Evaluation of Next-Generation H3 Influenza Vaccines in Ferrets Pre-Immune to Historical H3N2 Viruses

Multivalent H3 COBRA-based influenza vaccine elicits enhanced immune response in a pre-immune elderly ferret model

Influenza viruses cause significant mortality in humans, especially among people 65 years and older. The outbreaks of A(H3N2) influenza viruses or viruses of vaccine-mismatched strains are usually associated with more severe diseases in elderly population. Vaccination is the practical countermeasure for controlling influenza virus infection in humans. However, the immune responses elicited by current influenza vaccines in elderly are not as robust as those responses elicited in younger adults. There is an urgent need for a universal influenza virus vaccine that can induce broadly protective immunity against viral infection in elderly individuals. Currently, influenza virus vaccines that target conserved epitopes on a variety of influenza virus antigens are under evaluation. However, almost all these vaccine candidates are evaluated in adult animal models. In this study, we evaluated Computationally Optimized Broadly Reactive Antigen (COBRA)-based influenza vaccines in elderly ferrets with pre-existing immunity to historical influenza viruses to assess the breadth of vaccine induced protective antibody responses. Vaccination of elderly ferrets with Infectimune® adjuvanted mixtures of COBRA hemagglutinin (HA) and neuraminidase (NA) recombinant protein vaccines elicited robust binding antibodies against all components in the vaccine. Vaccine formulations with multiple H3 COBRA HA components significantly enhanced hemagglutination-inhibition (HAI) activity against H3N2 viruses. In addition, elderly ferrets vaccinated with multivalent COBRA HA and NA vaccines were protected from infection with reduced nasal virus shedding. Overall, a multivalent COBRA HA and NA vaccine may be an effective vaccine strategy to reduce morbidity and mortality in the elderly.

Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin

Monoclonal antibodies (mAbs) represent one of the most prevalent FDA-approved treatments for autoimmune, infectious, and cancer diseases. However, their discovery and development remains a time-consuming and costly process. Recent advancements in machine learning (ML) and artificial intelligence (AI) have shown significant promise in revolutionizing antibody discovery field. Models that predict antibody biological activity enable in silico evaluation of binding and functional properties; such models can prioritize antibodies with the highest likelihood of success in laboratory testing procedures. We explore an AI model for predicting the binding and receptor blocking activity of antibodies against influenza A hemagglutinin (HA) antigens. Our model is developed with the Molecular Aligned Multi-Modal Architecture and Language (MAMMAL) framework for biologics discovery to predict antibody-antigen interactions using only sequence information. To evaluate the model's performance, we tested it under various data split conditions to mimic real-world scenarios. Our model achieved an area under the receiver operating characteristic (AUROC) score of ≥ 0.91 for predicting the activity of existing antibodies against seen HAs and an AUROC score of 0.9 for unseen HAs. For novel antibody activity prediction, the AUROC was 0.73, which further declined to 0.63-0.66 under stringent constraints on similarity to existing antibodies. These results demonstrate the potential of AI foundation models to transform antibody design by reducing dependence on extensive laboratory testing and enabling more efficient prioritization of antibody candidates. Moreover, our findings emphasize the critical importance of diverse and comprehensive antibody datasets to improve the generalization of prediction models, particularly for novel antibody development.

A single dose of inactivated influenza virus vaccine expressing COBRA hemagglutinin elicits broadly-reactive and long-lasting protection

Influenza virus infections present a pervasive global health concern resulting in millions of hospitalizations and thousands of fatalities annually. To address the influenza antigenic variation, the computationally optimized broadly reactive antigen (COBRA) methodology was used to design influenza hemagglutinin (HA) or neuraminidase (NA) for universal influenza vaccine candidates. In this study, whole inactivated virus (WIV) or split inactivated virus (SIV) vaccine formulations expressing either the H1 COBRA HA or H3 COBRA HA were formulated with or without an adjuvant and tested in ferrets with pre-existing anti-influenza immunity. A single dose of the COBRA-WIV vaccine elicited a robust and broadly reactive antibody response against H1N1 and H3N2 influenza viruses. In contrast, the COBRA-SIV elicited antibodies that recognized fewer viruses, but with R-DOATP, its specificity was expanded. Vaccinated ferrets were protected against morbidity and mortality following challenge with A/California/07/2009 at 14 weeks post-vaccination with reduced viral shedding post-infection compared to the naïve ferrets. However, the COBRA-IIVs did not block the viral transmission to naïve ferrets. The contact infection induced less severe disease and delayed viral shedding than direct infection. Overall, the COBRA HA WIV or the COBRA HA SIV plus R-DOTAP elicited broadly reactive antibodies with long-term protection against viral challenge and reduced viral transmission following a single dose of vaccine in ferrets pre-immune to historical H1N1 and H3N2 influenza viruses. IMPORTANCE The goal of the next-generation influenza vaccine is to provide broadly reactive protection against various drifted influenza strains. With the previous studies evaluating the COBRA HA-based vaccines, the breadth of antibody activities was confirmed following two or three vaccinations. However, for the commercial influenza vaccine, only one shot is required. In this study, only one shot was administrated to the pre-immune ferrets and the COBRA-WIV efficiently elicited broadly reactive antibodies and long-lasting protection against the pdm09 strain. Moreover, this study showed that different infection methods can lead to different disease severity, which emphasizes the significance of the model selection. The infection was conducted 14 weeks post-vaccination to evaluate the long-term protection elicited by only one vaccination. This is the first longevity study describing the immune responses elicited by COBRA-IIVs in ferrets and provides promising results for the potential clinical utilization.

