Influenza Research Research Articles

Delay of innate immune responses following influenza B virus infection affects the development of a robust antibody response in ferrets.

The ferret is the primary animal model for human influenza research. Using a ferret model, we studied the differences in both innate and adaptive immune responses following infection with influenza A and B viruses (IAV and IBV). Antibodies generated following infection of ferrets is used for surveillance assays to detect antigenic drift and cross-reactivity with vaccine viruses and circulating influenza strains. IAV infection of ferrets to generate these reagents resulted in a strong antibody response, but IBV infection generated weak antibody responses. In this study using influenza-infected ferrets, we found that IAV resulted in an early activation of the interferon (IFN) and pro-inflammatory response, whereas IBV showed a delay and reduction in these responses. Serum levels of IFNs and other cytokines or chemokines were much higher in ferrets following IAV infection. These reduced innate responses were reflected the subsequent delayed and reduced antibody responses to IBV in the sera. These findings may help in understanding low antibody responses in humans following influenza B vaccination and infection and may warrant the use of innate immunomodulators to overcome these weak responses.

Global research trends in the relationship between influenza and CD4+ T/CD8+ T cells: A bibliometric analysis

ABSTRACT Influenza pathogens cause many illnesses and deaths yearly, posing a serious threat to global public health. As a result, most studies are increasingly focusing on the role of specific CD4+ T/CD8+ T cells in combating influenza. This study examines the key themes and trends in this field using bibliometric analysis. Literature on influenza and CD4+ T/CD8+ T cells were searched (from 1985 to 2023) in the Web of Science Core Collection (WoSCC) database. Eligible articles were screened according to the inclusion and exclusion criteria for bibliometric analysis using VOSviewer, CiteSpace, and the R package “bibliometrix.” A total of 1,071 publications from 47 countries or regions and 1,148 institutions associated with 5,728 authors in the disciplines of immunology, virology, biochemistry, and molecular biology were included. The findings indicate a yearly increase in publications related to influenza and CD4+ T/CD8+ T cells, with the United States, Australia, and China leading in publication volume. The University of Melbourne had the highest volume of publications. Only a few researchers collaborated, and the collaborations were mostly concentrated in the same countries/regions. Professor Katherine Kedzierska, associated with The Peter Doherty Institute for Infection and Immunity, was the most productive academic in this field. According to the analysis of highly cited literature and keywords, the application of cellular immunity in formulating pioneering influenza vaccines is a key direction for future research.The role of CD4+ T/CD8+ T cells in combating the influenza virus has emerged as a significant focus within influenza research literature. This article summarizes the research institutions, authors, journals, hotspots, and application trends of CD4+ T/CD8+ T cells in influenza.

Analysis of influenza epidemics during the COVID-19 pandemic using an improved surveillance system (from 2021 to 2024)

Aim. Assessing the effectiveness of new baselines and intensity thresholds of epidemics based on rates of incidence and hospitalization with a diagnosis of “influenza” to clarify the timing of epidemics and their spread throughout the Russian Federation against the backdrop of the COVID-19 pandemic (from 2021 to 2024). Materials and methods. At the A.A. Smorodintsev Influenza Research Institute, the software was reformed taking into account the need to solve the tasks set during the COVID-19 pandemic. Due to changes in influenza surveillance in relation to the diagnosis of “influenza”, and hence the increase in the registration of influenza cases, the baseline and threshold of epidemics were adjusted for the influenza incidence and hospitalization rates in the surveyed cities in total (61) and for each Federal districts (over the entire population and by age groups) for 3 epidemics against the background of COVID-19 pandemic (2021–2022, 2022–2023, and 2023–2024). Results. A comparison of baselines calculated over the previous 6 seasons based on the incidence and hospitalization rates of mostly clinically diagnosed influenza and new baseline levels of incidence and hospitalization rates of mostly laboratory-confirmed influenza during the pandemic showed minor changes in the indicators of baseline incidence and hospitalization rates while epidemic thresholds for these indicators increased. Conclusion. Against the backdrop of the COVID-19 pandemic during the 2020–2021 season, there was no influenza epidemic. In 2021–2022, the A(H3N2) epidemic was of low intensity in terms of incidence, hospitalization rates and low mortality (2 cases). In 2022–2023, the influenza A(H1N1)pdm09 and B epidemic was of moderate intensity in terms of incidence, with a high frequency of hospitalizations and mortality (120 cases). Influenza A(H3N2) and B epidemic in 2023–2024 was of a “very high” level in terms of the influenza incidence, but average in terms of the frequency of hospitalizations and mortality (41 cases), with higher incidence rate compared to the previous epidemic (0.28% and 0.19% of the total population), including persons over 15 years of age (0.19% and 0.12%).

