Influenza Virus Neuraminidase Structure and Functions

Marked neurotropism and potential adaptation of H5N1 clade 2.3.4.4.b virus in naturally infected domestic cats

In April 2024, ten cats died in a rural South Dakota (SD) residence, showing respiratory and neurological symptoms. Necropsy and laboratory testing of two cats confirmed H5N1 clade 2.3.4.4b infection. The viral genome sequences are closely related to recent SD cattle H5N1 sequences. Cat H5N1 genomes had unique mutations, including T143A in haemagglutinin, known to affect infectivity and immune evasion, and two novel mutations in PA protein (F314L, L342Q) that may affect polymerase activity and virulence, suggesting potential virus adaptation. Dead cats showed systemic infection with lesions and viral antigens in multiple organs. Higher viral RNA and antigen in the brain indicated pronounced neurotropism. Lectin-histochemistry revealed widespread co-expression of sialic acid α-2,6 and α-2,3 receptors, suggesting cats could serve as mixing vessels for reassortment of avian and mammalian influenza viruses. No differences in clade 2.2 or 2.3.4.4b H5 pseudoviruses binding to cat lung/brain tissues indicated the neurotropism is unlikely mediated by receptor binding affinity.

A fluorometric and naked eye readable neuraminidase probe for influenza virus detection

Rapid diagnostic methods are crucial for effective influenza therapy and the prevention of flu pandemics. Neuraminidase (NA), a key protein on the surface of influenza virions, plays a vital role in the replication of the influenza virus (IV). Herein, we present SANP, a multimode NA-activatable fluorescent probe designed for rapid influenza detection and live-cell imaging. This probe demonstrated a high sensitivity with a limit of detection (LOD) of 15.4 mU/mL for NA and 2-2 hemagglutination units (0.25 HAU) for influenza virus samples. SANP also exhibited a LOD of 20 HAU (1 HAU) when detected influenza virus samples by the naked eye without the aid of equipment. Moreover, SANP facilitated real-time visualization of NA activity in influenza-infected cells through fluorescence imaging.

Systematic Comparison of Commercial Uranyl-Alternative Stains for Negative- and Positive-Staining Transmission Electron Microscopy of Organic Specimens

Negative- and positive-staining transmission electron microscopy (ns/psTEM) is a cornerstone of research and diagnostics, enabling nanometer-resolution analysis of organic specimens from nanoparticles to cells without requiring costly cryo-equipment. For nearly 70 years, uranyl salts like uranyl acetate (UA) have been the gold-standard ns/psTEM-stains. However, mounting safety concerns due to their high toxicity and radioactivity have led to stricter regulations and expensive licensing requirements. Consequently, there is an urgent global demand for safer, more sustainable stains that deliver uranyl-comparable, high-quality ns/psTEM. Here, the commercially available stain-alternatives UranyLess, UAR, UA-Zero, PTA, STAIN 77, Nano-W, NanoVan, and lead citrate are systematically assessed against UA. The stains are evaluated regarding their contrast, resolution, stain-distribution, and ease-of-use in ns/psTEM across a diverse sample set, including polymethylmethacrylate-nanoplastics, phosphatidylcholine-liposomes, Influenza-A viruses, globular ferritin, fibrillar pyruvate kinase amyloids, and human lung-carcinoma cell-sections. It is shown that for this variety of samples, a ready-to-use uranyl-alternative is commercially available with comparable or even superior ns/psTEM-performance to UA using an efficient staining-protocol. Furthermore, the GUIDE4U tool is developed for the fast identification of the appropriate uranyl-replacements for each sample of interest, saving ns/psTEM-users time and costs while ensuring excellent staining results for ultrastructural analysis, thereby further catalyzing the use of safer stains.

An intranasally administered IgM protects against antigenically distinct subtypes of influenza A viruses

Engineering broadly neutralizing monoclonal antibodies (mAbs) targeting the hemagglutinin (HA) of Influenza A virus (IAV) is a promising approach for intervention of seasonal flu. However, HA plasticity often leads to resistant strains that compromise mAb potency as bivalent IgGs. Here we hypothesize that multimerization of anti-IAV antibodies as IgMs can enhance coverage and neutralization potency. Here, we construct 18 IgM antibodies from known broadly neutralizing IgGs targeting different IAV HA epitopes and evaluate their breadth and potency of neutralization against distinct H1N1 and H3N2 IAVs. The IgM version of receptor binding site-specific IgG F045-092 shows increased breadth and antiviral potency compared to its parental IgG. Engineered IgM molecules overcome IAV strain resistance by expanded avidity, providing potent neutralization in vitro at sub-nanomolar ranges while retaining parental IgG specificity. Intranasal delivery of engineered IgM-F045-092 in female mice demonstrates efficient bio-retention in nasal cavities and lungs, offering protection against lethal doses of H1N1 and H3N2 IAV when administered prophylactically. Optimal epitope selection, trans-crosslinking, decavalent avidity, and intranasal administration contribute to the broader protection and potency of engineered IgM antibodies against diverse IAV subtypes.

Efficient discovery of frequently co-occurring mutations in a sequence database with matrix factorization

We have developed a robust method for efficiently tracking multiple co-occurring mutations in a sequence database. Evolution often hinges on the interaction of several mutations to produce significant phenotypic changes that lead to the proliferation of a variant. However, identifying numerous simultaneous mutations across a vast database of sequences poses a significant computational challenge. Our approach leverages a matrix factorization technique to automatically and efficiently pinpoint subsets of positions where co-mutations occur, appearing in a substantial number of sequences within the database. We validated our method using SARS-CoV-2 receptor-binding domains, comprising approximately seven hundred thousand sequences of the Spike protein, demonstrating superior performance compared to a reasonably exhaustive brute-force method. Furthermore, we explore the biological significance of the identified co-mutational positions (CMPs) and their potential impact on the virus's evolution and functionality, identifying key mutations in Delta and Omicron variants. This analysis underscores the significant role of identified CMPs in understanding the evolutionary trajectory. By tracking the "birth" and "death" of CMPs, we can elucidate the persistence and impact of specific groups of mutations across different viral strains, providing valuable insights into the virus' adaptability and thus, possibly aiding vaccine design strategies.

Glucosidase alpha neutral C promotes influenza virus replication by inhibiting proteosome-dependent degradation of hemagglutinin

The H7N9 influenza virus poses a significant threat to human health, and the mechanism by which it infects humans remains incompletely understood. Our investigation has unveiled significant insights into the role of glucosidase alpha, neutral C (GANC) gene in human H7N9 infections. Through whole genome sequencing (WGS), we identified five low-frequency functional and heterozygous variants of GANC strongly associated with human H7N9 infections compared to healthy controls. Furthermore, we observed a reduction in mRNA and protein expression of GANC following H7N9 virus infection in vitro and in vivo. Subsequent experiments involving GANC demonstrated the promotion of H7N9 virus replication in a stable strain with GANC overexpression. Conversely, GANC knockdown exhibited the ability to restrict influenza A virus (IAV) replication, including H7N9, H9N2, and H1N1, both in vitro and in vivo. This inhibition was mediated by GANC's ability to promote the degradation of H7N9 hemagglutinin (HA). Moreover, we discovered that GANC knockdown facilitated the degradation of HA in a proteasome-dependent manner. The inhibition caused by GANC knockdown was mediated by promoting direct binding of HA with the proteasome 26S subunit, non-ATPase, 1 (PSMD1) and PSMD2. All five variants in the GANC gene reduced their ability to promote H7N9 virus replication, and also diminished the levels of GANC-induced HA protein expression. Our findings revealed a novel mechanism by which GANC inhibits the proteasome-dependent degradation of HA to promote H7N9 virus replication. These results suggest that GANC may play an important role in IAV replication.

