Influenza Hemagglutinin Structures and Antibody Recognition

De novo design and discovery of broad-spectrum affinity peptide ligands for influenza A vaccines

Seasonal Influenza viruses, owing to their continued evolution and high level of contagion, present a significant threat to public health around world each year. Vaccination remains the most effective strategy for preventing complications of influenza virus infection, particularly for vulnerable populations such as elderly individuals, children, and individuals with underlying health conditions. In this study, we described the de novo design for the discovery of affinity ligands targeting the conserved receptor binding site (RBS) of the influenza virus hemagglutinin (HA). Based on three-round of molecular docking, three candidate peptides, pep1, pep3 and pep4, with top-rankings were identified. Molecular dynamic simulation and per-residue decomposition further revealed the different binding mechanisms of the three peptides with HA and the key residue's contribution to the binding. The result of microscale thermophoresis indicated that the three peptides had broad-spectrum affinity for various influenza A strains and, among them, pep1 had the highest binding affinity for HA (Kd = 0.58-0.73 μmol/L). By coupling pep1 onto Sepharose gels, the affinity gel was applied to the evaluation of the chromatographic performance in the purification of HA and influenza A vaccine from mimic egg- and mammalian-based feedstocks. A recovery of 68.3 %-72.2 % at the purity of 95.9 %-97.2 % was obtained in vaccine purification, demonstrating the excellent feature of the peptide ligand. This work provided new insight into the rational design of broad-spectrum affinity peptide targeting HA and the result has potential application in the production of influenza vaccines.

A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface

Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here, we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal influenza infection in mice. These antibodies bind to most influenza A subtypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to "universal" influenza immunity.

IMPORTANCE

Antibodies to the influenza virus hemagglutinin (HA) protein confer the strongest protection against infection. Human antibodies elicited by infection and/or vaccination fail to protect against antigenically novel animal, pandemic, or human seasonal viruses. Improved vaccines are needed. We identify a novel class of antibodies that bind most divergent HA subtypes and all seasonal human HA antigenic variants tested. These antibodies confer protection from lethal influenza challenge in animal models. The corresponding epitope on the HA head is occluded by its interaction with the stem and is inaccessible in the well-resolved prefusion state. The immunogenicity of this head-stem interface indicates that poorly understood conformations of HA presenting widely conserved surfaces are explored in biochemical, cell-based, and in vivo assays. Head-stem interface antibodies warrant further investigation as an avenue to improve influenza vaccines and therapeutics.

Kinetic MUNANA assay reveals functionally relevant antibody epitopes on Influenza A virus neuraminidase

Influenza A virus neuraminidase (NA) is drawing attention as a target for vaccine development. In this study, we propose kinetic MUNANA assay as a tool to identify monoclonal antibodies (mAbs) that specifically target functional epitopes on NA. By analyzing changes in the parameters of the Michaelis-Menten curve (Km and Vmax), we revealed distinct mechanisms of Ab-mediated inhibition. Additionally, we developed a web-based application facilitating efficient processing of the assay results and enabling statistical inference. We employed the kinetic MUNANA assay to test newly developed mAbs targeting NA of the widely used PR8 H1N1 strain. Among these, mAbs with strong effect on NA enzymatic parameters were more likely to select for escape mutants that had a substantial impact on the overall enzymatic activity of the virus. In summary, when combined with ELLA, kinetic MUNANA is a rapid method to profile the putative binding site and the effect of NA-specific mAbs.

Species-specific RNA barcoding technology for rapid and accurate identification of four types of influenza virus

BACKGROUND

The influenza virus (IV) is responsible for seasonal flu epidemics. Constant mutation of the virus results in new strains and widespread reinfections across the globe, bringing great challenges to disease prevention and control. Research has demonstrated that barcoding technology efficiently and cost-effectively differentiates closely related species on a large scale. We screened and validated species-specific RNA barcode segments based on the genetic relationships of four types of IVs, facilitating their precise identification in high-throughput sequencing viral samples.

RESULTS

Through the analysis of single nucleotide polymorphism, population genetic characteristics, and phylogenetic relationships in the training set, 7 IVA type, 29 IVB type, 40 IVC type, and 5 IVD type barcode segments were selected. In the testing set, the nucleotide-level recall rate for all barcode segments reached 96.86%, the average nucleotide-level specificity was approximately 55.27%, the precision rate was 100%, and the false omission rate was 0%, demonstrating high accuracy, specificity, and generalization capabilities for species identification. Ultimately, all four types of IVs were visualized in a combination of one-dimensional and two-dimensional codes and stored in an online database named Influenza Virus Barcode Database (FluBarDB, http://virusbarcodedatabase.top/database/index.html ).

CONCLUSION

This study validates the effective application of RNA barcoding technology in the detection of IVs and establishes criteria and procedures for selecting species-specific molecular markers. These advancements enhance the understanding of the genetic and epidemiological characteristics of IVs and enable rapid responses to viral genetic mutations.

Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryoelectron tomography

Influenza viruses are enveloped, negative-sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80 to 90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of purified receptor-free and receptor-bound HA, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryoelectron tomography to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even interglycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and the formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8 to 10 Å reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.

A novel tetravalent influenza vaccine based on one chimpanzee adenoviral vector

Highly effective and broad-spectrum influenza vaccines are urgently required to prevent influenza outbreaks. Hemagglutinin (HA), M2 ectodomain (M2e), and nucleoprotein (NP) are crucial target antigens for the development of universal influenza vaccines. To generate a novel multivalent influenza vaccine, the HA genes of influenza B Yamagata (BY) and Victoria (BV) strains, and the NP gene of H1N1 were cloned into the E1 region of the chimpanzee adenoviral vector, AdC68, and M2e epitopes of H1N1 and H3N2 were fused to the loop region of the AdC68 fiber, resulting in the recombinant adenoviral vector vaccine, AdC-Flu-Tet. The immunoprotective effects of AdC-Flu-Tet were evaluated in the mouse models. The results showed that AdC-Flu-Tet successfully induced robust humoral and cellular immune responses and conferred full protection against H1N1, H3N2, BY, and BV infections. In conclusion, AdC-Flu-Tet is a promising candidate as a novel influenza vaccine with high protective efficacy.

Catch, Cut, or Block? Versatile 4-N-Derivatized Sialyl Glycosides for Influenza Virus Neuraminidase Detection and Purification

Seasonal influenza continues to threaten human lives and pose a significant burden to healthcare systems and the economy, emphasizing the need for developing better influenza vaccines, diagnostics, and antiviral therapeutics. To address these challenges, we generated a library of structurally diverse sialyl glycosides containing 4-N-derivatized sialic acids by a highly efficient one-pot two-enzyme chemoenzymatic sialylation strategy. Sialosides containing 4-azido-substituted sialic acid were selectively cleaved by sialidases from influenza viruses, whereas sialosides containing 4-acetamido-modified sialic acid were resistant to sialidase cleavage. Interestingly, sialosides containing 4-amino- or 4-guanidino-substituted sialic acid were effective inhibitors moderately or highly resistant to cleavage by influenza sialidases (also called neuraminidases). The sialosides containing the 4-guanidino-substituted sialic acid represent a new class of sialidase substrate analog-based inhibitors. We took advantage of this unique property to create a ligand-based approach for efficiently isolating influenza virions from egg allantoic fluid with high purity. Together, these compounds are versatile probes and ligands for developing new approaches to detect, profile, isolate, and characterize influenza viruses via neuraminidases on their surface.