Computationally Optimized Hemagglutinin Proteins Adjuvanted with Infectimune® Generate Broadly Protective Antibody Responses in Mice and Ferrets

Background/Objectives: Standard-of-care influenza vaccines contain antigens that are typically derived from components of wild type (WT) influenza viruses. Often, these antigens elicit strain-specific immune responses and are susceptible to mismatch in seasons where antigenic drift is prevalent. Thanks to advances in viral surveillance and sequencing, influenza vaccine antigens can now be optimized using computationally derived methodologies and algorithms to enhance their immunogenicity. Methods: Mice and ferrets that had been previously exposed to historical H1N1 and H3N2 influenza viruses were vaccinated intramuscularly with bivalent mixtures of H1 and H3 recombinant hemagglutinin (rHA) proteins, which were generated using a computationally optimized broadly reactive antigen (COBRA) design methodology. The vaccine antigens were mixed with a cationic lipid nanoparticle adjuvant, Infectimune®, which promotes both humoral and cellular immune responses. Results: Mice and ferrets vaccinated with Infectimune® and COBRA rHAs elicited protective antibody titers against panels of H1N1 and H3N2 influenza viruses isolated over the past 10 years. These animals also had antibodies that neutralized numerous modern H1N1 and H3N2 influenza viruses in vitro. When challenged with the A/Victoria/2570/2019 H1N1 influenza virus, the COBRA rHA vaccinated animals had minimal weight loss, and no detectable virus was present in their respiratory tissues on day 3 post-infection. Conclusions: These results demonstrate that COBRA rHA vaccines formulated with Infectimune® elicit protective antibody responses against influenza strains, which were isolated across periods of time when standard-of-care vaccines were frequently reformulated, thus reducing the need to update vaccines on a nearly annual basis.

Pre-existing immunity to influenza aids ferrets in developing stronger and broader H3 vaccine-induced antibody responses

Influenza seasons occur annually, building immune history for individuals, but the influence of this history on subsequent influenza vaccine protection remains unclear. We extracted data from an animal trial to study its potential impact. The trial involved 80 ferrets, each receiving either one type of infection or a placebo before vaccination. We quantified the vaccine protection by evaluating hemagglutination inhibition (HAI) antibody titer responses. We tested whether hosts with different infection histories exhibited similar level of responses when receiving the same vaccine for all homologous and heterologous outcomes. We observed that different pre-existing immunities were generally beneficial to vaccine induced responses, but varied in magnitude. Without pre-immunity, post-vaccination HAI titers after the 1st dose of the vaccine were less likely to be above 1:40, and a booster shot was needed. Our study suggests that pre-existing immunity may strengthen and extend the homologous and heterologous vaccine responses.

Flu-COVID combo recombinant protein vaccines elicited protective immune responses against both influenza and SARS-CoV-2 viruses infection

SARS-CoV-2 and Influenza viruses are both highly transmissible airborne viruses and causing high morbidity and mortality. Co-infection of these two viruses results in severe disease that have been observed when influenza and SARS-CoV-2 viruses cocirculated in the past three years, and vaccination is still the effective way to prevent these two diseases. However, influenza and COVID-19 vaccines are designed and manufactured in different platforms, all the individuals will need to get two shots in order to prevent those two severe respiratory diseases. Therefore, it is urgent to develop a Flu-COVID combo vaccine to provide an efficient way for receiving immunization against those two diseases. In this study, we developed a flu-COVID combo vaccine that includes both influenza virus haemagglutinin (HA) proteins and SARS-CoV-2 Spike (S) protein which formulated with AddaVax. K18-hACE-2 transgenic mice were intramuscularly vaccinated with either combo vaccine or mono Flu (HA) or COVID (S) recombinant protein vaccine in a prime-boost-boost regimen, and then were challenged with lethal doses of influenza virus or SARS-CoV-2 to evaluate vaccine efficacy. The results showed that Flu-COVID combo vaccine protected mice from both Influenza and SARS-CoV-2 challenge by preventing body weight loss and clinical signs progression. The protective immune responses elicited by Flu-COVID combo vaccine were equivalent to those elicited by mono flu or COVID recombinant protein vaccines. In conclusion, our study highlights the effectiveness of the FLU-COVID combo recombinant protein vaccine in preventing both influenza and COVID-19 infections.