Molecular and ecological determinants of mammalian adaptability in avian influenza virus

The avian influenza virus (AIV) primarily affects birds and poses an increasing concern due to its growing adaptability to other hosts, heightening zoonotic risks. The adaptability is a key factor in AIV to infect multiple non-avian species, including humans, companion animals, aquatic mammals, carnivores, and other mammals. The virus is evolving through genetic mutations and reassortments, leading to the emergence of AIV strains with enhanced virulence and adaptability in mammals. This highlights the critical need to understand the genetic factors of AIV, including mutations in polymerase proteins, surface antigens, and other regulatory proteins, as well as the dynamics of AIV-host interactions and environmental factors such as temperature, humidity, water salinity, and pH that govern the cross-species adaptability of the virus. This review provides comprehensive insights into the molecular/genetic changes AIV undergoes to adapt in mammalian hosts including bovines, swine, equines, canines, and felines. The adaptive mutations in viral polymerase proteins, such as PB2-E627K, and receptor specificity shift facilitate the virus adaptability in mammals. Since AIVs interact with specific receptors on host cells, therefore the type and distribution of receptors are crucial in determining the host range of the virus and its adaptability by facilitating attachment and entry of the virus. This review examines sialic acid receptor distribution and binding patterns in various mammalian hosts, emphasizing how the presence and structure of specific receptors influence viral interaction, adaptation, and transmission. The review concludes that the differential distribution and expression of SA receptors are vital in the mammalian adaptability and tissue tropism of viral strains. Notably, during the adaptation to mammals, AIVs show a shift in preference from α-2,3 to α-2,6 receptors. This review further emphasizes the role of ecological determinants in the adaptation of viruses to mammalian hosts. Low temperatures, high humidity, and neutral to slightly acidic pH levels enhance virus stability, facilitating its persistence in the environment and spread among susceptible hosts. Overall, AIV remains a global health threat, necessitating coordinated efforts in research, surveillance, and public health strategies.

RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry

The composition and organization of the cell surface determine how cells interact with their environment. Traditionally, glycosylated transmembrane proteins were thought to be the major constituents of the external surface of the plasma membrane. Here, we provide evidence that a group of RNA-binding proteins (RBPs) is present on the surface of living cells. These cell-surface RBPs (csRBPs) precisely organize into well-defined nanoclusters enriched for multiple RBPs and glycoRNAs, and their clustering can be disrupted by extracellular RNase addition. These glycoRNA-csRBP clusters further serve as sites of cell-surface interaction for the cell-penetrating peptide trans-activator of transcription (TAT). Removal of RNA from the cell surface, or loss of RNA-binding activity by TAT, causes defects in TAT cell internalization. Together, we provide evidence of an expanded view of the cell surface by positioning glycoRNA-csRBP clusters as a regulator of communication between cells and the extracellular environment.

Emergence, migration and spreading of the high pathogenicity avian influenza virus H5NX of the Gs/Gd lineage into America

The high pathogenicity avian influenza virus H5N1, which first emerged in the winter of 2021, has resulted in multiple outbreaks across the American continent through the summer of 2023 and they continue based on early 2025 records, presenting significant challenges for global health and food security. The viruses causing the outbreaks belong to clade 2.3.4.4b, which are descendants of the lineage A/Goose/Guangdong/1/1996 (Gs/Gd) through genetic reassortments with several low pathogenicity avian influenza viruses present in populations of Anseriformes and Charadriiformes orders. This review addresses these issues by thoroughly analysing available epidemiological databases and specialized literature reviews. This project explores the mechanisms behind the resurgence of the H5N1 virus. It provides a comprehensive overview of the origin, timeline and factors contributing to its prevalence among wild bird populations on the American continent.

Identification of Novel Neuraminidase Inhibitors as Potential Anti-Influenza Agents: Virtual Screening, Molecular Docking, in vitro Validation and Molecular Dynamic Simulation Studies

The influenza virus causes approximately hundreds of thousands of deaths annually. Coupled with the emergence of drug resistance, there is an urgent need to develop new drugs for the treatment of influenza. Neuraminidase (NA) has long been recognized as a valid drug target for anti-influenza therapy. Herein, in order to identify potential NA inhibitors with novel structures, we employed a structure-based virtual screening strategy to screen a library containing 1.6 million compounds. Based on XP docking score and free energy calculation results, the three compounds E570-1769, K788-4718, and C071-0424 were selected that may have better binding affinity for the NA protein compared to oseltamivir. Amongst, E570-1769 was identified to be the most potential hit. Docking study showed that E570-1769 bound to NA with a binding energy of -10.3 kcal/mol. Moreover, in silico ADME/T studies demonstrated the druggability of E570-1769 was quite well. Furthermore, in vitro assay demonstrated that E570-1769 inhibited the wild-type and H274Y-muatated NAs with IC50 values of 72.6 μM and 229 μM, respectively. Additionally, molecular dynamic (MD) simulation studies were performed to gain a deep insight into the binding modes of E570-1769 in complex with NA. While less potent than oseltamivir, the novel structure of E570-1769 and promising ADME/T properties indicates it as a promising lead for future research.

Sustained Vaccine Exposure Elicits More Rapid, Consistent, and Broad Humoral Immune Responses to Multivalent Influenza Vaccines

With the ever-present threat of pandemics, it is imperative vaccine technologies eliciting broad and durable immunity to high-risk pathogens are developed. Yet, current annual influenza vaccines, for example, fail to provide robust immunity against the 3-4 homologous strains they contain, let alone heterologous strains. Herein, this study demonstrates that sustained delivery of multivalent influenza vaccines from an injectable polymer-nanoparticle (PNP) hydrogel technology induces more rapid, consistent, and potent humoral immune responses against multiple homologous viruses, as well as potent responses against heterologous viruses and potential pandemic subtypes H5N1, H7N9 and H9N2. Further, admixing PNP hydrogels with commercial influenza vaccines results in stronger hemagglutination inhibition against both heterologous and homologous viruses. Additional investigation shows this enhanced potency and breadth arise from higher affinity antibodies targeting both the hemagglutinin stem and head. Overall, this simple and effective sustained delivery platform for multivalent annual influenza vaccines generates durable, potent, and remarkably broad immunity to influenza.

Structural mapping of polyclonal IgG responses to HA after influenza virus vaccination or infection

Cellular and molecular characterization of immune responses elicited by influenza virus infection and seasonal vaccination have informed efforts to improve vaccine efficacy, breadth, and longevity. Here, we use negative stain electron microscopy polyclonal epitope mapping (nsEMPEM) to structurally characterize the humoral IgG antibody responses to hemagglutinin (HA) from human patients vaccinated with a seasonal quadrivalent flu vaccine or infected with influenza A viruses. Our data show that both vaccinated and infected patients had humoral IgGs targeting highly conserved regions on both H1 and H3 subtype HAs, including the stem and anchor, which are targets for universal influenza vaccine design. Responses against H1 predominantly targeted the central stem epitope in infected patients and vaccinated donors, whereas head epitopes were more prominently targeted on H3. Responses against H3 were less abundant, but a greater diversity of H3 epitopes were targeted relative to H1. While our analysis is limited by sample size, on average, vaccinated donors responded to a greater diversity of epitopes on both H1 and H3 than infected patients. These data establish a baseline for assessing polyclonal antibody responses in vaccination and infection, providing a context for future vaccine trials and emphasizing the need for further characterization of protective responses toward conserved epitopes. (201 words)IMPORTANCESeasonal influenza viruses cause hundreds of thousands of deaths each year and up to a billion infections; under the proper circumstances, influenza A viruses with pandemic potential could threaten the lives of millions more. The variable efficacies of traditional influenza virus vaccines and the desire to prevent pandemic influenzas have motivated work toward finding a universal flu vaccine. Many promising universal flu vaccine candidates currently focus on guiding immune responses to highly conserved epitopes on the central stem of the influenza hemagglutinin viral fusion protein. To support the further development of these stem-targeting vaccine candidates, in this study, we use negative stain electron microscopy to assess the prevalence of central stem-targeting antibodies in individuals who were exposed to influenza antigens through traditional vaccination and/or natural infection during the 2018-2019 flu season.

Native Capillary Nanogel Electrophoresis Assay of Inhibitors of Neuraminidases Derived from H1N1 and H5N1 Influenza A Pandemics

Tetrameric neuraminidases cleave the end-capping sialylated monomer from oligosaccharide ligands at the surface of a host cell infected by the influenza A virus. This cleavage releases the replicated virions from the host cell, making drugs that inhibit neuraminidase function effective to treat influenza A infections. A capillary electrophoresis separation-based assay is reported that maintains the native structure of tetrameric viral neuraminidases derived from H1N1 or H5N1 influenza A pandemics which convert, in-real time, a substrate that mimics 6'-sialyllated threonine-linked glycans on human cells. The assay integrates the enzyme reaction with the separation and is operated using a background electrolyte containing 100 mM NaCl with a thermally reversible nanogel in a 10 μm inner diameter fused silica capillary. In addition to defining the 0.4 nL reaction zone maintained at 37 °C, the nanogel medium resolves the substrate from contaminants as well as the substrate from the product before and after the enzymatic conversion. The enzyme activity is quantifiable based on the percent conversion observed in the presence of a range of inhibitor concentrations. For 1918 H1N1 (A/Brevig Mission/1/18) neuraminidase, the inhibition constant of the transition state analog 2,3-dehydro-2-deoxy-N-acetylneuraminic acid (DANA) is 3.5 ± 0.8 μM (n = 5). The inhibition constants for oseltamivir acid (inhibiting compound of Tamiflu) and peramivir (Rapivab) are 18.2 ± 0.5 nM (n = 3) and 67 ± 8 nM (n = 3), respectively. For 2004 H5N1 (A/Vietnam/1203/2004) neuraminidase, which contained a foreign tetramerization domain to maintain the structure, the inhibition constant for peramivir is 5.4 nM.