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.

Recombinant probiotic Escherichia coli delivers the polymeric protein of swine influenza virus for protection

Swine influenza virus invades the host through the respiratory mucosa, which severely restricts the development of the pig breeding industry. To construct monomeric and trimeric vaccines, we developed recombinant Escherichia coli Nissle 1917 (EcN) strains that express the receptor binding site (RBS) of the hemagglutinin (HA) antigen from H1N1 swine influenza virus. After the mucosal immunization of mice, we found that probiotics activated CD40 and CD86 in DCs and increased the levels of IL-4 and IFN-γ secretion by T cells. Furthermore, the probiotics improved the function of the mucosal immune system, increased the level of SIgA, level of IgG and number of B220+IgA+, and activated germinal center B cells. The challenge experiment revealed that the probiotics alleviated weight loss, reduced pathological injury to the lungs, and protected the mice from virus infection. We also observed that the serum neutralizing antibodies of immunized piglets significantly increased, which reduced the shedding frequency of swine influenza virus in the nose of the piglets and reduced the pathological damage by activating the T cell immune response in infected piglets. Thus, the constructed probiotics are promising candidates for effective non-traditional swine influenza vaccines.

Influenza A(H5N1) Immune Response among Ferrets with Influenza A(H1N1)pdm09 Immunity

The emergence of highly pathogenic avian influenza A(H5N1) virus in dairy cattle herds across the United States in 2024 caused several human infections. Understanding the risk for spillover infections into humans is crucial for protecting public health. We investigated whether immunity from influenza A(H1N1)pdm09 (pH1N1) virus would provide protection from death and severe clinical disease among ferrets intranasally infected with H5N1 virus from dairy cows from the 2024 outbreak. We observed differential tissue tropism among pH1N1-immune ferrets. pH1N1-immune ferrets also had little H5N1 viral dissemination to organs outside the respiratory tract and much less H5N1 virus in nasal secretions and the respiratory tract than naive ferrets. In addition, ferrets with pH1N1 immunity produced antibodies that cross-reacted with H5N1 neuraminidase protein. Taken together, our results suggest that humans with immunity to human seasonal influenza viruses may experience milder disease from the 2024 influenza A(H5N1) virus strain.

High-throughput synthesis and specificity characterization of natively paired antibodies using oPool+ display

Antibody discovery is crucial for developing therapeutics and vaccines as well as understanding adaptive immunity. However, the lack of approaches to synthesize antibodies with defined sequences in a high-throughput manner represents a major bottleneck in antibody discovery. Here, we presented oPool+ display, a high-throughput cell-free platform that combined oligo pool synthesis and mRNA display to rapidly construct and characterize many natively paired antibodies in parallel. As a proof-of-concept, we applied oPool+ display to probe the binding specificity of >300 uncommon influenza hemagglutinin (HA) antibodies against 9 HA variants through 16 different screens. Over 5,000 binding tests were performed in 3-5 days with further scaling potential. Follow-up structural analysis of two HA stem antibodies revealed the previously unknown versatility of IGHD3-3 gene segment in recognizing the HA stem. Overall, this study established an experimental platform that not only accelerate antibody characterization, but also enable unbiased discovery of antibody molecular signatures.

A capless hairpin-protected mRNA vaccine encoding the full-length Influenza A hemagglutinin protects mice against a lethal Influenza A infection

The success of mRNA vaccines in controlling the COVID 19 pandemic has confirmed the efficacy of synthetically synthesized mRNA in humans and has also provided a blueprint on how to design them in terms of molecular structure and cost. We describe a mRNA vector that, unlike linear mRNAs used in current vaccines/therapeutics, does not require a 5' cap to function. The described mRNA vector initiates translation from an internal ribosomal entry site (IRES) and contains specially designed self-folding secondary structures (hairpins) to protect the 5' end against degradation, dramatically improving its stability. The produced mRNA did not require any additional modifications for functionality. The 5' hairpins completely inhibited cap-dependent translation, and all vectors containing them required an IRES to express protein. When this capless mRNA vector was constructed to express the full-length Influenza A membrane protein hemagglutinin (HA), complexed with pre-formed lipid-based nanoparticles, and then injected into mice as a vaccine, it generated high titers of anti-HA antibodies and protected mice against a lethal dose of Influenza A.

Probing the Role of Membrane in Neutralizing Activity of Antibodies Against Influenza Virus

Influenza poses a major health issue globally. Neutralizing antibodies targeting the highly conserved stem region of hemagglutinin (HA) of the influenza virus provide considerable protection against the infection. Using an array of advanced simulation technologies, we developed a high-resolution structural model of full-length, Fab-bound HA in a native viral membrane to characterize direct membrane interactions that govern the efficacy of the antibody. We reveal functionally important residues beyond the antibody's complementary-determining regions that contribute to its membrane binding. Mutagenesis experiments and infectivity assays confirm that deactivating the membrane-binding residues of the antibody decreases its neutralization activity. Therefore, we propose that the association with the viral membrane plays a key role in the neutralization activity of these antibodies. Given the rapid evolution of the influenza virus, the developed model provides a structural framework for the rational design and development of more effective therapeutic antibodies.

Enhanced and Prolonged Immunogenicity in Mice of Thermally Stabilized Fatty Acid-Conjugated Vaccine Antigen

BACKGROUND/OBJECTIVES

Influenza vaccines require good thermal stability without the need for refrigerator storage. Although the fatty acid-conjugated hemagglutinin (Heg) vaccine antigen provides good stability in both solid and liquid states, its therapeutic effectiveness must be validated in vivo. This study aimed to investigate the immunogenicity of the thermally stabilized Heg-oleic acid conjugate (HOC) and compare it with native Heg as a reference.

METHOD

To evaluate HOC immunogenicity, an enzyme-linked immunosorbent assay was used to measure hemagglutinin inhibition (HI) titers, serum IgG antibody titers (IgG1, IgG2a), and cytokine secretion levels (IFN-γ, IL-4) in BALB/c mice after intramuscular (IM) injection.

RESULTS

Thermally stabilized HOC induced higher and more sustained serum IgG1 and IgG2a responses than the native Heg vaccine antigen. IgG1 is typically associated with a Th2 response, whereas IgG2a is associated with a Th1 response. HOC appeared to enhance both responses, inducing a more balanced immune response. Moreover, HOC antigens stimulate broader immune responses, suggesting stronger and longer-lasting immune memory. The cytokine levels of IFN-γ (2.8-fold) and IL-4 (6-fold) were significantly increased in the HOC-immunized group compared to the Heg group. IFN-γ, a cytokine that activates the Th1 immune response, demonstrated the enhanced ability of HOC to induce a Th1 response. IL-4, a cytokine that promotes the Th2 response, indicated that HOC also strongly induced a Th2 response. The thermal stability of HOC antigens was crucial for maintaining their structural integrity, enabling the continuous exposure to the stable antigen without denaturation. This allows immune cells to recognize stable antigens efficiently and form long-term immune memory.