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

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

Research on influenza epidemic and clinical characteristics based on influenza research database.

To compare the epidemic trends of different types of influenza viruses and the clinical characteristics of patients, so as to provide reference for influenza prevention and control. This was descriptive research. The human monitoring data collected from the Influenza Research Database (IRD) from 2006 to 2016 were used to descriptively analyze the distribution of influenza viruses in terms of time, geography, gender and age. The positive samples were divided into three groups based on the type of pathogen (H1N1 influenza A viruses, H3N2 influenza A viruses, and influenza B viruses). Compared and analyzed the distribution and clinical characteristics among groups. There were statistically significant differences in the positive rates among different countries (p< 0.001). The proportion of positive samples gradually decreased with age. The proportion of oseltamivir resistance was significantly higher in H1N1-positive patients compared with that in H3N2-positive patients (p< 0.001). Significant differences were observed in the vaccination status among H1N1, H3N2 and influenza B viruses (p< 0.001). Cough was common in all cases with H1N1, H3N2 and influenza B infections, while cough, fever and running nose occurred more frequently in influenza B-positive cases than those of H1N1-positive and H3N2-positive cases (p< 0.001). People aged 0-18 years are the major susceptible population to influenza, and H1N1 influenza viruses are the main pathogens of infection in this population, with major clinical manifestations of fever, cough and headache. The findings in this study highlight the necessity to strengthen the protection for this age group in clinical practice.

Generation of antigen-specific memory CD4 T cells by heterologous immunization enhances the magnitude of the germinal center response upon influenza infection.

Current influenza vaccine strategies have yet to overcome significant obstacles, including rapid antigenic drift of seasonal influenza viruses, in generating efficacious long-term humoral immunity. Due to the necessity of germinal center formation in generating long-lived high affinity antibodies, the germinal center has increasingly become a target for the development of novel or improvement of less-efficacious vaccines. However, there remains a major gap in current influenza research to effectively target T follicular helper cells during vaccination to alter the germinal center reaction. In this study, we used a heterologous infection or immunization priming strategy to seed an antigen-specific memory CD4+ T cell pool prior to influenza infection in mice to evaluate the effect of recalled memory T follicular helper cells in increased help to influenza-specific primary B cells and enhanced generation of neutralizing antibodies. We found that heterologous priming with intranasal infection with acute lymphocytic choriomeningitis virus (LCMV) or intramuscular immunization with adjuvanted recombinant LCMV glycoprotein induced increased antigen-specific effector CD4+ T and B cellular responses following infection with a recombinant influenza strain that expresses LCMV glycoprotein. Heterologously primed mice had increased expansion of secondary Th1 and Tfh cell subsets, including increased CD4+ TRM cells in the lung. However, the early enhancement of the germinal center cellular response following influenza infection did not impact influenza-specific antibody generation or B cell repertoires compared to primary influenza infection. Overall, our study suggests that while heterologous infection or immunization priming of CD4+ T cells is able to enhance the early germinal center reaction, further studies to understand how to target the germinal center and CD4+ T cells specifically to increase long-lived antiviral humoral immunity are needed.

Public Health Risk from Influenza Viruses: A Scientometric Analysis of Influenza Research.

Seasonal influenza and novel H1N1 influenza from 2009 present worldwide difficulties for public health sectors. It is difficult to distinguish between significant research output due to the rising quantity of papers mentioning this infectious disease. We aimed to identify a scientometric analysis of influenza diseases. We aimed to highlight the progress made in the discipline by the researchers affiliated with most documents. The h-index was used to evaluate the publication performance of highly cited papers. We retrieved the scientometric data using the keywords "Influenza" OR "Flu" OR "Orthomyxoviridae" AND "Antiviral agents" OR "Antiviral drugs." In all, 59013 documents were retrieved from the Web of Science between 2011 and 2020. The exported data to Biblioshiny and Microsoft Excel tools included sources by year, active authors, active journals, and countries. Also, we made use of quantitative analysis with scientometric indicators and knowledge mapping through the VOSviewer visualization software for creating the network visualization maps. We found most papers written in English and other languages were from 402027 authors and listed in 4443 core journals. The researchers found that Palese P produced 155 and received an h-index of 55. The author Li Y has the highest contributions, with 313 publications. In global influenza research, Europe and North America are the most productive and impactful continents. The influenza research has been published in very few journals. This study will help hospital librarians and other library professionals to understand the status of research on influenza at any given point in time.