Influenza Neuraminidase Virus-Like Particle-Based Nanocarriers as a New Platform for the Delivery of Small-Peptide Antigens

A new and simple platform to produce a nanocarrier for small-peptide antigen delivery was developed. Virus-like particles (VLPs) were of interest due to their good cell-penetrating properties and ability to protect target molecules from degradation. In this study, the VLP that was entirely formed by influenza neuraminidase (NA), NA-VLPs, was employed. The platform construction includes the genetic engineering of target peptides into the NA structure immediately above its stalk, at the bottom of the NA head, by an overlap extension PCR. The resulting chimeric gene is next expressed in stably transformed insect cells. The recombinant NA protein produced by the insect cells is then naturally assembled into the NA-VLPs that display those peptides on their surfaces. For the platform demonstration, Angiotensin II (AngII) octapeptide hormones that raise blood pressure were chosen as a model peptide antigen. The NA-VLPs displaying AngII peptides were successfully produced by the stably transformed insect cells. The AngII octapeptides were successfully delivered by the NA-AngII VLPs as the anti-AngII antibodies were raised in hypertensive rats. The antibodies effectively neutralized the AngII peptide hormone in these rats, as demonstrated by the decrease in systolic blood pressure of the immunized rats. Thus, NA-VLP nanocarriers represent a promising platform for delivering small-peptide antigens to stimulate antibody production.

1H-NMR and molecular networking-guided dereplication of phloroglucinol meroterpenoids from Cleistocalyx operculatus buds as neuraminidase inhibitors

A dereplication strategy guided by 1H-NMR and molecular networking resulted in the isolation of two unusual phloroglucinols [(±)-1 and (±)-2], which possess a rare decahydro-2H-cyclopenta[i]chromene skeleton, along with five undescribed phloroglucinol meroterpenoids [(±)-3-(±)-7] from the buds of Cleistocalyx operculatus. The chemical structures of isolated compounds were determined by 1D and 2D NMR spectroscopy, ECD, X-ray crystallography, and DP4+ probability calculations. Compounds (±)-1-(±)-7 were naturally found as enantiomeric pairs, which were successfully separated using chiral phase HPLC. Structural analysis of these compounds suggested a plausible biosynthetic pathway, involving the late-stage incorporation of acetoacetyl-CoA into the 2,2,4-trimethylcinnamyl-β-triketone core, followed by a series of functionalization steps leading to compounds (±)-1-(±)-4. Compounds (±)-1 and (±)-2 exhibited moderate neuraminidase inhibitory activity against neuraminidase enzymes from both H1N1 and H9N2 influenza strains. Kinetic experiments suggested a non-competitive binding mechanism for compound (±)-1.

Integrative computational analysis of anti-influenza potential in Caesalpinia mimosoides Lamk hydroethanolic extract

In a recent study, we used chemical analysis to show that the Caesalpinia mimosoides aqueous extract, which contains a high concentration of simple phenolics, has strong anti-influenza activity. We determined through molecular docking methods that its potential target inhibitor is the neuraminidase. Therefore, our study objectives were to evaluate whether the aqueous-ethanol extract (30% v/v) of this plant species exhibits greater antiviral activity than the aqueous plant extract. The C. mimosoides hydroethanolic extract exhibited potent antioxidant activity in the DPPH assay, with an IC50 value of 15.01 µg/mL, comparable to authentic quercetin (IC50 = 12.72 µg/mL) and approximately 4.91 times greater than standard gallic acid (IC50 = 3.06 µg/mL). Through untargeted metabolomic analyses (UPLC-ESI(±)-QTOF-MS/MS) and subsequent stepwise computational metabolomics analyses, we identified the extract as primarily containing simple phenolics (e.g., gallic acid, ellagic acid, shikimic acid, and chlorogenic acid), flavonoid derivatives (e.g., quercetin, taxifolin, myricitrin, and afzelin), and other bioactive components, including dicarboxylic acids and germacrone. The polyphenol-rich extract showed strong anti-influenza activity, with an IC50 of 2.33 µg/mL against the influenza A/PR/8/34 virus and no cytotoxic effects, as indicated by a CC50 greater than 50 µg/mL. This represents an approximately 3.35-fold increase in effectiveness compared to its corresponding aqueous extract (IC50 = 7.81 µg/mL). Furthermore, the extract demonstrated no hemolytic activity, even at a maximum concentration of 2,000 µg/mL, suggesting its potential as a safe antiviral agent. Molecular docking analyses revealed that the identified phytochemicals can simultaneously interact with the "drug-target binding sites" of neuraminidase (NA) and PB2 subunit of influenza RNA polymerase, indicating their potential polypharmacological effects. The antiviral activity of the ethanolic-aqueous extract against other strains is being explored due to the versatile biological effects of phenolic substances.

Genetic characterization of influenza B virus and oseltamivir resistance in pediatric patients with acute respiratory infections: a cross-sectional study

Influenza virus neuraminidase inhibitors (NAIs) drug usage can result in NAI resistance, especially in children and individuals with weakened immune systems. The aim of the present study was to identify NAI-resistant variants of IBV and to introduce probable novel mutations, phylogenetic study, and its epitope mapping based on NA gene in patients from Shiraz, Iran. A cross-sectional study was conducted between 2017 and 2018 on symptomatic children. A real-time PCR was run for IBV screening. Then, making use of direct sequencing, amplified 1401 bases of NA gene and phylogenetic tree reconstructed. Epitopes were predicted using ABCpred server. From among a total of 235 specimens, 9.7% were identified with IBV infection. Of them, sequence of NA gene for 17 isolates were analyzed. Phylogenetic analysis showed that 15 isolates belonged to Yamagata clade 3 Wisconsin/01-like subclade and 2 were related to Victoria clade 1 Brisbane/60-like subclade (Vic-1A-2). NA gene sequence analysis showed a total of 52 substitutions in which 27 were for BVic and 37 were for BYam isolates and 19 were novel substitutions. Only one substitution (S198N) was found in NA active site and T49M, I120V, N198S, N219K, S295R, D320K N340D, E358K, D384G, and D463N were found as probable resistance variants to NAIs. Epitope mapping showed some major differences in our isolates NA gene. Present study was one of the rare comprehensive studies conducted in Shiraz/Iran on IBV resistant associated variants to NAIs. We reported 11.7% mutation in NA active site and some probable NAIs resistant mutations. Epitope mapping confirmed major changes in NA gene which needs broader studies to confirm.

Identification of a broad-inhibition influenza neuraminidase antibody from pre-existing memory B cells

Identifying broadly reactive B precursor cells and conserved epitopes is crucial for developing a universal flu vaccine. In this study, using influenza neuraminidase (NA) mutant probes, we find that human pre-existing NA-specific memory B cells (MBCs) account for ∼0.25% of total MBCs, which are heterogeneous and dominated by class-unswitched MBCs. In addition, we identify three NA broad-inhibition monoclonal antibodies (mAbs) (BImAbs) that block the activity of NA derived from different influenza strains, including the recent cow H5N1. The cryoelectron microscopy (cryo-EM) structure shows that the BImAb targets the conserved NA enzymatic pocket and a separate epitope in the neighboring NA monomer. Furthermore, the NA BImAbs protect mice from the lethal challenge of the human pandemic H1N1 and H5N1. Our work demonstrates that the NA broad-inhibition precursor MBCs exist in healthy adults and could be targeted by the NA-based universal flu vaccine.