CONCLUSIONS

The stability of HOC antigens enhanced the antigen processing efficiency of antigen-presenting cells (APCs) and stimulated immune responses. The fatty acid-conjugated vaccine antigen could provide improved storage stability but also enhance immunogenic efficacy compared to the native antigen, supporting its potential for further applications.

Are we serologically prepared against an avian influenza pandemic and could seasonal flu vaccines help us?

The current situation with H5N1 highly pathogenic avian influenza virus (HPAI) is causing a worldwide concern due to multiple outbreaks in wild birds, poultry, and mammals. Moreover, multiple zoonotic infections in humans have been reported. Importantly, HPAI H5N1 viruses with genetic markers of adaptation to mammals have been detected. Together with HPAI H5N1, avian influenza viruses H7N9 (high and low pathogenic) stand out due to their high mortality rates in humans. This raises the question of how prepared we are serologically and whether seasonal vaccines are capable of inducing protective immunity against these influenza subtypes. An observational study was conducted in which sera from people born between years 1925-1967, 1968-1977, and 1978-1997 were collected before or after 28 days or 6 months post-vaccination with an inactivated seasonal influenza vaccine. Then, hemagglutination inhibition, viral neutralization, and immunoassays were performed to assess the basal protective immunity of the population as well as the ability of seasonal influenza vaccines to induce protective responses. Our results indicate that subtype-specific serological protection against H5N1 and H7N9 in the representative Spanish population evaluated was limited or nonexistent. However, seasonal vaccination was able to increase the antibody titers to protective levels in a moderate percentage of people, probably due to cross-reactive responses. These findings demonstrate the importance of vaccination and suggest that seasonal influenza vaccines could be used as a first line of defense against an eventual pandemic caused by avian influenza viruses, to be followed immediately by the use of more specific pandemic vaccines.IMPORTANCEInfluenza A viruses (IAV) can infect and replicate in multiple mammalian and avian species. Avian influenza virus (AIV) is a highly contagious viral disease that occurs primarily in poultry and wild water birds. Due to the lack of population immunity in humans and ongoing evolution of AIV, there is a continuing risk that new IAV could emerge and rapidly spread worldwide, causing a pandemic, if the ability to transmit efficiently among humans was gained. The aim of this study is to analyze the basal protection and presence of antibodies against IAV H5N1 and H7N9 subtypes in the population from different ages. Moreover, we have evaluated the humoral response after immunization with a seasonal influenza vaccine. This study is strategically important to evaluate the level of population immunity that is a major factor when assessing the impact that an emerging IAV strain would have, and the role of seasonal vaccines to mitigate the effects of a pandemic.

Disparities in Influenza Control and Surveillance in Latin America and the Caribbean

To identify measures that mitigate the impact of influenza in Latin America and the Caribbean, we compared the burden and detection capacity in humans and animals after the 2009 pandemic. The incidence rate in people was higher in Chile (23.72 per 100,000 people), but the impact was greater for Guatemala (503.78 disability-adjusted life years per 100,000 people). Brazil, Peru, Argentina, and Mexico built better medical testing, with typing being less frequent in Chile and Argentina, where costs for medical care were higher. The positivity rate among avian and nonhuman mammals was 5.8%, with more cases in Mexico, but constant testing in Chile. H5N1, H5N2, and H7N6 are deadly to poultry, whereas H1N1 is common in swine, and H3N8 in equines. By June 2023, H5N1 had caused severe influenza in two persons and killed millions of birds and hundreds of mammals with aquatic lifestyles. An analysis of the efforts in response to this outbreak revealed that handling of outbreaks in animals needs homogeneity and reinforcement of vaccination. Surveillance in exposed individuals requires articulation of medical and animal health authorities, and the region also demands decentralized typing and networks for genomic characterization.

Structurally convergent antibodies derived from different vaccine strategies target the influenza virus HA anchor epitope with a subset of VH3 and VK3 genes

H1N1 influenza viruses are responsible for both seasonal and pandemic influenza. The continual antigenic shift and drift of these viruses highlight the urgent need for a universal influenza vaccine to elicit broadly neutralizing antibodies (bnAbs). Identification and characterization of bnAbs elicited in natural infection and immunization to influenza virus hemagglutinin (HA) can provide insights for development of a universal influenza vaccine. Here, we structurally and biophysically characterize four antibodies that bind to a conserved region on the HA membrane-proximal region known as the anchor epitope. Despite some diversity in their VH and VK genes, the antibodies interact with the HA through germline-encoded residues in HCDR2 and LCDR3. Somatic mutations on HCDR3 also contribute hydrophobic interactions with the conserved HA epitope. This convergent binding mode provides extensive neutralization breadth against H1N1 viruses and suggests possible countermeasures against H1N1 viruses.

Isolation, identification, and challenges of extracellular vesicles: emerging players in clinical applications

Extracellular vesicles (EVs) serve as critical mediators of intercellular communication, encompassing exosomes, microvesicles, and apoptotic vesicles that play significant roles in diverse physiological and pathological contexts. Numerous studies have demonstrated that EVs derived from mesenchymal stem cells (MSC-EVs) play a pivotal role in facilitating tissue and organ repair, alleviating inflammation and apoptosis, enhancing the proliferation of endogenous stem cells within tissues and organs, and modulating immune function-these functions have been extensively utilized in clinical applications. The precise classification, isolation, and identification of MSC-EVs are essential for their clinical applications. This article provides a comprehensive overview of the biological properties of EVs, emphasizing both their advantages and limitations in isolation and identification methodologies. Additionally, we summarize the protein markers associated with MSC-EVs, emphasizing their significance in the treatment of various diseases. Finally, this article addresses the current challenges and dilemmas in developing clinical applications for MSC-EVs, aiming to offer valuable insights for future research.