A computationally optimized broadly reactive hemagglutinin vaccine elicits neutralizing antibodies against influenza B viruses from both lineages

Influenza B viruses (IBV) can cause severe disease and death much like influenza A viruses (IAV), with a disproportionate number of infections in children. Despite moving to a quadrivalent vaccine to include strains from both the B/Victoria and B/Yamagata lineages, vaccine effectiveness rates continue to be variable and low in many past seasons. To develop more effective influenza B virus vaccines, three novel IBV hemagglutinin (HA) vaccines were designed using a computationally optimized broadly reactive antigen (COBRA) methodology. These IBV HA proteins were expressed on the surface of a virus-like particle (VLP) and used to vaccinate ferrets that were pre-immune to historical B/Victoria or B/Yamagata lineage viruses. Ferrets vaccinated with B-COBRA HA vaccines had neutralizing antibodies with high titer HAI titer against all influenza B viruses regardless of pre-immunization history. Conversely, VLPs expressing wild-type IBV HA antigens preferentially boosted titers against viruses from the same lineage and there was little-to-no seroprotective antibodies detected in ferrets with mismatched IBV pre-immune infections. Overall, a single IBV HA developed using the COBRA methodology elicited protective broadly-reactive antibodies against current and future drifted IBVs from both lineages.

Evaluation of Pre-Pandemic Trivalent COBRA HA Vaccine in Mice Pre-Immune to Historical H1N1 and H3N2 Influenza Viruses

Initial exposure to influenza virus(es) during early childhood produces protective antibodies that may be recalled following future exposure to subsequent viral infections or vaccinations. Most influenza vaccine research studies use immunologically naïve animal models to assess vaccine effectiveness. However, most people have an extensive influenza immune history, with memory cells produced by viruses or vaccines representing multiple influenza viruses. In this study, we explored the effect influenza seasonal virus-induced immunity has on pre-pandemic influenza virus vaccination. The mice that were pre-immune to historical H1N1 and H3N2 seasonal influenza viruses were vaccinated with adjuvanted pre-pandemic (H2, H5, and H7) HA-based computationally optimized broadly reactive antigen (COBRA) vaccines, and were fully protected from lethal challenge, whereas the mock-vaccinated mice, with or without pre-immunity, were not protected from morbidity or mortality. Detectable antibody titers were present in the pre-immune mice vaccinated with a single dose of vaccine, but not in the immunologically naïve mice. The mice vaccinated twice with the trivalent COBRA HA vaccine had similar antibody titers regardless of their pre-immune status. Overall, seasonal pre-immunity did not interfere with the immune responses elicited by pre-pandemic COBRA HA vaccines or the protection against pre-pandemic viruses.

Broadly Protective Neuraminidase-Based Influenza Vaccines and Monoclonal Antibodies: Target Epitopes and Mechanisms of Action

Neuraminidase (NA) is an important surface protein on influenza virions, playing an essential role in the viral life cycle and being a key target of the immune system. Despite the importance of NA-based immunity, current vaccines are focused on the hemagglutinin (HA) protein as the target for protective antibodies, and the amount of NA is not standardized in virion-based vaccines. Antibodies targeting NA are predominantly protective, reducing infection severity and viral shedding. Recently, NA-specific monoclonal antibodies have been characterized, and their target epitopes have been identified. This review summarizes the characteristics of NA, NA-specific antibodies, the mechanism of NA inhibition, and the recent efforts towards developing NA-based and NA-incorporating influenza vaccines.

