using high-throughput sequencing. The analysis revealed 133 significantly differentially regulated snoRNAs (131 upregulated and 2 downregulated), including 93 SNORD, 38 SNORA, and 2 SCARNA. The most upregulated was SNORD58 (log2FoldChange = 9.61), while the only downregulated snoRNAs were SNORD3 (log2FC = −2.98) and SNORA74 (log2FC = −2.67). Several snoRNAs previously described as involved in viral infections were upregulated, including SNORD27, SNORD28, SNORD29, SNORD58, and SNORD44. In total, 533 interactors of dysregulated snoRNAs were identified using the RNAinter database with an assigned confidence score ≥ 0.25. The main groups of predicted interactors were transcription factors (TFs, 169 interactors) and RNA-binding proteins (RBPs, 130 interactors). Among the most important were pioneer TFs such as POU5F1, SOX2, CEBPB, and MYC, while in the RBP category, notable interactors included Polr2a, TNRC6A, IGF2BP3, and FMRP. Our results suggest that snoRNAs are involved in pro-viral activity, although follow-up studies including experimental validation would be beneficial. [ABSTRACT FROM AUTHOR]

Influenza A virus (IAV) remains a pandemic threat. Particularly, the evolution and increased interspecies and intercontinental transmission of avian IAV H5N1 subtype highlight the importance of continuously studying the IAV and identifying the determinants of its pathogenesis. Host innate antiviral response is the first line of defense against IAV infection, and the transcription factor, the signal transducer and activator of transcription 3 (STAT3), has emerged as a critical component of this response. Also, histone deacetylase 1 (HDAC1) and HDAC2 have been identified as important components of IAV-induced host innate antiviral response. Upon IAV infection, STAT3 is activated and translocated to the nucleus to initiate the transcription of innate response genes. Also, the HDAC1 and HDAC2 are localized to the nucleus. In this study, we sought to investigate the role of HDAC1 and HDAC2 in IAV-induced STAT3 nuclear translocation. We employed a quantitative confocal microscopy approach and analyzed the nuclear translocation of plasmid-expressed STAT3-GFP in IAV-infected cells depleted with the expression of HDAC1 or HDAC2. We found that the depletion of both HDAC1 and HDAC2 expression inhibits the IAV-induced nuclear translocation of STAT3-GFP. These findings will help elucidate the significance of the emerging role of acetylation in IAV infection and disease severity. [ABSTRACT FROM AUTHOR]

Disrupting the conserved multivalent binding of hemagglutinin (HA) on influenza A virus (IAV) to sialic acids (SAs) on the host cell membrane offers a robust strategy to block viral attachment and infection, irrespective of antigenic evolution or drug resistance. In this study, we exploit red blood cell‐derived small extracellular vesicles (RBC sEVs) as nanodecoys by harnessing their high abundance of surface‐displayed SAs to interact with IAV through multivalent HA‐SA interactions. This high‐avidity binding inhibits viral adhesion to the cell surface, effectively preventing both attachment and infection in a dose‐dependent manner. Notably, enzymatic removal of SAs from RBC sEVs significantly diminishes their anti‐IAV efficacy. Our findings indicate that RBC sEVs possess intrinsic anti‐IAV properties due to their native multivalent SAs and hold considerable promise as antiviral therapeutics. [ABSTRACT FROM AUTHOR]

Exploration of the hydroethanolic extracts from the halophyte Limonium densiflorum, led to the isolation of seven phenolic compounds: gallic acid, epigallocatechin gallate (EGCG), quercitrin, a mixture of myricetin 3-O-α-rhamnopyranoside + myricetin 3-O-L-arabinofuranoside, dihydrokaempferol, pinoresinol, and trans-N-ferulolyl tyramine. These compounds were assessed for anticancer, anti-influenza A virus, antioxidant, and anti-inflammatory properties. The results indicated that these compounds do not exhibit toxicity towards healthy cells (WS-1 and MDCK). Furthermore, they displayed strong antioxidant properties. Among these compounds, gallic acid, the mixture of myricetin 3-O-α-rhamnopyranoside + myricetin 3-O-L-arabinofuranoside, dihydrokaempferol, and pinoresinol, showed significant cytotoxicity against colon cancer cells (IC50: 1-39 µg/mL). EGCG, gallic acid, dihydrokaempferol, pinoresinol, and trans-N-ferulolyl tyramine demonstrated potent anti-inflammatory activity by reducing nitric oxide (NO) production and also inhibited the replication of the influenza A virus. Biological activities varied based on compound structure, with phenolic acids and flavonoid aglycones showing stronger effects than glycosylated compounds and lignans. [ABSTRACT FROM AUTHOR]