Immune responses to avian influenza viruses in chickens

Chickens are a key species in both the manifestation of avian influenza and the potential for zoonotic transmission. Avian influenza virus (AIV) infection in chickens can range from asymptomatic or mild disease with low pathogenic AIVs (LPAIVs) to systemic fatal disease with high pathogenic AIVs (HPAIVs). During AIV infection in chickens, Toll-like receptor 7 and melanoma differentiation-associated gene 5 are upregulated to detect the single-stranded ribonucleic acid genomes of AIV, triggering a signaling cascade that produces interferons (IFNs) and pro-inflammatory cytokines. These inflammatory mediators induce the expression of antiviral proteins and recruit immune system cells, such as macrophages and dendritic cells, to the infection site. AIV evades these antiviral responses primarily through its non-structural protein 1, which suppresses type I IFNs, influencing viral pathogenicity. The uncontrolled release of pro-inflammatory cytokines may contribute to the pathogenicity and high mortality associated with HPAIV infections. AIV modulates apoptosis in chicken cells to enhance its replication, with variations in apoptosis pathways influenced by viral strain and host cell type. The presentation of AIV antigens to T and B cells leads to the production of neutralizing antibodies and the targeted destruction of infected cells by CD8+ T cells, respectively, which enhances protection and establishes immunological memory. This review explores the diverse innate and adaptive immune responses in chickens to different AIVs, focusing on the dynamics of these responses relative to protection, susceptibility, and potential immunopathology. By understanding these immune mechanisms, informed strategies for controlling AIV infection and improving chicken health can be developed.

Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model

Understanding how immune history influences influenza immunity is essential for developing effective vaccines and therapeutic strategies. This study examines the antigenic imprinting of influenza hemagglutinin (HA) and neuraminidase (NA) using a mouse model with sequential infections by H1N1 virus strains exhibiting substantial antigenic differences in HA. In our pre-2009 influenza infection model, we observed that mice with more extensive infection histories produced higher levels of functional NA-inhibiting antibodies (NAI). However, following further infection with the 2009 pandemic H1N1 strain, these mice demonstrated a reduced NAI to the challenged virus. Interestingly, prior exposure to older strains resulted in a lower HA antibody response (neutralization and HAI) to the challenged virus in both pre- and post-2009 scenarios, potentially due to faster viral clearance facilitated by immune memory recall. Overall, our findings reveal distinct trajectories in HA and NA immune responses, suggesting that immune imprinting can differentially impact these proteins based on the extent of antigenic variation in influenza viruses.

IMPORTANCE

Influenza viruses continue to pose a significant threat to human health, with vaccine effectiveness remaining a persistent challenge. Individual immune history is a crucial factor that can influence antibody responses to subsequent influenza exposures. While many studies have explored how pre-existing antibodies shape the induction of anti-HA antibodies following influenza virus infections or vaccinations, the impact on anti-NA antibodies has been less extensively studied. Using a mouse model, our study demonstrates that within pre-2009 H1N1 strains, an extensive immune history negatively impacted anti-HA antibody responses but enhanced anti-NA antibody responses. However, in response to the 2009 pandemic H1N1 strain, which experienced an antigenic shift, both anti-HA and anti-NA antibody responses were hindered by antibodies from prior pre-2009 H1N1 virus infections. These findings provide important insights into how antigenic imprinting affects both anti-HA and anti-NA antibody responses and underscore the need to consider immune history in developing more effective influenza vaccination strategies.

Pre-exposure antibody prophylaxis protects macaques from severe influenza

Influenza virus pandemics and seasonal epidemics have claimed countless lives. Recurrent zoonotic spillovers of influenza viruses with pandemic potential underscore the need for effective countermeasures. In this study, we show that pre-exposure prophylaxis with broadly neutralizing antibody (bnAb) MEDI8852 is highly effective in protecting cynomolgus macaques from severe disease caused by aerosolized highly pathogenic avian influenza H5N1 virus infection. Protection was antibody dose-dependent yet independent of Fc-mediated effector functions at the dose tested. Macaques receiving MEDI8852 at 10 milligrams per kilogram or higher had negligible impairment of respiratory function after infection, whereas control animals were not protected from severe disease and fatality. Given the breadth of MEDI8852 and other bnAbs, we anticipate that protection from unforeseen pandemic influenza A viruses is achievable.

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.

Evaluation of Influenza Vaccine Effectiveness from 2021 to 2024: A Guangdong-Based Test-Negative Case-Control Study

BACKGROUND

The influenza virus's high mutation rate requires the annual reformulation and administration of the vaccine. Therefore, its vaccine effectiveness (VE) must be evaluated annually.

AIM

Estimate the effectiveness of the influenza vaccine and analyze the impact of age, seasonal variations, and the vaccination to sample collection interval on VE.

METHODS

The study used a test-negative case-control (TNCC) design to collect data from patients under 18 years of age who presented with acute respiratory infection (ARI) symptoms and underwent influenza virus testing at a national children's regional medical center in Guangdong Province between October 2021 and January 2024, spanning three influenza seasons. VE was estimated using unconditional logistic regression.

RESULTS

A total of 27,670 patient data entries were analyzed. The VE against all influenza viruses across the three seasons was 37% (95% CI: 31-43), with the lowest VE of 24% (95% CI: 8-37) observed in the 2021-2022 season. In children aged 0.5 to <3 years, the VE was 32% (95% CI: 19-43). The effectiveness for samples collected at intervals of 0.5-2 months, 3-6 months, and over 6 months after vaccination was 39% (95% CI: 32-46), 30% (95% CI: 19-40), and 28% (95% CI: 5-46).

CONCLUSIONS

Across three influenza seasons, at least one-third of vaccinated individuals were protected from influenza in outpatient settings. Given that children are at high risk, improving vaccination management is recommended, and parents should be encouraged to vaccinate their children before each influenza season.

Use of equine H3N8 hemagglutinin as a broadly protective influenza vaccine immunogen

Development of an efficacious universal influenza vaccines remains a long-sought goal. Current vaccines have shortfalls such as mid/low efficacy and needing yearly strain revisions to account for viral drift/shift. Horses undergo bi-annual vaccines for the H3N8 equine influenza virus, and surveillance of sera from vaccinees demonstrated very broad reactivity and neutralization to many influenza strains. Subsequently, vaccinating mice using the equine A/Kentucky/1/1991 strain or recombinant hemagglutinin (HA) induced similar broadly reactive and neutralizing antibodies to seasonal and high pathogenicity avian influenza strains. Challenge of vaccinated mice protected from lethal virus challenges across H1N1 and H3N2 strains. This protection correlated with neutralizing antibodies to the HA head, esterase, and stem regions. Vaccinated ferrets were also protected after challenge with H1N1 influenza A/07/2009 virus using whole viral or HA. These data suggest that equine H3N8 induces broad protection against multiple influenzas using a unique antigen that diverges from other universal vaccine approaches.

mRNA Vaccines Against COVID-19 as Trailblazers for Other Human Infectious Diseases

mRNA vaccines represent a milestone in the history of vaccinology, because they are safe, very effective, quick and cost-effective to produce, easy to adapt should the antigen vary, and able to induce humoral and cellular immunity.

METHODS

To date, only two COVID-19 mRNA and one RSV vaccines have been approved. However, several mRNA vaccines are currently under development for the prevention of human viral (influenza, human immunodeficiency virus [HIV], Epstein-Barr virus, cytomegalovirus, Zika, respiratory syncytial virus, metapneumovirus/parainfluenza 3, Chikungunya, Nipah, rabies, varicella zoster virus, and herpes simplex virus 1 and 2), bacterial (tuberculosis), and parasitic (malaria) diseases.