Hemagglutinin 3 and 8 can be the most efficient influenza subtypes for human host invasion; a comparative in silico approach

The severity of the influenza virus infection is largely determined by its ability to invade the human host receptor. This critical step is conducted by utilizing hemagglutinin (HA) due to its binding with sialic acid 2,6 (SA). Though 18 subtypes (H1-H18) of HA have been identified, the most efficient one for conducting the host entry has not yet been resolved. This study aims to assess the severity of infections for HA variants by conducting a comparative docking of H1-H18 with the human SA receptor. Eighteen viral 3D structures were retrieved, minimized, and optimized for docking with human SA. In all retrieved structures, five conserved amino acid residues were selected for docking with human SA. Special protein grids were prepared by locating these five residues in the 18 selected subtypes. Results showed that H3 and H8 exerted the highest standard precision and extra precision docking scores, and the highest binding affinities with the human SA, respectively. Phylogenetic analyses confirmed the actual positioning of the selected 3D structures and showed these docked structures belonged to their usual classes due to the extremely close distances found in each docked subtype compared with its corresponding non-docked structures. H8-SA showed slightly better RMSD and SASA values than H3-SA, while H3-SIA showed more favourable radius of gyration scores than H8-SIA in the majority of the simulation period. Due to the highest affinity of binding of H3 and H8 with the human receptor, special caution should be exercised regarding any possible outbreak mediated by these subtypes in human populations. However, it is important to acknowledge a limitation inherent to the computational approach; it may hold relative rather than absolute significance. Further research is needed to deepen our understanding of the intricate interplay between HA variants and the host receptor, taking into account the broader context of viral infection dynamics.Communicated by Ramaswamy H. Sarma.

Formulation development of a stable influenza recombinant neuraminidase vaccine candidate

Current influenza vaccines could be augmented by including recombinant neuraminidase (rNA) protein antigen to broaden protective immunity and improve efficacy. Toward this goal, we investigated formulation conditions to optimize rNA physicochemical stability. When rNA in sodium phosphate saline buffer (NaPBS) was frozen and thawed (F/T), the tetrameric structure transitioned from a "closed" to an "open" conformation, negatively impacting functional activity. Hydrogen deuterium exchange experiments identified differences in anchorage binding sites at the base of the open tetramer, offering a structural mechanistic explanation for the change in conformation and decreased functional activity. Change to the open configuration was triggered by the combined stresses of acidic pH and F/T. The desired closed conformation was preserved in a potassium phosphate buffer (KP), minimizing pH drop upon freezing and including 10% sucrose to control F/T stress. Stability was further evaluated in thermal stress studies where changes in conformation were readily detected by ELISA and size exclusion chromatography (SEC). Both tests were suitable indicators of stability and antigenicity and considered potential critical quality attributes (pCQAs). To understand longer-term stability, the pCQA profiles from thermally stressed rNA at 6 months were modeled to predict stability of at least 24-months at 5°C storage. In summary, a desired rNA closed tetramer was maintained by formulation selection and monitoring of pCQAs to produce a stable rNA vaccine candidate. The study highlights the importance of understanding and controlling vaccine protein structural and functional integrity.

COBRA N2 NA vaccines induce protective immune responses against influenza viral infection

Influenza neuraminidase (NA) is a promising target for a broadly protective vaccine. In this study, the Computationally Optimized Broadly Reactive Antigen (COBRA) methodology was used to develop N2 NA vaccine candidates. The unique wild type (WT) N2 sequences of human and swine influenza strains isolated between 1957 and 2019 were used to design the COBRA N2-A NA vaccine, while the unique WT N2 sequences of human influenza strains isolated between 2000 and 2019 were used to design the COBRA N2-B NA vaccine. Sera collected from COBRA N2 NA vaccinated mice showed more broadly reactive antibody responses against a broad panel of H×N2 influenza virus strains than sera collected from mice vaccinated with WT N2 NA vaccines. Antibodies elicited by COBRA or WT N2 NA antigens cross react with recent human H3N2 influenza viruses from different clades, while the antibodies elicited by A/Switzerland/9715293/2013 hemagglutinin (HA) reacted with viruses from the same clade. Furthermore, mice vaccinated with COBRA N2-B NA vaccine had lower viral lung titers compared to mock vaccinated mice when challenged with human H3N2 influenza viruses. Thus, the COBRA N2 NA vaccines elicit broadly protective murine anti-NA antibodies against multiple strains across subtypes and the viral loads were significantly decreased in the lungs of the mice in the COBRA N2 NA vaccine groups, compared to the mice in the mock vaccinated group, indicating that the COBRA-based N2 subtype NA vaccines have a potential to be a component in a universal influenza vaccine.

Unlocking cell surface enzymes: A review of chemical strategies for detecting enzymatic activity

BACKGROUND

Cell surface enzymes are important proteins that play essential roles in controlling a wide variety of biological processes, such as cell-cell adhesion, recognition and communication. Dysregulation of enzyme-catalyzed processes is known to contribute to numerous diseases, including cancer, cardiovascular diseases and neurodegenerative disease. From the perspective of drug discovery and development, there is a growing interest in detecting the cell surface enzyme activity, propelled by the arising need for innovative diagnostic and therapeutic approaches to address various health conditions.

RESULTS

In this review, we focus on advances in chemical strategies for the detection of cell surface enzyme activity. Firstly, this comprehensive review delves into the diverse landscape of cell surface enzymes, detailing their structural features and diverse biological functions. Various enzyme families on the cell surface are examined in depth, elucidating their roles in cellular homeostasis and signaling cascades. Subsequently, various biosensors, including electrochemical biosensors, optical biosensors and dual-mode biosensors, used for detecting the cell surface enzyme activity are described. Exemplars are provided to illustrate the mechanisms, limit of detection and prospective applications of these different biosensors. Furthermore, this review unravels the intricate interplay between cell surface enzymes and cellular physiology, contributing to the development of novel diagnostic and therapeutic strategies for various diseases. In the end, the review provides insights into the ongoing challenges and future prospects associated with the detection of cell surface enzyme activity.

SIGNIFICANCE

Detecting cell surface enzyme activity holds pivotal significance in biomedical research, offering valuable insights into cellular physiology and disease pathology. Understanding enzyme activity aids in elucidating signaling pathways, drug interactions and disease mechanisms. This knowledge informs the development of diagnostic tools and therapeutic interventions targeting various ailments, from cancer to neurodegenerative disease. Additionally, it contributes to the advancement of drug screening and personalized medicine approaches.

Phlorotannin-Rich Ascophyllum nodosum Seaweed Extract Inhibits Influenza Infection

Seaweed-derived compounds are a renewable resource utilised in the manufacturing and food industry. This study focuses on an enriched seaweed extract (ESE) isolated from Ascophyllum nodosum. The ESE was screened for antiviral activity by plaque reduction assays against influenza A/Puerto Rico/8/1934 H1N1 (PR8), A/X-31 H3N2 (X31) and A/England/195/2009 H1N1 (Eng195), resulting in the complete inhibition of infection. Time of addition assays and FACS analysis were used to help determine the modes of action. The therapeutic potential of ESE was then explored using differentiated human bronchiole epithelial cells at the air-liquid interphase and a murine model challenged with IAV. The data indicates that ESE primarily interacts directly with virions, reducing mean virus-cell binding by 79.3% with 0.01 mg/mL ESE. Interestingly, ESE also inhibits the early and late stages of the influenza A lifecycle when treatment occurs after cell binding. This inhibitory effect appears to reduce the internalisation of the virus and the release of progeny virus by targeting neuraminidase activity, with IC50 values of 0.5 μg/mL for X31, 3.2 μg/mL for Eng195 and 12.8 μg/mL for PR8. The intranasal administration of 5 mg/kg ESE in mice infected with IAV reduced the viral load in lung tissue. ESE may be a promising broad-acting antiviral agent in the treatment of influenza infections.

Structural Convergence and Water-Mediated Substrate Mimicry Enable Broad Neuraminidase Inhibition by Human Antibodies

Influenza has been responsible for multiple global pandemics and seasonal epidemics and claimed millions of lives. The imminent threat of a panzootic outbreak of avian influenza H5N1 virus underscores the urgent need for pandemic preparedness and effective countermeasures, including monoclonal antibodies (mAbs). Here, we characterize human mAbs that target the highly conserved catalytic site of viral neuraminidase (NA), termed NCS mAbs, and the molecular basis of their broad specificity. Cross-reactive NA-specific B cells were isolated by using stabilized NA probes of non-circulating subtypes. We found that NCS mAbs recognized multiple NAs of influenza A as well as influenza B NAs and conferred prophylactic protections in mice against H1N1, H5N1, and influenza B viruses. Cryo-electron microscopy structures of two NCS mAbs revealed that they rely on structural mimicry of sialic acid, the substrate of NA, by coordinating not only amino acid side chains but also water molecules, enabling inhibition of NA activity across multiple influenza A and B viruses, including avian influenza H5N1 clade 2.3.4.4b viruses. Our results provide a molecular basis for the broad reactivity and inhibitory activity of NCS mAbs targeting the catalytic site of NA through substrate mimicry.