Targeting interactions between a virus and a host protein is one of the important approaches to developing antiviral therapies. We previously identified host nucleolin as a novel interacting partner of the influenza A virus nucleoprotein, and it was demonstrated that this interaction restricts virus replication. In the current study, we examined the interaction of nucleolin with the viral nucleoprotein at the domain and amino acid levels using in vitro and in silico approaches. Both approaches demonstrated a direct and specific interaction between these two proteins. Furthermore, it was observed that previous pandemic strains of influenza A virus had specific amino acid residues in their nucleoproteins that were predicted to be critical for interaction with nucleolin. This preliminary analysis provides insights into the binding process, which could be explored for developing antiviral strategies. [ABSTRACT FROM AUTHOR]

In March 2024, highly pathogenic avian influenza A(H5N1) virus, clade 2.3.4.4b, was detected in dairy cows in the United States, and at the same time in resident cats on affected farms. To help guide sample collection and diagnosis in cats, here we report the distribution of lesions and detection of H5N1 clade 2.3.4.4b influenza A virus (IAV) infection by PCR, immunohistochemistry (IHC), and serology in samples from 4 deceased and 2 living cats from 3 separate affected dairy farms. Although gross lesions were not diagnostic, histologically, all 4 deceased cats had nonsuppurative and necrotizing encephalitis and subtle interstitial pneumonia, and some also had significant myocarditis (3 of 4), chorioretinitis (2 of 4), and sialadenitis (1 of 2). The virus was detected by IHC in the aforementioned tissues, and by PCR in each brain (Ct = 9.9–25.1), lung (17.4–32.7), oropharyngeal swab (28.3–30.5), urine (30.3–34.4), and nasal swab (33.5–34.1) collected postmortem; fecal swabs were PCR-negative. In the antemortem samples, the virus was detected by PCR in the oropharyngeal swabs (34.1–36.1), whole-blood samples (30.8–36.6), and one serum sample (31.7). Seroconversion was detected in one cat. Our results support histologic evaluation of brain, lung, eyes, and heart, and PCR testing of brain and lung for postmortem diagnosis, and show that oropharyngeal swabs, urine, serum, and whole blood are suitable samples for antemortem detection of IAV infection in clinically affected cats. [ABSTRACT FROM AUTHOR]

Background: The Influenza A virus (IAV), a pathogen affecting the respiratory system, represents a major risk to public health worldwide. Immunization remains the foremost strategy to control the transmission of IAV. The virus has two primary antigens: hemagglutinin (HA) and neuraminidase (NA). Our previous studies have demonstrated that an IAV NA mRNA vaccine can induce Th1-type immune responses in mice. This research examined the immune responses elicited by an mRNA vaccine targeting both HA and NA antigens in murine models. Methods: In this study, we used two dual-antigen immunization strategies: single-site immunization with an IAV HA+NA mRNA vaccine and multi-site immunization with an IAV HA mRNA vaccine and IAV NA mRNA vaccine. Hemagglutination-inhibiting antibody titer and neutralizing antibody titer in the sera of immunized mice were evaluated, and a viral challenge experiment was conducted. Additionally, the immune responses elicited by the two immunization strategies were characterized using flow cytometry and ELISA. Comparative analyses were performed with mice immunized individually with the IAV HA mRNA vaccine, IAV NA mRNA vaccine, and inactivated vaccine. Results: The results showed that by using a multi-site immunization strategy, mice were able to generate higher levels of hemagglutination-inhibiting and neutralizing antibodies, and were protected in a viral challenge experiment. Moreover, the multi-site regimen also promoted the generation of cytotoxic T cells and maintained a balanced Th1/Th2 immune response. Conclusions: Using mRNA vaccine based on a HA and NA antigen with multi-site immunization strategy can induce higher levels of hemagglutination-inhibiting and neutralizing antibodies, and multi-type immune responses in mice, providing new theoretical and experimental support for advancing upcoming influenza vaccines. [ABSTRACT FROM AUTHOR]

Background/Objectives: An effective universal influenza vaccine is urgently needed to overcome the limitations of current seasonal influenza vaccines, which are ineffective against mismatched strains and unable to protect against pandemic influenza. Methods: In this study, bovine and human adenoviral vector-based vaccine platforms were utilized to express various combinations of antigens. These included the H5N1 hemagglutinin (HA) stem region or HA2, the extracellular domain of matrix protein 2 of influenza A virus, HA signal peptide (SP), trimerization domain, excretory peptide, and the autophagy-inducing peptide C5 (AIP-C5). The goal was to identify the optimal combination for enhanced immune responses and cross-protection. Mice were immunized using a prime-boost strategy with heterologous adenoviral (Ad) vectors. Results: The heterologous Ad vectors induced robust HA stem-specific humoral and cellular immune responses in the immunized mice. Among the tested combinations, Ad vectors expressing SP + HA stem + AIP-C5 conferred significant protection against group 1 (H1N1 and H5N1) and group 2 (H3N2) influenza A viruses. This protection was demonstrated by lower lung viral titers and reduced morbidity and mortality. Conclusions: The findings support further investigation of heterologous Ad vaccine platforms expressing SP + HA stem + AIP-C5. This combination shows promise as a potential universal influenza vaccine, providing broader protection against influenza A viruses. [ABSTRACT FROM AUTHOR]