RESULTS

RNA viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV)-2, HIV, and influenza, are characterized by high variability, thus creating the need to rapidly adapt the vaccines to the circulating viral strain, a task that mRNA vaccines can easily accomplish; however, the speed of variability may be higher than the time needed for a vaccine to be adapted. mRNA vaccines, using lipid nanoparticles as the delivery system, may act as adjuvants, thus powerfully stimulating innate as well as adaptive immunity, both humoral, which is rapidly waning, and cell-mediated, which is highly persistent. Safety profiles were satisfactory, considering that only a slight increase in prognostically favorable anaphylactic reactions in young females and myopericarditis in young males has been observed.

CONCLUSIONS

The COVID-19 pandemic determined a shift in the use of RNA: after having been used in medicine as micro-RNAs and tumor vaccines, the new era of anti-infectious mRNA vaccines has begun, which is currently in great development, to either improve already available, but unsatisfactory, vaccines or develop protective vaccines against infectious agents for which no preventative tools have been realized yet.

Trivalent oleanolic acid-glucose conjugates: Synthesis and efficacy against Influenza A virus

Influenza A virus (IAV) leads to significant morbidity and mortality due to the seasonal epidemics and spread. We have demonstrated that oleanolic acid (OA) C28 glucose conjugates and OA trimers are capable of effectively blocking the recognition and interaction between the influenza virus and host cells. In this study, a series of OA-glucose trimers were designed and synthesized through the CuAAC reaction. All trimers underwent screening for anti-IAV activities in vitro. Among these, compounds 13a and 13b showed inhibitory activity against the influenza virus, with IC50 values of 0.68 μM and 0.47 μM, respectively, demonstrating greater potency than oseltamivir (IC50 = 1.36 μM). Results from the time-of-addition experiment and hemagglutination inhibition assay suggest that these OA-glucose trimers may disrupt the recognition between the HA protein of IAV and sialic acid receptors on host cells, thus blocking viral entry. Furthermore, it was found that compound 13b effectively inhibits IAV infection in BALB/c mice. This study has elucidated the structure-activity relationships of OA trimers against the influenza virus and highlighted the utility of multivalent OA conjugates for enhancing ligand-target interactions in anti-influenza virus drug design, laying a groundwork for future research into the antiviral applications of these natural products.

Influenza A virus continues to circulate among children in Linyi, northern China, after the relaxation of COVID-19 control measures

Following the relaxation of control measures for COVID-19 in China in December 2022, there was a resurgence of influenza A among children in Linyi. This research aims to analyze the epidemiology and genetic characteristics of influenza A viruses circulating among children in Linyi from April 2022 to March 2024. Throat swab specimens were collected from children with influenza-like illness (ILI), and the types of influenza were identified. The hemagglutinin (HA) genes of influenza A viruses were amplified using reverse transcription-polymerase chain reaction (RT-PCR) and then sequenced. Subsequently, the gene characteristics and phylogenetics of these sequences were analyzed. A total of 6258 cases of influenza A were tested from 54,926 children with ILI over two years, showing three epidemic waves: one in summer 2022 and two in spring and winter 2023. The epidemic waves in summer 2022 and winter 2023 were caused by influenza A(H3N2) viruses. In spring 2023, influenza A(H1N1)pdm09 viruses accounted for 77.1% and A(H3N2) viruses accounted for 22.9%, respectively. The influenza A(H1N1)pdm09 viruses belonged to clade 6B.1A.5a.2a, while the influenza A(H3N2) viruses evolved from clade 3C.2a1b.2a.1a to 3C.2a1b.2a.2a.3a.1. Compared with the vaccine strain of the Northern Hemisphere of the current year, multiple amino acid substitutions and glycosylation sites changes were observed in the HA protein that most likely resulted in antigenic drift. The influenza A viruses have been circulating and evolving persistently in Linyi from 2022 to 2024. Continuous surveillance is essential for comprehending the dynamics of influenza in the post-COVID-19 era.

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.

Whole-genome analysis of circulating influenza A virus (H3N2) strains in Shanghai, China from 2005 to 2023

Seasonal influenza A virus subtype H3N2 (A/H3N2) circulates globally and has been linked to higher hospitalization rates and summer outbreaks in temperate regions. Here, A/H3N2 circulation in Shanghai, China was systematically studied using data and materials generated by the Shanghai influenza surveillance network from 2005 to 2023. Time-series analysis of incidence and subtyping data showed that A/H3N2 co-circulated with other (sub)types and dominated in multiple seasonal influenza peaks, preferentially in summer. Whole genomes of 528 representative strains were sequenced, and spatiotemporal phylodynamic analysis using these and GISAID-archived sequences demonstrated that in the years before the COVID-19 pandemic, phylogenetically similar strains were circulating locally and elsewhere. However, clade 1a.1 (within 3C.2a.1b.2a), circulated in and only in Shanghai and domestically in 2022, while the sibling clade 2 predominated in other regions. Interestingly, clade 1a.1 was swiftly and completely replaced by clade 2, mostly 2a.3a.1, at the start of 2023. In hemagglutination inhibition and neutralization assays, sera from healthy donors collected in 2022 displayed higher or similar reactivity against 2a.3a.1 compared to 1a.1. By contrast, transcription and replication competence of 2a.3a.1 in MDCK cells was higher than 1a.1. These results indicated that instead of antigenicity differences enabling evasion of pre-existing immunity, higher replicative capability more likely contributed to 2a.3a.1 viruses achieving dominance in China. In addition to summarizing patterns of A/H3N2 local circulation in Shanghai, this work revealed an unusual episode in A/H3N2 global circulation and evolution dynamics in connection to the COVID-19 pandemic and explored possible mechanistic explanations.

Hemagglutinin glycosylation pattern-specific effects: implications for the fitness of H9.4.2.5-branched H9N2 avian influenza viruses

Since 2007, h9.4.2.5 has emerged as the most predominant branch of H9N2 avian influenza viruses (AIVs) that affects the majority of the global poultry population. The spread of this viral branch in vaccinated chicken flocks has not been considerably curbed despite numerous efforts. The evolutionary fitness of h9.4.2.5-branched AIVs must consequently be taken into consideration. The glycosylation modifications of hemagglutinin (HA) play a pivotal role in regulating the balance between receptor affinity and immune evasion for influenza viruses. Sequence alignment showed that five major HA glycosylation patterns have evolved over time in h9.4.2.5-branched AIVs. Here, we compared the adaptive phenotypes of five virus mutants with different HA glycosylation patterns. According to the results, the mutant with 6 N-linked glycans displayed the best acid and thermal stability and a better capacity for multiplication, although having a relatively lower receptor affinity than 7 glycans. The antigenic profile between the five mutants revealed a distinct antigenic distance, indicating that variations in glycosylation level have an impact on antigenic drift. These findings suggest that changes in the number of glycans on HA can not only modulate the receptor affinity and antigenicity of H9N2 AIVs, but also affect their stability and multiplication. These adaptive phenotypes may underlie the biological basis for the dominant strain switchover of h9.4.2.5-branched AIVs. Overall, our study provides a systematic insight into how changes in HA glycosylation patterns regulate the evolutionary fitness and epidemiological dominance drift of h9.4.2.5-branched H9N2 AIVs, which will be of great benefit for the glycosylation-dependent vaccine design.