Influenza neuraminidase mutations and resistance to neuraminidase inhibitors

Mutations in influenza virus neuraminidase (NA) can lead to viral resistance to NA inhibitors (NAIs). To update global influenza NA mutations and resistance to NAIs, we investigated epidemic information from global regions for NAIs-resistant influenza strains and analyzed their NA mutations. Drug-resistant mutations in NA, especially new mutations occurred in 2016-2024, were updated. The H274Y mutation in N1, a major contributor to NAI resistance, peaked in 2008, significantly impacting public health in countries like Japan and the USA. Three main mechanisms of NAI resistance were identified: catalytic site mutations, structural hindrance, and monomer stability changes. Although global resistance rates of H1N1pdm09, H3N2, and influenza B have remained stable at around 1%, sporadic emergence of resistant strains highlights the need for continued vigilance. The evolution of drug-resistant, transmissible strains through compensatory mutations underscores the urgency of new antiviral strategies. Strengthening global surveillance and adjusting public health policies, such as improving vaccine coverage and prudent antiviral use, remain essential to mitigating future risks.

Optimized production of a truncated form of the recombinant neuraminidase of influenza virus in Escherichia coli as host with suitable functional activity

BACKGROUND

To discover effective drugs for treating Influenza (a disease with high annual mortality), large amounts of recombinant neuraminidase (NA) with suitable catalytic activity are needed. However, the functional activity of the full-length form of this enzyme in the bacterial host (as producing cells with a low cost) in a soluble form is limited. Thus, in the present study, a truncated form of the neuraminidase (derived from California H1N1 influenza strain) was designed, then biosynthesized in Escherichia coli BL21 (DE3), Shuffle T7, and SILEX systems. E. coli BL21 (DE3) was selected as a best host for statistical optimization. Using central composite design methodology, neuraminidase expression level was measured at 20 different runs considering most effective factors including; concentration of isopropyl-β-D-thiogalactopyranoside (IPTG), temperature, and induction time.

RESULT

The recombinant neuraminidase was purified using Ni-affinity chromatography in soluble form. The neuraminidase expression was confirmed by western blot technique with a molecular mass of 48 kDa. The optimum expression condition was at temperature (30°C), induction time (3 h), and concentration of IPTG (0.6 mM) resulting in maximum neuraminidase expression (7.6 µg/mL) with P < 0.05. The analysis of variance with the significant value of R2 (0.97) indicated that the quadratic model utilized for this prediction was highly significant (p < 0.0001). Applying the optimized condition led to a ~ 2.2-fold increase in NA expression level (from 3.4 to 7.6 µg/ml). The kinetic parameters were also confirmed by fluorescent signals (by 2'-(4-Methylumbelliferyl)-α-D-N acetyl neuraminic acid substrate) with specific activity; ~3.5 IU/mg and Km: 86.49 ± 0.1 µ, close to the Vibrio Cholera neuraminidase with specific activity; 4 IU/mg. The neuraminidase inhibition test confirmed the inhibition of the neuraminidase activity by the drug inhibitor (Oseltamivir) compared to the control sample.

CONCLUSION

The high quality and proper functional activity of the truncated neuraminidase described in this research show that E. coli can be a suitable host for a wide range of applications with less cost and risk compared to eukaryotic expression systems.

A facile access to aliphatic trifluoromethyl ketones via photocatalyzed cross-coupling of bromotrifluoroacetone and alkenes

Biological molecules incorporating trifluoromethyl ketones (TFMKs) have emerged as reversible covalent inhibitors, aiding in the management and treatment of inflammatory diseases, cancer, and respiratory conditions. TFMKs, renowned for their versatile binding properties and adaptability, are pivotal in the rational design of novel drugs for diverse diseases. The photocatalytic insertion of alkenes, abundant feedstocks, into the α-carbon of trifluoromethylacetone represents a highly effective and atom-economical method for synthesizing valuable TFMKs. However, these processes typically necessitate high-energy photoirradiation (λ > 300 nm, Hg lamp) and stoichiometric oxidants to generate the acetonyl radical from acetone. In our study, we demonstrate the visible-light photocatalytic radical addition into olefins using bromotrifluoroacetone as the trifluoroacetonyl radical precursor under mild conditions. Aliphatic trifluoromethyl ketones or the corresponding bromo-substituted products can be obtained by selecting an appropriate photocatalyst and solvent. Comprehensive experimental investigations, including cyclic voltammetry, Stern-Volmer quenching studies, and kinetic isotope effects, corroborate the synthesis of trifluoroacetonyl radical species from bromotrifluoroacetone under photoredox conditions. Further, we demonstrate the efficient synthesis of an oseltamivir derivative bearing a trifluoromethylketone moiety, which shows promising biological activity. Hence, this methodology will streamline the direct introduction of trifluoromethyl ketone into biological target molecules during drug discovery.

Evolutionary analysis of Hemagglutinin and neuraminidase gene variation in H1N1 swine influenza virus from vaccine intervention in China

Influenza poses a significant threat to the global economy and health. Inactivated virus vaccines were introduced in China for prevention in 2018. In this study, three pairs of hemagglutinin (HA) and neuraminidase (NA) gene sequences were obtained from three Swine influenza virus (IAV-S) inactivated vaccine strains that were marketed in China in 2018. Phylogenetic analysis was carried out with HA and NA gene sequences to investigate the relationship between vaccine use and virus genetic drift. The findings showed that the evolutionary rate of HA remained relatively stable from 2012 to 2017, with an average genetic distance of approximately 0.020731195. However, following the introduction of the swine influenza vaccine, there was a notable acceleration in the evolutionary rate of HA, accompanied by a significant increase in the genetic distance. In 2018, the value was 0.111750269, while in 2019 it was 0.176389393. In contrast, the evolution of NA was relatively smooth, with an average genetic distance of approximately 0.030386708. Finally, we demonstrated that commercial vaccines are weak neutralizers of wild strains through immunization experiments in animals. Thus, we have reason to believe that mutations in the virus favor virus evasion of vaccine immunity. Our findings suggest that vaccine use may significantly impact the evolution of the influenza virus by potentially stimulating mutations. The selection pressure of vaccine antibodies played a role in regulating the variation of IAV-S-H1N1.

Boosting neuraminidase immunity in the presence of hemagglutinin with the next generation of influenza vaccines

Neuraminidase (NA), the second most abundant surface glycoprotein on the influenza virus, plays a key role in viral replication and propagation. Despite growing evidence showing that NA-specific antibodies correlate with resistance to disease in humans, current licensed vaccines focus almost entirely on the hemagglutinin (HA) antigen. Here, we demonstrate that recombinant NA (rNA) protein is highly immunogenic in both naïve mice and ferrets, as well as in pre-immune ferrets, irrespective of the level of match with preexisting immunity. Ferrets vaccinated with rNA developed mild influenza disease symptoms upon challenge with human H3N2 influenza virus, and anti-NA antibody responses appeared correlated with reduction in disease severity. The addition of rNA to a quadrivalent HA-based vaccine induced robust NA-specific humoral immunity in ferrets, while retaining the ability to induce HA-specific immunity. These results demonstrate that the addition of rNA is a viable option to increase immunogenicity and potentially efficacy versus currently licensed influenza vaccines by means of boosting NA immunity.