Intranasal SARS-CoV-2 Omicron variant vaccines elicit humoral and cellular mucosal immunity in female mice

In order to prevent the emergence and spread of future variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), developing vaccines capable of stopping transmission is crucial. The SARS-CoV-2 vaccine NDV-HXP-S can be administered live intranasally (IN) and thus induce protective immunity in the upper respiratory tract. The vaccine is based on Newcastle disease virus (NDV) expressing a stabilised SARS-CoV-2 spike protein. NDV-HXP-S can be produced as influenza virus vaccine at low cost in embryonated chicken eggs. The NDV-HXP-S vaccine was genetically engineered to match the Omicron variants of concern (VOC) BA.1 and BA.5 and tested as an IN two or three dose vaccination regimen in female mice. Furthermore, female mice intramuscularly (IM) vaccinated with mRNA-lipid nanoparticles (LNPs) were IN boosted with NDV-HXP-S. Systemic humoral immunity, memory T cell responses in the lungs and spleens as well as immunoglobulin A (IgA) responses in distinct mucosal tissues were characterised. NDV-HXP-S Omicron variant vaccines elicited high mucosal IgA and serum IgG titers against respective SARS-CoV-2 VOC in female mice following IN administration and protected against challenge from matched variants. Additionally, antigen-specific memory B cells and local T cell responses in the lungs were induced. Host immunity against the NDV vector did not interfere with boosting. Intramuscular vaccination with mRNA-LNPs was enhanced by IN NDV-HXP-S boosting resulting in improvement of serum neutralization titers and induction of mucosal immunity. We demonstrate that NDV-HXP-S Omicron variant vaccines utilised for primary immunizations or boosting efficiently elicit humoral and cellular immunity. The described induction of systemic and mucosal immunity has the potential to reduce infection and transmission. This work was partially funded by the NIAIDCenters of Excellence for Influenza Research and Response (CEIRR) and by the NIAID Collaborative Vaccine Innovation Centers and by institutional funding from the Icahn School of Medicine at Mount Sinai. See under Acknowledgements for details.

Establishment of a humanized ST6GAL1 mouse model for influenza research.

This study aimed to construct and characterize a humanized influenza mouse model expressing hST6GAL1. Humanized fragments, consisting of the endothelial cell-specific K18 promoter, human ST6GAL1-encoding gene, and luciferase gene, were microinjected into the fertilized eggs of mice. The manipulated embryos were transferred into the oviducts of pseudopregnant female mice. The offspring were identified using PCR. Mice exhibiting elevated expression of the hST6GAL1 gene were selectively bred for propagation, and invivo analysis was performed for screening. Expression of the humanized gene was tested by performing immunohistochemical (IHC) analysis. Hematologic and biochemical analyses using the whole blood and serum of humanized hST6GAL1 mice were performed. Successful integration of the human ST6GAL1 gene into the mouse genome led to the overexpression of human SiaT ST6GAL1. Seven mice were identified as carrying copies of the humanized gene, and the invivo analysis indicated that hST6GAL1 gene expression in positive mice mirrored influenza virus infection characteristics. The IHC results revealed that hST6GAL1 was expressed in the lungs of humanized mice. Moreover, the hematologic and biochemical parameters of the positive mice were within the normal range. A humanized influenza mouse model expressing the hST6GAL1 gene was successfully established and characterized.

Sex-based differences in persistent lung inflammation following influenza infection of juvenile outbred mice.

Children are susceptible to influenza infections and can experience severe disease presentation due to a lack of or limited pre-existing immunity. Despite the disproportionate impact influenza has on this population, there is a lack of focus on pediatric influenza research, particularly when it comes to identifying the pathogenesis of long-term outcomes that persist beyond the point of viral clearance. In this study, juvenile outbred male and female mice were infected with influenza and analyzed following viral clearance to determine how sex impacts the persistent inflammatory responses to influenza. It was found that females maintained a broader cytokine response in the lung following clearance of influenza, with innate, type I and type II cytokine signatures in almost all mice. Males, on the other hand, had higher levels of IL-6 and other macrophage-related cytokines, but no evidence of a type I or type II response. The immune landscape was similar in the lungs between males and females postinfection, but males had a higher regulatory T cell to TH1 ratio compared with female mice. Cytokine production positively correlated with the frequency of TH1 cells and exudate macrophages, as well as the number of cells in the bronchoalveolar lavage fluid. Furthermore, female lungs were enriched for metabolites involved in the glycolytic pathway, suggesting glycolysis is higher in female lungs compared with males after viral clearance. These data suggest juvenile female mice have persistent and excessive lung inflammation beyond the point of viral clearance, whereas juvenile males had a more immunosuppressive phenotype.NEW & NOTEWORTHY This study identifies sex-based differences in persistent lung inflammation following influenza infection in an outbred, juvenile animal model of pediatric infection. These findings indicate the importance of considering sex and age as variable in infectious disease research.