Ferret model to mimic the sequential exposure of humans to historical H3N2 influenza viruses

Mutations accumulate in influenza A virus proteins, especially in the main epitopes on the virus surface glycoprotein hemagglutinin (HA). For influenza A(H3N2) viruses, in particular, the antigenicity of their HA has altered since their emergence in 1968, requiring changes of vaccine strains every few years. Most adults have been exposed to several antigenically divergent H3N2 viruses through infection and/or vaccination, and those exposures affect the immune responses of those individuals. However, animal models reflecting this 'immune history' in humans are lacking and naïve animals are generally used for vaccination and virus challenge studies. Here, we describe a ferret model to mimic the serial exposure of humans to antigenically different historical H3HA proteins. In this model, ferrets were sequentially immunized with adjuvanted recombinant H3HA proteins from two or three different H3HA antigenic clusters in chronological order, and serum neutralizing antibody titers were examined against the homologous virus and viruses from different antigenic clusters. For ferrets immunized with a single HA antigen, serum neutralizing antibody titers were elevated specifically against the homologous virus. However, after immunization with the second or third antigenically distinct HA antigen in chronological order, the ferrets showed an increase in more broadly cross-reactive neutralizing titers against the antigenically distinct viruses and against the homologous virus. Sequentially immunized animals challenged with an antigenically advanced H3N2 virus showed attenuated virus growth and less body temperature increase compared with naïve animals. These results suggest that sequential exposure to antigenically different HAs elicits broader neutralizing activity in sera and enhances immune responses against more antigenically distinct viruses Our findings may partly explain why adults who have been exposed to antigenically divergent HAs are less likely to be infected with influenza virus and have severe symptoms than children.

Development of a broadly active influenza intranasal vaccine adjuvanted with self-assembled particles composed of mastoparan-7 and CpG

Currently licensed vaccine adjuvants offer limited mucosal immunity, which is needed to better combat respiratory infections such as influenza. Mast cells (MCs) are emerging as a target for a new class of mucosal vaccine adjuvants. Here, we developed and characterized a nanoparticulate adjuvant composed of an MC activator [mastoparan-7 (M7)] and a TLR ligand (CpG). This novel nanoparticle (NP) adjuvant was co-formulated with a computationally optimized broadly reactive antigen (COBRA) for hemagglutinin (HA), which is broadly reactive against influenza strains. M7 was combined at different ratios with CpG and tested for in vitro immune responses and cytotoxicity. We observed significantly higher cytokine production in dendritic cells and MCs with the lowest cytotoxicity at a charge-neutralizing ratio of nitrogen/phosphate = 1 for M7 and CpG. This combination formed spherical NPs approximately 200 nm in diameter with self-assembling capacity. Mice were vaccinated intranasally with COBRA HA and M7-CpG NPs in a prime-boost-boost schedule. Vaccinated mice had significantly higher antigen-specific antibody responses (IgG and IgA) in serum and mucosa compared with controls. Splenocytes from vaccinated mice had significantly increased cytokine production upon antigen recall and the presence of central and effector memory T cells in draining lymph nodes. Finally, co-immunization with NPs and COBRA HA induced influenza H3N2-specific HA inhibition antibody titers across multiple strains and partially protected mice from a challenge against an H3N2 virus. These results illustrate that the M7-CpG NP adjuvant combination can induce a protective immune response with a broadly reactive influenza antigen via mucosal vaccination.

Influenza and Universal Vaccine Research in China

Influenza viruses usually cause seasonal influenza epidemics and influenza pandemics, resulting in acute respiratory illness and, in severe cases, multiple organ complications and even death, posing a serious global and human health burden. Compared with other countries, China has a large population base and a large number of influenza cases and deaths. Currently, influenza vaccination remains the most cost-effective and efficient way to prevent and control influenza, which can significantly reduce the risk of influenza virus infection and serious complications. The antigenicity of the influenza vaccine exhibits good protective efficacy when matched to the seasonal epidemic strain. However, when influenza viruses undergo rapid and sustained antigenic drift resulting in a mismatch between the vaccine strain and the epidemic strain, the protective effect is greatly reduced. As a result, the flu vaccine must be reformulated and readministered annually, causing a significant drain on human and financial resources. Therefore, the development of a universal influenza vaccine is necessary for the complete fight against the influenza virus. By statistically analyzing cases related to influenza virus infection and death in China in recent years, this paper describes the existing marketed vaccines, vaccine distribution and vaccination in China and summarizes the candidate immunogens designed based on the structure of influenza virus, hoping to provide ideas for the design and development of new influenza vaccines in the future.