Computational Evidence for Bisartan Arginine Blockers as Next-Generation Pan-Antiviral Therapeutics Targeting SARS-CoV-2, Influenza, and Respiratory Syncytial Viruses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, and respiratory syncytial virus (RSV) are significant global health threats. The need for low-cost, easily synthesized oral drugs for rapid deployment during outbreaks is crucial. Broad-spectrum therapeutics, or pan-antivirals, are designed to target multiple viral pathogens simultaneously by focusing on shared molecular features, such as common metal cofactors or conserved residues in viral catalytic domains. This study introduces a new generation of potent sartans, known as bisartans, engineered in our laboratories with negative charges from carboxylate or tetrazolate groups. These anionic tetrazoles interact strongly with cationic arginine residues or metal cations (e.g., Zn2+) within viral and host target sites, including the SARS-CoV-2 ACE2 receptor, influenza H1N1 neuraminidases, and the RSV fusion protein. Using virtual ligand docking and molecular dynamics, we investigated how bisartans and their analogs bind to these viral receptors, potentially blocking infection through a pan-antiviral mechanism. Bisartan, ACC519TT, demonstrated stable and high-affinity docking to key catalytic domains of the SARS-CoV-2 NSP3, H1N1 neuraminidase, and RSV fusion protein, outperforming FDA-approved drugs like Paxlovid and oseltamivir. It also showed strong binding to the arginine-rich furin cleavage sites S1/S2 and S2', suggesting interference with SARS-CoV-2's spike protein cleavage. The results highlight the potential of tetrazole-based bisartans as promising candidates for developing broad-spectrum antiviral therapies.

Drug resistance and possible therapeutic options against influenza A virus infection over past years

Influenza A virus infection, commonly known as the flu, has persisted in the community for centuries. Although we have yearly vaccinations to prevent seasonal flu, there remains a dire need for antiviral drugs to treat active infections. The constantly evolving genome of the influenza A virus limits the number of effective antiviral therapeutic options. Over time, antiviral drugs become inefficient due to the development of resistance, as seen with adamantanes, which are now largely ineffective against most circulating strains of the virus. Neuraminidase inhibitors have long been the drug of choice, but due to selection pressure, strains are becoming resistant to this class of drugs. Baloxavir marboxil, a drug with a novel mode of action, can be used against strains resistant to other classes of drugs but is still not available in many countries. Deep research into nanoparticles has shown they are effective as antiviral drugs, opening a new avenue of research to use them as antiviral agents with novel modes of action. As this deadly virus, which has killed millions of people in the past, continues to develop resistance, there is an urgent need for new therapeutic agents with novel modes of action to halt active infections in patients. This review article covers the available therapeutic antiviral drug options with different modes of action, their effectiveness, and resistance to various strains of influenza A virus.

Indole-core inhibitors of influenza a neuraminidase: iterative medicinal chemistry and molecular modeling

Influenza viruses that cause seasonal and pandemic flu are a permanent health threat. The surface glycoprotein, neuraminidase, is crucial for the infectivity of the virus and therefore an attractive target for flu drug discovery campaigns. We have designed and synthesized more than 40 3-indolinone derivatives. We mainly investigated the role of substituents at the 2 position of the core as well as the introduction of substituents or a nitrogen atom in the fused phenyl ring of the core for inhibition of influenza virus neuraminidase activity and replication in vitro and in vivo. After evaluating the compounds for their ability to inhibit the viral neuraminidase, six potent inhibitors 3c, 3e, 7c, 12o, 12v, 18d were progressed to evaluate for cytotoxicity and inhibition of influenza virus A/PR/8/34 replication in in MDCK cells. Two hit compounds 3e and 12o were tested in an animal model of influenza virus infection. Molecular mechanism of the 3-indolinone derivatives interactions with the neuraminidase was revealed in molecular dynamic simulations. Proposed inhibitors bind to the 430-cavity that is different from the conventional binding site of commercial compounds. The most promising 3-indolinone inhibitors demonstrate stronger interactions with the neuraminidase in molecular models that supports proposed binding site.

Inhibition of influenza virus infection in mice by pulmonary administration of a spray dried antiviral drug

Increasing resistance to antiviral drugs approved for the treatment of influenza urges the development of novel compounds. Ideally, this should be complemented by a careful consideration of the administration route. 6'siallyllactosamine-functionalized β-cyclodextrin (CD-6'SLN) is a novel entry inhibitor that acts as a mimic of the primary attachment receptor of influenza, sialic acid. In this study, we aimed to develop a dry powder formulation of CD-6'SLN to assess its in vivo antiviral activity after administration via the pulmonary route. By means of spray drying the compound together with trileucine, a dispersion enhancer, we created a powder that retained the antiviral effect of the drug, remained stable under elevated temperature conditions and performed well in a dry powder inhaler. To test the efficacy of the dry powder drug against influenza infection in vivo, infected mice were treated with CD-6'SLN using an aerosol generator that allowed for the controlled administration of powder formulations to the lungs of mice. CD-6'SLN was effective in mitigating the course of the disease compared to the control groups, reflected by lower disease activity scores and by the prevention of virus-induced IL-6 production. Our data show that CD-6'SLN can be formulated as a stable dry powder that is suitable for use in a dry powder inhaler and is effective when administered via the pulmonary route to influenza-infected mice.

The Effects of Viral Structural Proteins on Acidic Phospholipids in Host Membranes

Enveloped viruses rely on host membranes for trafficking and assembly. A substantial body of literature published over the years supports the involvement of cellular membrane lipids in the enveloped virus assembly processes. In particular, the knowledge regarding the relationship between viral structural proteins and acidic phospholipids has been steadily increasing in recent years. In this review, we will briefly review the cellular functions of plasma membrane-associated acidic phospholipids and the mechanisms that regulate their local distribution within this membrane. We will then explore the interplay between viruses and the plasma membrane acidic phospholipids in the context of the assembly process for two enveloped viruses, the influenza A virus (IAV) and the human immunodeficiency virus type 1 (HIV-1). Among the proteins encoded by these viruses, three viral structural proteins, IAV hemagglutinin (HA), IAV matrix protein-1 (M1), and HIV-1 Gag protein, are known to interact with acidic phospholipids, phosphatidylserine and/or phosphatidylinositol (4,5)-bisphosphate. These interactions regulate the localization of the viral proteins to and/or within the plasma membrane and likely facilitate the clustering of the proteins. On the other hand, these viral proteins, via their ability to multimerize, can also alter the distribution of the lipids and may induce acidic-lipid-enriched membrane domains. We will discuss the potential significance of these interactions in the virus assembly process and the property of the progeny virions. Finally, we will outline key outstanding questions that need to be answered for a better understanding of the relationships between enveloped virus assembly and acidic phospholipids.

A recombinant N2 neuraminidase-based CpG 1018® adjuvanted vaccine provides protection against challenge with heterologous influenza viruses in mice and hamsters

Recombinant influenza virus neuraminidase (NA) is a promising broadly protective influenza vaccine candidate. However, the recombinant protein alone is not sufficient to induce durable and protective immune responses and requires the coadministration of immunostimulatory molecules. Here, we evaluated the immunogenicity and cross-protective potential of a recombinant influenza virus N2 neuraminidase vaccine construct, adjuvanted with a toll-like receptor 9 (TLR9) agonist (CpG 1018® adjuvant), and alum. The combination of CpG 1018 adjuvant and alum induced a balanced and robust humoral and T-cellular immune response against the NA, which provided protection and reduced morbidity against homologous and heterologous viral challenges in mouse and hamster models. This study supports Syrian hamsters as a useful complementary animal model to mice for pre-clinical evaluation of influenza virus vaccines.

Enhancing NA immunogenicity through novel VLP designs

Current influenza virus vaccines poorly display key neuraminidase (NA) epitopes and do not robustly induce NA-reactive antibodies; instead, they focus on the induction of hemagglutinin (HA)-reactive antibodies. Next-generation influenza vaccines should be optimized in order to activate NA-reactive B cells and to induce a broadly cross-reactive and protective antibody response. We aimed at enhancing the immunogenicity of the NA on vaccines by two strategies: (i) modifying the HA:NA ratio of the vaccine preparation and (ii) exposing epitopes on the lateral surface or beneath the head of the NA by extending the NA stalk. The H1N1 glycoproteins from the influenza virus A/California/04/2009 strain were displayed on human immunodeficiency virus 1 (HIV-1) gag-based virus-like particles (VLP). Using the baculovirus insect cell expression system, we biased the quantity of surface glycoproteins employing two different promoters, the very late baculovirus p10 promoter and the early and late gp64 promoter. This led to a 1:1 to 2:1 HA:NA ratio, which was approximately double or triple the amount of NA as present on the wild-type influenza A virus (HA:NA ratio 3:1 to 5:1). Furthermore, by insertion of 15 amino acids from the A-New York/61/2012 strain (NY12) which prolongates the NA stalk (NA long stalk; NA-LS), we intended to improve the accessibility of the NA. Six different types of VLPs were produced and purified using a platform downstream process based on Capto-Core 700™ followed by Capto-Heparin™ affinity chromatography combined with ultracentrifugation. These VLPs were then tested in a mouse model. Robust titers of antibodies that inhibit the neuraminidase activity were elicited even after vaccination with two low doses (0.3 μg) of the H1N1 VLPs without compromising the anti-HA responses. In conclusion, our results demonstrate the feasibility of the two developed strategies to retain HA immunogenicity and improve NA immunogenicity as a future influenza vaccine candidate.