Genomic surveillance and evolutionary dynamics of influenza a virus in Sri Lanka

BACKGROUND

Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza seasons in Sri Lanka. Therefore, we sought to understand the molecular epidemiology of the influenza viruses in the Western Province of Sri Lanka, including mutational analysis to investigate the evolutionary dynamics.

METHODOLOGY

A total of 349 individuals presenting with fever and respiratory symptoms were enrolled in this study from November 2022 to May 2024. Nasopharyngeal and oropharyngeal specimens were collected and screened using quantitative PCR to detect Influenza A, Influenza B, and SARS-CoV-2. Subtyping and genomic sequencing was carried out on influenza A strains using Oxford Nanopore Technology.

RESULTS

Influenza A was detected in 49 (14%) patients, influenza B in 20 (5.7%) and SARS-CoV-2 in 41 (11.7%). Co-infections were observed in five participants. The phylogenetic analysis assigned the H1N1 HA gene sequences within the 6B.1 A.5a.2a clade. The HA gene of the H1N1 sequences in 2023 were assigned as belonging to the subclades C.1, C.1.2, and C.1.8, while the 2024 sequences were assigned to subclades C.1.8 and C.1.9. The H3N2 sequences from 2023 were assigned to the 3 C.2a1b.2a.2a.1b clade and subclade G.1.1.2, while the 2024 sequences were assigned to the 3 C.2a1b.2a.2a.3a.1 clade and subclade J.2. The K54Q, A186T, Q189E, E224A, R259K, K308R, I418V, and X215A amino acid substitutions were seen in the H1N1 in the 2023 and 2024 sequences. The 2024 H1N1 sequences additionally exhibited further substitutions, such as V47I, I96T, T120A, A139D, G339X, K156X, and T278S.

CONCLUSION

In this first study using genomic sequencing to characterize the influenza A strains in Sri Lanka, which showed different influenza A viruses circulating in an 18-month period. As the Sri Lankan strains also had certain mutations of unknown significance, it would be important to continue detailed surveillance of the influenza strains in Sri Lanka to choose the most suitable vaccines for the population and the timing of vaccine administration.

Comprehensive molecular epidemiology of influenza viruses in Brazil: insights from a nationwide analysis

Influenza A and B viruses represent significant global health threats, contributing substantially to morbidity and mortality rates. However, a comprehensive understanding of the molecular epidemiology of these viruses in Brazil, a continental-size country and a crucial hub for the entry, circulation, and dissemination of influenza viruses within South America, still needs to be improved. This study addresses this gap by consolidating data and samples across all Brazilian macroregions, as part of the Center for Viral Surveillance and Serological Assessment project, together with an extensive number of other Brazilian sequences provided by a public database during the epidemic seasons spanning 2021-23. Phylogenetic analysis of the hemagglutinin segment of influenza A/H1N1pdm09, A/H3N2, and influenza B/Victoria-lineage viruses revealed that in 2021 and in the first semester of 2022, the A/H3N2 2a.3 strain was the predominant circulating strain. Subsequently, the A/H3N2 2b became the prevalent strain until October, when it was substituted by A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. This scenario was maintained during the year of 2023. B/Victoria emerged and circulated at low levels between December 2021 and September 2022 and then became coprevalent with A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. The comparison between the vaccine strain A/Darwin/9/2021 and circulating viruses revealed shared mutations to aspartic acid at residues 186 and 225 across all A/H3N2 lineages from 2021 to 2023, altering the charge in the receptor-binding domain. For A/H1N1pdm09, the 2022 consensus of 5a.2a.1 and the vaccine strain A/Victoria/2570/2019 showed 14 amino acid substitutions. Key residues H180, D187, K219, R223, E224, and T133 are involved in hydrogen interactions with sialic acids, while N130, K142, and D222 may contribute to distance interactions based on docking analyses. Importantly, distinct influenza A lineage frequency patterns were observed across Brazil's macroregions, underscoring the regional variations in virus circulation. This study characterizes influenza A and B viruses circulating in Brazil, providing insights into their circulation patterns and dynamics across Brazilian macroregions. These findings hold significant implications for public health interventions, informing strategies to mitigate transmission risks, optimize vaccination efforts, and enhance outbreak control measures.

Advances in protein subunit vaccines against H1N1/09 influenza

The A/H1N1pdm09 influenza virus, which caused the 2009 pandemic, has since become a recurring strain in seasonal influenza outbreaks. Given the ongoing threat of influenza, protein subunit vaccines have garnered significant attention for their safety and effectiveness. This review seeks to highlight the latest developments in protein subunit vaccines that specifically target the A/H1N1pdm09 virus. It will also examine the structure and replication cycle of influenza A viruses and compare different types of influenza vaccines. Additionally, the review will address key aspects of H1N1 protein subunit vaccine development, such as antigen selection, protein expression systems, and the use of adjuvants. The role of animal models in evaluating these vaccines will also be discussed. Despite challenges like antigenic variability and the complexities of vaccine production and distribution, protein subunit vaccines remain a promising option for future influenza prevention efforts.

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.

Multifaceted virus-like particles: Navigating towards broadly effective influenza A virus vaccines

The threat of influenza A virus (IAV) remains an annual health concern, as almost 500,000 people die each year due to the seasonal flu. Current flu vaccines are highly dependent on embryonated chicken eggs for production, which is time consuming and costly. These vaccines only confer moderate protections in elderly people, and they lack cross-protectivity; thereby requiring annual reformulation to ensure effectiveness against contemporary circulating strains. To address current limitations, new strategies are being sought, with great emphasis given on exploiting IAV's conserved antigens for vaccine development, and by using different vaccine technologies to enhance immunogenicity and expedite vaccine production. Among these technologies, there are growing pre-clinical and clinical studies involving virus-like particles (VLPs), as they are capable to display multiple conserved IAV antigens and augment their immune responses. In this review, we outline recent findings involving broadly effective IAV antigens and strategies to display these antigens on VLPs. Current production systems for IAV VLP vaccines are comprehensively reviewed. Pain-free methods for administration of IAV VLP vaccines through intranasal and transdermal routes, as well as the mechanisms in stimulating immune responses are discussed in detail. The future perspectives of VLPs in IAV vaccine development are discussed, particularly concerning their potentials in overcoming current immunological limitations of IAV vaccines, and their inherent advantages in exploring intranasal vaccination studies. We also propose avenues to expedite VLP vaccine production, as we envision that there will be more clinical trials involving IAV VLP vaccines, leading to commercialization of these vaccines in the near future.

Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes in Acidic pH

The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding ability and evasion of the host immune response. In this study, we conducted extensive equilibrium microsecond-level all-atom molecular dynamics (MD) simulations of the HA protein to explore the influence of low pH on its conformational dynamics. Specifically, we investigated the impact of protonation on conserved histidine residues (H1062) located in the hinge region of HA2. Our analysis encompassed comparisons between nonprotonated (NP), partially protonated (1P, 2P), and fully protonated (3P) conditions. Our findings reveal substantial pH-dependent conformational alterations in the HA protein, affecting its receptor-binding capability and immune evasion potential. Notably, the nonprotonated form exhibits greater stability compared to protonated states. Conformational shifts in the central helices of HA2 involve outward movement, counterclockwise rotation of protonated helices, and fusion peptide release in protonated systems. Disruption of hydrogen bonds between the fusion peptide and central helices of HA2 drives this release. Moreover, HA1 separation is more likely in the fully protonated system (3P) compared to nonprotonated systems (NP), underscoring the influence of protonation. These insights shed light on influenza virus infection mechanisms and may inform the development of novel antiviral drugs targeting HA protein and pH-responsive drug delivery systems for influenza.

Emergence of highly pathogenic avian influenza viruses H5N1 and H5N5 in white-tailed eagles, 2021-2023

Highly pathogenic avian influenza (HPAI) poses a substantial threat to several raptors. Between 2021 and 2023, HPAI viruses (HPAIVs) of the Goose/Guangdong lineage H5 clade 2.3.4.4b became widespread in wild birds in Norway, and H5N1 and H5N5 viruses were detected in 31 white-tailed eagles (Haliaeetus albicilla, WTEs). Post-mortem examinations of four WTEs revealed no macroscopic pathological findings. Microscopic examinations showed the presence of myocardial and splenic necroses and a few lesions in the brain. In situ hybridization revealed the presence of the virus in several organs, suggesting a multisystemic infection. The detection of HPAIV H5N5 in a WTE in February 2022 marked the first recorded occurrence of this subtype in Norway. Since then, the virus has persisted, sporadically being detected in WTEs and other wild bird species. Phylogenetic analyses reveal that at least two distinct incursions of HPAIV H5N1 Eurasian (EA) genotype C affected WTEs, likely introduced by migratory birds from Eurasia and seabirds entering from Western and Central Europe. Some WTE isolates from 2021 to 2022 clustered with those from Canada and Ireland, aligning with the transatlantic spread of H5N1. Others were related to the 2021 mass mortality of great skuas in the UK or outbreaks in seabird populations, including gannets, gulls and terns, during 2022 in the North Sea region. This suggests that the WTEs were likely preying on the affected birds. Our study highlights that WTEs can act as sentinels for some HPAIV strains, but the absence of several known circulating genotypes in WTEs suggests varying pathogenic effects on this species.

Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies

Glycans linked to proteins and lipids and also occurring in free forms have many functions, and these are partly elicited through specific interactions with glycan-binding proteins (GBPs). These include lectins, adhesins, toxins, hemagglutinins, growth factors, and enzymes, but antibodies can also bind glycans. While humans and other animals generate a vast repertoire of GBPs and different glycans in their glycomes, other organisms, including phage, microbes, protozoans, fungi, and plants also express glycans and GBPs, and these can also interact with their host glycans. This can be termed the protein-glycan interactome, and in nature is likely to be vast, but is so far very poorly described. Understanding the breadth of the protein-glycan interactome is also a key to unlocking our understanding of infectious diseases involving glycans, and immunology associated with antibodies binding to glycans. A key technological advance in this area has been the development of glycan microarrays. This is a display technology in which minute quantities of glycans are attached to the surfaces of slides or beads. This allows the arrayed glycans to be interrogated by GBPs and antibodies in a relatively high throughput approach, in which a protein may bind to one or more distinct glycans. Such binding can lead to novel insights and hypotheses regarding both the function of the GBP, the specificity of an antibody and the function of the glycan within the context of the protein-glycan interactome. This article focuses on the types of glycan microarray technologies currently available to study animal glycobiology and examples of breakthroughs aided by these technologies.

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.

Investigate the potential impact of Hemagglutinin from the H1N1 strain on severe pneumonia

The most prevalent glycoprotein on the influenza virus envelope is called hemagglutinin (HA), yet little is known about its involvement in the pathophysiology and etiology of severe influenza pneumonia. Here, after stimulating human bronchial epithelial cells (16-HBE) and mice with HA of H1N1 for 12 h, we investigated the proliferation, migration, inflammatory cytokines expression, and apoptosis in 16-HBE and the pathological damage in mouse lung tissue. The expression of inflammatory cytokines plasminogen activator inhibitor 1(PAI-1), urokinase-type (uPA) and tissue-type (tPA) plasminogen activators, and apoptosis were all enhanced by HA, which also prevented the proliferation and migration of bronchial epithelial cells. HA enhanced up-regulated PAI-1, uPA, and tPA protein expression within mouse lung tissue and caused lung injury. In conclusion, HA alone, but not the whole H1N1 virus, induces lung tissue injury by inhibiting cell proliferation and migration, while promoting the expression of inflammatory cytokines and apoptosis.

Pre-existing H1N1 immunity reduces severe disease with bovine H5N1 influenza virus

The emergence of highly pathogenic H5N1 avian influenza in dairy cattle herds across the United States has caused multiple mild human infections. There is an urgent need to understand the risk of spillover into humans. Here, we show that pre-existing immunity from the 2009 H1N1 pandemic influenza virus provided protection from mortality and severe clinical disease to ferrets intranasally infected with bovine H5N1. H1N1 immune ferrets exhibited a differential tissue tropism with little bovine H5N1 viral dissemination to organs outside the respiratory tract and significantly less H5N1 virus found in nasal secretions and the respiratory tract. Additionally, ferrets with H1N1 prior immunity produced antibodies that cross-reacted with H5N1 neuraminidase protein. Taken together, these results suggest that mild disease in humans may be linked to prior immunity to human seasonal influenza viruses.

Effects of Alkaline Solutions on the Structure and Function of Influenza A Virus

Influenza A virus (IAV) infection contributes to high annual morbidity and mortality, thus necessitating measures aimed at protecting against the disease. Alcohol-based disinfectants are commonly used to inactivate IAV, but they have several undesirable properties. In search of other means which would inactivate IAV, we focused on the effect of alkaline solutions on IAV. We found the viral infectivity remarkably decreased with treatment of an alkaline solution at pH 12.0 for 1 min, where destruction of the viral spikes was observed using an electron microscope. A more detailed examination revealed that the infectivity of IAV was remarkedly reduced by brief treatment with the alkaline solution at pH 11.75 or above, most likely due to the degradation of viral hemagglutinin protein. These results show that at a high pH, the haemagglutinin protein is degraded, resulting in very rapid inactivation of IAV.

Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryo-electron tomography

Influenza viruses are enveloped, negative sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80-90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of receptor-free and receptor-bound HA in vitro, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryo-electron tomography (cryoET) to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even inter-glycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8-10 Å reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present new structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.