Differential Recognition of Computationally Optimized H3 Hemagglutinin Influenza Vaccine Candidates by Human Antibodies

Among circulating influenza viruses in humans, H3N2 viruses typically evolve faster than other subtypes and have caused disease in millions of people since emerging in 1968. Computationally optimized broadly reactive antigen (COBRA) technology is one strategy to broaden vaccine-elicited antibody responses among influenza subtypes. In this study, we determined the structural integrity of an H3N2 COBRA hemagglutinin (HA), TJ5, and we probed the antigenic profile of several H3N2 COBRA HAs by assessing recognition of these immunogens by human B cells from seasonally vaccinated human subjects. Of three recently described COBRA H3 HA antigens (TJ5, NG2, and J4), we determined that TJ5 and J4 HA proteins recognize pre-existing B cells more effectively than NG2 HA and a wild-type Hong Kong/4801/2014 protein. We also isolated a panel of 12 H3 HA-specific human monoclonal antibodies (MAbs) and identified that most MAbs recognize both wild-type and COBRA HA proteins and have functional activity against a broad panel of H3N2 viruses. Most MAbs target the receptor-binding site, and one MAb targets the HA stem. MAb TJ5-5 recognizes TJ5 and J4 COBRA HA proteins but has poor recognition of NG2 HA, similar to the global B-cell analysis. We determined a 3.4 Å structure via cryo-electron microscopy of Fab TJ5-5 complexed with the H3 COBRA TJ5, which revealed residues important to the differential binding. Overall, these studies determined that COBRA H3 HA proteins have correct antigenic and structural features, and the proteins are recognized by B cells and MAbs isolated from seasonally vaccinated humans. IMPORTANCE Vaccine development for circulating influenza viruses, particularly for the H3N2 subtype, remains challenging due to consistent antigenic drift. Computationally optimized broadly reactive antigen (COBRA) technology has proven effective for broadening influenza hemagglutinin (HA)-elicited antibody responses compared to wild-type immunogens. Here, we determined the structural features and antigenic profiles of H3 COBRA HA proteins. Two H3 COBRA HA proteins, TJ5 and J4, are better recognized by pre-existing B cells and monoclonal antibodies from the 2017 to 2018 vaccine season compared to COBRA NG2 and a wild-type A/Hong Kong/2014 HA protein. We determined a cryo-electron microscopy (cryo-EM) structure of one MAb that poorly recognizes NG2, MAb TJ5-5, in complex with the TJ5 COBRA HA protein and identified residues critical to MAb recognition. As NG2 is more effective than TJ5 for the recent Hong Kong/2019 virus, these data provide insights into the diminished effectiveness of influenza vaccines across vaccine seasons.

Bivalent H1 and H3 COBRA Recombinant Hemagglutinin Vaccines Elicit Seroprotective Antibodies against H1N1 and H3N2 Influenza Viruses from 2009 to 2019

Commercial influenza virus vaccines often elicit strain-specific immune responses and have difficulties preventing illness caused by antigenically drifted viral variants. In the last 20 years, the H3N2 component of the annual vaccine has been updated nearly twice as often as the H1N1 component, and in 2019, a mismatch between the wild-type (WT) H3N2 vaccine strain and circulating H3N2 influenza strains led to a vaccine efficacy of ∼9%. Modern methods of developing computationally optimized broadly reactive antigens (COBRAs) for H3N2 influenza viruses utilize current viral surveillance information to design more broadly reactive vaccine antigens. Here, 7 new recombinant hemagglutinin (rHA) H3 COBRA hemagglutinin (HA) antigens were evaluated in mice. Subsequently, two candidates, J4 and NG2, were selected for further testing in influenza-preimmune animals based on their ability to elicit broadly reactive antibodies against antigenically drifted H3N2 viral isolates. In the preimmune model, monovalent formulations of J4 and NG2 elicited broadly reactive antibodies against recently circulating H3N2 influenza viruses from 2019. Bivalent mixtures of COBRA H1 and H3 rHA, Y2 + J4, and Y2 + NG2 outperformed multiple WT H1+H3 bivalent rHA mixtures by eliciting seroprotective antibodies against H1N1 and H3N2 isolates from 2009 to 2019. Overall, the newly generated COBRA HA antigens, namely, Y2, J4, and NG2, had the ability to induce broadly reactive antibodies in influenza-naive and preimmune animals in both monovalent and bivalent formulations, and these antigens outperformed H1 and H3 WT rHA vaccine antigens by eliciting seroprotective antibodies against panels of antigenically drifted historical H1N1 and H3N2 vaccine strains from 2009 to 2019. IMPORTANCE Standard-of-care influenza virus vaccines are composed of a mixture of antigens from different influenza viral subtypes. For the first time, lead COBRA H1 and H3 HA antigens, formulated as a bivalent vaccine, have been investigated in animals with preexisting immunity to influenza viruses. The cocktail of COBRA HA antigens elicited more broadly reactive anti-HA antibodies than those elicited by a comparator bivalent wild-type HA vaccine against H1 and H3 influenza viruses isolated between 2009 and 2019.