Insights into Genetic and Antigenic Characteristics of Influenza A(H1N1)pdm09 Viruses Circulating in Sicily During the Surveillance Season 2023-2024: The Potential Effect on the Seasonal Vaccine Effectiveness

After disruption in the influenza circulation due to the emergence of SARS-CoV-2, the intensity of seasonal outbreaks has returned to the pre-pandemic levels. This study aimed to evaluate the evolution and variability of whole-genome sequences of A(H1N1)pdm09, the predominant influenza virus in Sicily (Italy) during the season 2023-2024. The potential vaccine efficacy was calculated using the pepitope model based on amino acid changes in the dominant epitope of hemagglutinin. The HA gene sequences showed several amino acid substitutions, some of which were within the major antigenic sites. The phylogenetic analysis showed that Sicilian strains grouped into two main genetic clades (6B.1A.5a.2a.1 and 6B.1A.5a.2a) and several subclades. Notably, about 40% of sequences partially drifted from the WHO-recommended vaccine strain A/Victoria/4897/2022 for the Northern Hemisphere. These sequences mostly belonged to the subclades C.1.8 and C.1.9 and harboured the amino acid mutations responsible for the modest predicted vaccine efficacy (E = 38.12% of 53%, pepitope = 0) against these viruses. Amino acid substitutions in other gene segments were also found. Since influenza viruses are constantly evolving, genomic surveillance is crucial in monitoring their molecular evolution and the occurrence of genetic and antigenic changes, and, thus, their potential impact on vaccine efficacy.

Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites

The hemagglutinin (HA) glycoprotein of influenza virus binds host cell receptors and mediates viral entry. Here we present cryo-EM structures of fully glycosylated HAs from H5N1 and H5N8 influenza viruses. We find that the H5N1 HA can form filaments that comprise two head-to-head HA trimers. Multivalent interactions between the two HA trimers are mediated by glycans attached to N158. The distal Sia1-Gal2-NAG3 sugar moiety of N158 interacts with the receptor binding site on the opposing HA trimer. Additional interactions are observed between NAG3 and residues K222 and K193. The H5N8 HA lacks the N158 glycosylation site and does not form the filamentous structure. However, the H5N8 HA exhibits an auto-inhibition conformation, where the receptor binding site is occupied by the glycan chain attached to residue N169 from a neighboring protomer. These structures represent native HA-glycan interactions, which may closely mimic the receptor-HA interactions on the cell surface.

Improved influenza vaccine responses after expression of multiple viral glycoproteins from a single mRNA

Influenza viruses cause substantial morbidity and mortality every year despite seasonal vaccination. mRNA-based vaccines have the potential to elicit more protective immune responses, but for maximal breadth and durability, it is desirable to deliver both the viral hemagglutinin and neuraminidase glycoproteins. Delivering multiple antigens individually, however, complicates manufacturing and increases cost, thus it would be beneficial to express both proteins from a single mRNA. Here, we develop an mRNA genetic configuration that allows the simultaneous expression of unmodified, full-length NA and HA proteins from a single open reading frame. We apply this approach to glycoproteins from contemporary influenza A and B viruses and, after vaccination, observe high levels of functional antibodies and protection from disease in female mouse and male ferret challenge models. This approach may further efforts to utilize mRNA technology to improve seasonal vaccine efficacy by efficiently delivering multiple viral antigens simultaneously and in their native state.

Dual neutralization of influenza virus hemagglutinin and neuraminidase by a bispecific antibody leads to improved antiviral activity

Targeting multiple viral proteins is pivotal for sustained suppression of highly mutable viruses. In recent years, broadly neutralizing antibodies that target the influenza virus hemagglutinin and neuraminidase glycoproteins have been developed, and antibody monotherapy has been tested in preclinical and clinical studies to treat or prevent influenza virus infection. However, the impact of dual neutralization of the hemagglutinin and neuraminidase on the course of infection, as well as its therapeutic potential, has not been thoroughly tested. For this purpose, we generated a bispecific antibody that neutralizes both the hemagglutinin and the neuraminidase of influenza viruses. We demonstrated that this bispecific antibody has a dual-antiviral activity as it blocks infection and prevents the release of progeny viruses from the infected cells. We show that dual neutralization of the hemagglutinin and the neuraminidase by a bispecific antibody is advantageous over monoclonal antibody combination as it resulted an improved neutralization capacity and augmented the antibody effector functions. Notably, the bispecific antibody showed enhanced antiviral activity in influenza virus-infected mice, reduced mice mortality, and limited the virus mutation profile upon antibody administration. Thus, dual neutralization of the hemagglutinin and neuraminidase could be effective in controlling influenza virus infection.

Modulation of human-to-swine influenza a virus adaptation by the neuraminidase low-affinity calcium-binding pocket

Frequent interspecies transmission of human influenza A viruses (FLUAV) to pigs contrasts with the limited subset that establishes in swine. While hemagglutinin mutations are recognized for their role in cross-species transmission, the contribution of neuraminidase remains understudied. Here, the NA's role in FLUAV adaptation was investigated using a swine-adapted H3N2 reassortant virus with human-derived HA and NA segments. Adaptation in pigs resulted in mutations in both HA (A138S) and NA (D113A). The D113A mutation abolished calcium (Ca2+) binding in the low-affinity Ca2+-binding pocket of NA, enhancing enzymatic activity and thermostability under Ca2+-depleted conditions, mirroring swine-origin FLUAV NA behavior. Structural analysis predicts that swine-adapted H3N2 viruses lack Ca2+ binding in this pocket. Further, residue 93 in NA (G93 in human, N93 in swine) also influences Ca2+ binding and impacts NA activity and thermostability, even when D113 is present. These findings demonstrate that mutations in influenza A virus surface proteins alter evolutionary trajectories following interspecies transmission and reveal distinct mechanisms modulating NA activity during FLUAV adaptation, highlighting the importance of Ca2+ binding in the low-affinity calcium-binding pocket.

Fighting the flu: a brief review on anti-influenza agents

The influenza virus causes one of the most prevalent and lethal infectious viral diseases of the respiratory system; the disease progression varies from acute self-limiting mild fever to disease chronicity and death. Although both the preventive and treatment measures have been vital in protecting humans against seasonal epidemics or sporadic pandemics, there are several challenges to curb the influenza virus such as limited or poor cross-protection against circulating virus strains, moderate protection in immune-compromised patients, and rapid emergence of resistance. Currently, there are four US-FDA-approved anti-influenza drugs to treat flu infection, viz. Rapivab, Relenza, Tamiflu, and Xofluza. These drugs are classified based on their mode of action against the viral replication cycle with the first three being Neuraminidase inhibitors, and the fourth one targeting the viral polymerase. The emergence of the drug-resistant strains of influenza, however, underscores the need for continuous innovation towards development and discovery of new anti-influenza agents with enhanced antiviral effects, greater safety, and improved tolerability. Here in this review, we highlighted commercially available antiviral agents besides those that are at different stages of development including under clinical trials, with a brief account of their antiviral mechanisms.

Recombinant Influenza A Viruses Expressing Reporter Genes from the Viral NS Segment

Studying influenza A viruses (IAVs) requires secondary experimental procedures to detect the presence of the virus in infected cells or animals. The ability to generate recombinant (r)IAV using reverse genetics techniques has allowed investigators to generate viruses expressing foreign genes, including fluorescent and luciferase proteins. These rIAVs expressing reporter genes have allowed for easily tracking viral infections in cultured cells and animal models of infection without the need for secondary approaches, representing an excellent option to study different aspects in the biology of IAV where expression of reporter genes can be used as a readout of viral replication and spread. Likewise, these reporter-expressing rIAVs provide an excellent opportunity for the rapid identification and characterization of prophylactic and/or therapeutic approaches. To date, rIAV expressing reporter genes from different viral segments have been described in the literature. Among those, rIAV expressing reporter genes from the viral NS segment have been shown to represent an excellent option to track IAV infection in vitro and in vivo, eliminating the need for secondary approaches to identify the presence of the virus. Here, we summarize the status on rIAV expressing traceable reporter genes from the viral NS segment and their applications for in vitro and in vivo influenza research.