Genomic Surveillance and Evolutionary Dynamics of Influenza A Virus in Sri Lanka

Background

Influenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza seasons in Sri Lanka. Therefore, we sought to understand the molecular epidemiology of the influenza viruses in the Western Province of Sri Lanka, including mutational analysis to investigate the evolutionary dynamics.

Methods

A total of 349 individuals presenting with fever and respiratory symptoms were enrolled in this study from November 2022 to May 2024. Nasopharyngeal and oropharyngeal specimens were collected and screened using quantitative PCR to detect Influenza A, Influenza B, and SARS-CoV-2. Subtyping and genomic sequencing was carried out on influenza A strains using Oxford Nanopore Technology.

Results

Influenza A was detected in 49 (14%) patients, influenza B in 20 (5.7%) and SARS-CoV-2 in 41 (11.7%). Co-infections were observed in five participants. The phylogenetic analysis assigned the H1N1 HA gene sequences within the 6B.1A.5a.2a clade. The HA gene of the H1N1 sequences in 2023 were assigned as belonging to the subclades C.1, C.1.2, and C.1.8, while the 2024 sequences were assigned to subclades C.1.8 and C.1.9. The H3N2 sequences from 2023 were assigned to the 3C.2a1b.2a.2a.1b clade and subclade G.1.1.2, while the 2024 sequences were assigned to the 3C.2a1b.2a.2a.3a.1 clade and subclade J.2. The K54Q, A186T, Q189E, E224A, R259K, K308R, I418V, and X215A amino acid substitutions were seen in the H1N1 in the 2023 and 2024 sequences. The 2024 H1N1 sequences additionally exhibited further substitutions, such as V47I, I96T, T120A, A139D, G339X, K156X, and T278S.

Conclusion

In this first study using genomic sequencing to characterize the influenza A strains in Sri Lanka, which showed different influenza A viruses circulating in an 18-month period. As the Sri Lankan strains also had certain mutations of unknown significance, it would be important to continue detailed surveillance of the influenza strains in Sri Lanka to choose the most suitable vaccines for the population and the timing of vaccine administration.

LysoPE mediated by respiratory microorganism Aeromicrobium camelliae alleviates H9N2 challenge in mice

Influenza remains a severe respiratory illness that poses significant global health threats. Recent studies have identified distinct microbial communities within the respiratory tract, from nostrils to alveoli. This research explores specific anti-influenza respiratory microbes using a mouse model supported by 16S rDNA sequencing and untargeted metabolomics. The study found that transferring respiratory microbes from mice that survived H9N2 influenza to antibiotic-treated mice enhanced infection resistance. Notably, the levels of Aeromicrobium were significantly higher in the surviving mice. Mice pre-treated with antibiotics and then inoculated with Aeromicrobium camelliae showed reduced infection severity, as evidenced by decreased weight loss, higher survival rates, and lower lung viral titres. Metabolomic analysis revealed elevated LysoPE (16:0) levels in mildly infected mice. In vivo and in vitro experiments indicated that LysoPE (16:0) suppresses inducible nitric oxide synthase (INOS) and cyclooxygenase-2 (COX2) expression, enhancing anti-influenza defences. Our findings suggest that Aeromicrobium camelliae could serve as a potential agent for influenza prevention and a prognostic marker for influenza outcomes.

Ruhao Dashi granules exert therapeutic effects on H1N1 influenza virus infection by altering intestinal microflora composition

Objective

Antiviral medications for influenza could be ineffective due to the emergence of resistant influenza virus strains. Ruhao Dashi (RHDS) granules possess anti-inflammatory and antibacterial effects. The present study aimed to determine the efficacy of RHDS granules in treating influenza-infected mice and the mechanism underlying this treatment as well as its effect on the intestinal flora composition of the infected mice.

Methods

The HPLC-UV method was used to identify the active components of RHDS granules. ICR mice were infected with influenza A virus (IAV) H1N1 subtype through a nasal drip. After the influenza mice model was successfully established, the pathological changes in the lungs were observed for 5 days after gavage treatment with 0.9% sterile saline and low, medium, and high doses (0.07, 0.14, and 0.28 g/mL, respectively) of RHDS granules. The serum levels of the cytokines IL-6 and TNF-α and sIgA were detected by ELISA. Real-time fluorescence quantitative PCR and western blotting assay were performed to determine the expression levels of the tight junction (TJ) proteins claudin-1, occludin, and zonula occludens-1 (ZO-1) in colon tissues. Furthermore, 16S rRNA gene sequencing of feces samples was conducted to assess the effect of RHDS granules on the gut microbiota.

Results

RHDS granules exerted a protective effect on the lung tissues of IAV-infected mice; moreover, the granules reduced the synthesis of proinflammatory cytokines and increased the relative expression levels of claudin-1, occludin, and ZO-1 in colon tissues. Furthermore, RHDS granule treatment increased the relative abundance of Lactobacillus, Akkermansia, and Faecalibaculum and decreased the relative abundance of Muribaculaceae; thus, RHDS granules could stabilize the intestinal microbiota to some extent.

Conclusion

RHDS granules exert a therapeutic effect on IAV-infected mice probably by modifying the structural composition of their intestinal microbiota.

An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies

Despite decades of antibody research, it remains challenging to predict the specificity of an antibody solely based on its sequence. Two major obstacles are the lack of appropriate models and the inaccessibility of datasets for model training. In this study, we curated >5,000 influenza hemagglutinin (HA) antibodies by mining research publications and patents, which revealed many distinct sequence features between antibodies to HA head and stem domains. We then leveraged this dataset to develop a lightweight memory B cell language model (mBLM) for sequence-based antibody specificity prediction. Model explainability analysis showed that mBLM could identify key sequence features of HA stem antibodies. Additionally, by applying mBLM to HA antibodies with unknown epitopes, we discovered and experimentally validated many HA stem antibodies. Overall, this study not only advances our molecular understanding of the antibody response to the influenza virus but also provides a valuable resource for applying deep learning to antibody research.

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.

Structure-guided assembly of an influenza spike nanobicelle vaccine provides pan H1 intranasal protection

Development of intranasal vaccines for respiratory viruses has gained popularity. However, currently only a live-attenuated influenza vaccine is FDA-approved for intranasal administration. Here, we focused on influenza virus as it circulates seasonally, has pandemic potential, and has vaccine formulations that present hemagglutinin (HA) in different structural arrangements. These display differences have not been correlated with induction of pan-H1 antibodies or shown to provide intranasal protection. Using electron microscopy, biochemistry and animal studies, we identified HA complexes arranged as lipid discs with multiple trimeric HAs displayed along the perimeter, termed spike nanobicelles (SNB). We utilized a structure-guided approach to synthesize in vitro assembled spiked nanobicelles (IA-SNB) from a classical 1934 H1N1 influenza virus. IA-SNBs elicited pan-H1 antibodies and provided protection against antigenically divergent H1N1 viruses via intranasal immunizations. Viral glycoprotein spikes displayed as SNBs could aid in combating antigenic variation and provide innovative intranasal vaccines to aid universal influenza vaccine development.