Aptamers: precision tools for diagnosing and treating infectious diseases

Infectious diseases represent a significant global health challenge, with bacteria, fungi, viruses, and parasitic protozoa being significant causative agents. The shared symptoms among diseases and the emergence of new pathogen variations make diagnosis and treatment complex. Conventional diagnostic methods are laborious and intricate, underscoring the need for rapid, accurate techniques. Aptamer-based technologies offer a promising solution, as they are cost-effective, sensitive, specific, and convenient for molecular disease diagnosis. Aptamers, which are single-stranded RNA or DNA sequences, serve as nucleotide equivalents of monoclonal antibodies, displaying high specificity and affinity for target molecules. They are structurally robust, allowing for long-term storage without substantial activity loss. Aptamers find applications in diverse fields such as drug screening, material science, and environmental monitoring. In biomedicine, they are extensively studied for biomarker detection, diagnostics, imaging, and targeted therapy. This comprehensive review focuses on the utility of aptamers in managing infectious diseases, particularly in the realms of diagnostics and therapeutics.

Preparation and characterization of kelp polysaccharide and its research on anti-influenza a virus activity

The beneficial effects of kelp polysaccharide (KPS) have recently attracted attention. In this study, KPS was extracted from kelp using the enzyme hydrolysis combined with freeze-drying, namely, KPS-EF. The structural characterization showed that KPS-EF was a highly sulfated macromolecule with the Mw of 764.2 kDa and the sulfate content of 23.49 %. The antiviral activity of KPS-EF in vitro was verified, and the IC50 value of KPS against the PR8 virus was 0.58 mg/mL. Intranasal administration of KPS-EF significantly inhibited death and weight loss in IAV-infected mice and alleviated virus-induced pneumonia symptoms, meanwhile, KPS-EF (10 mg/kg/day) significantly decreased the production levels of chemokines (CXCL1, RANTES) and inflammatory cytokines (IL-6, TNF-α) in lungs (p < 0.05). KPS-EF could downregulate the activity of viral neuraminidase (NA) primarily in the late stage of viral adsorption with an IC50 value of 0.29 mg/mL. This study provides a theoretical basis for the using KPS as a supplement to NA inhibitors or anti-influenza drugs.

Comparative docking and molecular dynamics studies of molnupiravir (EIDD-2801): implications for novel mechanisms of action on influenza and SARS-CoV-2 protein targets

Molnupiravir (EIDD-2801) (MLN) is an oral antiviral drug for COVID-19 treatment, being integrated into viral RNA through RNA-dependent RNA polymerase (RdRp). Upon ingestion, MLN is transformed into two active metabolites: β-d-N4-hydroxycytidine (NHC) (EIDD-1931) in the host plasma, and EIDD-1931-triphosphate (MTP) within the host cells. However, recent studies provide increasing evidence of MLN's interactions with off-target proteins beyond the viral genome, suggesting that the complete mechanisms of action of MLN remain unclear. The aim of this study was therefore to investigate the molecular interactions of MLN in the form of NHC and MTP with the non-RNA structural components of avian influenza (hemagglutinin, neuraminidase) and SARS-CoV-2 (spike glycoprotein, Mpro, and RdRp) viruses and to elucidate whether these two metabolites possess the ability to form stable complexes with these major viral components. Molecular docking of NHC and MTP was performed using AutoDock 4.2.6 and the obtained protein-drug complexes were submitted to 200-ns molecular dynamics simulations in triplicate with subsequent free energy calculations using GROMACS. Docking scores, molecular dynamics and MM/GBSA results showed that MTP was tightly bound within the active site of SARS-CoV-2 RdRp and remained highly stable throughout the 200-ns simulations. Besides, it was also shown that NHC and MTP formed moderately-to-highly stable molecular complexes with off-target receptors hemagglutinin, neuraminidase and Mpro, but rather weak interactions with spike glycoprotein. Our computational findings suggest that NHC and MTP may directly inhibit these receptors, and propose that additional studies on the off-target effects of MLN, i.e. real-time protein binding assays, should be performed.Communicated by Ramaswamy H. Sarma.

Adaptation potential of H3N8 canine influenza virus in human respiratory cells

In 2004, the equine-origin H3N8 canine influenza virus (CIV) first caused an outbreak with lethal cases in racing greyhounds in Florida, USA, and then spread to domestic dogs nationwide. Although transmission of this canine virus to humans has not been reported, it is important to evaluate its zoonotic potential because of the high contact opportunities between companion dogs and humans. To gain insight into the interspecies transmissibility of H3N8 CIV, we tested its adaptability to human respiratory A549 cells through successive passages. We found that CIV acquired high growth properties in these cells mainly through mutations in surface glycoproteins, such as hemagglutinin (HA) and neuraminidase (NA). Our reverse genetics approach revealed that HA2-K82E, HA2-R163K, and NA-S18L mutations were responsible for the increased growth of CIV in human cells. Molecular analyses revealed that both HA2 mutations altered the optimum pH for HA membrane fusion activity and that the NA mutation changed the HA-NA functional balance. These findings suggest that H3N8 CIV could evolve into a human pathogen with pandemic potential through a small number of mutations, thereby posing a threat to public health in the future.

SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes

Segmented RNA viruses are a complex group of RNA viruses with multisegment genomes. Reconstructing complete segmented viruses is crucial for advancing our understanding of viral diversity, evolution, and public health impact. Using metatranscriptomic data to identify known and novel segmented viruses has sped up the survey of segmented viruses in various ecosystems. However, the high genetic diversity and the difficulty in binning complete segmented genomes present significant challenges in segmented virus reconstruction. Current virus detection tools are primarily used to identify nonsegmented viral genomes. This study presents SegVir, a novel tool designed to identify segmented RNA viruses and reconstruct their complete genomes from complex metatranscriptomes. SegVir leverages both close and remote homology searches to accurately detect conserved and divergent viral segments. Additionally, we introduce a new method that can evaluate the genome completeness and conservation based on gene content. Our evaluations on simulated datasets demonstrate SegVir's superior sensitivity and precision compared to existing tools. Moreover, in experiments using real data, we identified some virus segments missing in the NCBI database, underscoring SegVir's potential to enhance viral metagenome analysis. The source code and supporting data of SegVir are available via https://github.com/HubertTang/SegVir.

Ventricular-subventricular zone stem cell niche adaptations in a mouse model of post-infectious hydrocephalus

Congenital post-infectious hydrocephalus (PIH) is a condition characterized by enlargement of the ventricular system, consequently imposing a burden on the associated stem cell niche, the ventricular-subventricular zone (V-SVZ). To investigate how the V-SVZ adapts in PIH, we developed a mouse model of influenza virus-induced PIH based on direct intracerebroventricular injection of mouse-adapted influenza virus at two distinct time points: embryonic day 16 (E16), when stem cells line the ventricle, and postnatal day 4 (P4), when an ependymal monolayer covers the ventricle surface and stem cells retain only a thin ventricle-contacting process. Global hydrocephalus with associated regions of astrogliosis along the lateral ventricle was found in 82% of the mice infected at P4. Increased ependymogenesis was observed at gliotic borders and throughout areas exhibiting intact ependyma based on tracking of newly divided cells. Additionally, in areas of intact ependyma, stem cell numbers were reduced; however, we found no significant reduction in new neurons reaching the olfactory bulb following onset of ventriculomegaly. At P4, injection of only the non-infectious viral component neuraminidase resulted in limited, region-specific ventriculomegaly due to absence of cell-to-cell transmission. In contrast, at E16 intracerebroventricular injection of influenza virus resulted in death at birth due to hypoxia and multiorgan hemorrhage, suggesting an age-dependent advantage in neonates, while the viral component neuraminidase resulted in minimal, or no, ventriculomegaly. In summary, we tracked acute adaptations of the V-SVZ stem cell niche following onset of ventriculomegaly and describe developmental changes that help mitigate the severity of congenital PIH.

Advancements in Antiviral Drug Development: Comprehensive Insights into Design Strategies and Mechanisms Targeting Key Viral Proteins

Viral infectious diseases have always been a threat to human survival and quality of life, impeding the stability and progress of human society. As such, researchers have persistently focused on developing highly efficient, low-toxicity antiviral drugs, whether for acute or chronic infectious diseases. This article presents a comprehensive review of the design concepts behind virus-targeted drugs, examined through the lens of antiviral drug mechanisms. The intention is to provide a reference for the development of new, virus-targeted antiviral drugs and guide their clinical usage.