Effect of human H3N2 influenza virus reassortment on influenza incidence and severity during the 2017–18 influenza season in the USA: a retrospective observational genomic analysis

During the 2017-18 influenza season in the USA, there was a high incidence of influenza illness and mortality. However, no apparent antigenic change was identified in the dominant H3N2 viruses, and the severity of the season could not be solely attributed to a vaccine mismatch. We aimed to investigate whether the altered virus properties resulting from gene reassortment were underlying causes of the increased case number and disease severity associated with the 2017-18 influenza season. Samples included were collected from patients with influenza who were prospectively recruited during the 2016-17 and 2017-18 influenza seasons at the Johns Hopkins Hospital Emergency Departments in Baltimore, MD, USA, as well as from archived samples from Johns Hopkins Health System sites. Among 647 recruited patients with influenza A virus infection, 411 patients with whole-genome sequences were available in the Johns Hopkins Center of Excellence for Influenza Research and Surveillance network during the 2016-17 and 2017-18 seasons. Phylogenetic trees were constructed based on viral whole-genome sequences. Representative viral isolates of the two seasons were characterised in immortalised cell lines and human nasal epithelial cell cultures, and patients' demographic data and clinical outcomes were analysed. Unique H3N2 reassortment events were observed, resulting in two predominant strains in the 2017-18 season: HA clade 3C.2a2 and clade 3C.3a, which had novel gene segment constellations containing gene segments from HA clade 3C.2a1 viruses. The reassortant re3C.2a2 viruses replicated with faster kinetics and to a higher peak titre compared with the parental 3C.2a2 and 3C.2a1 viruses (48 h vs 72 h). Furthermore, patients infected with reassortant 3C.2a2 viruses had higher Influenza Severity Scores than patients infected with the parental 3C.2a2 viruses (median 3·00 [IQR 1·00-4·00] vs 1·50 [1·00-2·00]; p=0·018). Our findings suggest that the increased severity of the 2017-18 influenza season was due in part to twointrasubtypes, cocirculating H3N2 reassortant viruses with fitness advantages over the parental viruses. This information could help inform future vaccine development and public health policies. The Center of Excellence for Influenza Research and Response in the US, National Science and Technology Council, and Chang Gung Memorial Hospital in Taiwan.

Evaluating the Effectiveness of New Criteria for Early Detection of the Start and Intensity of Influenza Epidemics in Russian Federation

Relevance. During the COVID-19 pandemic, an early determination of the start of the influenza epidemic by the incidence of influenza and SARS in total is impossible, due to the similarity of the clinical picture of SARS and lung cases of COVID-19.Aim. The goal is to calculate and test new criteria for early detection of the start of influenza epidemics and their intensity for each of the cities–reference bases (61) of the 2 WHO National Influenza Centers based on the incidence of clinically diagnosed influenza.Tasks. To evaluate the effectiveness of baseline influenza incidence and epidemic intensity thresholds for the general population and age groups of each city in the epidemic of 2022–2023. To give a retrospective assessment of the effectiveness of influenza baselines for cities, compared with the baselines of the corresponding Federal Districts, for the seasons from 2009 to 2022. To estimate the intensity of epidemics by influenza incidence over the previous epidemies of the pandemic cycle of influenza A/California/H1N1/ virus.Materials and methods. By the 2022–2023 season. baseline lines and thresholds of influenza incidence intensity were calculated using the method of moving epidemics according to clinical diagnostic data not only for federal districts, but also for each of the observed cities (61). The calculation of the baselines was carried out according to the data of the computer database of the Influenza Research Institute on the incidence of influenza by age groups in each city over the previous 5 years in the season from 2016–2017 to 2021–2022.Results. In the 2022-23 season application of new criteria for the start of epidemics (prev.- and post-epidemic baseline influenza incidence) and their intensity revealed: early onset of the influenza epidemic (07–13.11 2022); simultaneous onset in all children's age groups; geographical spread of the epidemic in federal districts; intensity of the epidemic in the general population and age groups. The thresholds for the intensity of influenza morbidity made it possible to clarify the intensity levels of influenza epidemics from 2009 to 2023 and to show that the pandemic cycle of the influenza A(H1N1) virus continues. A comparison of the effectiveness of urban baselines with federal ones in the epidemic of 2022–2023 showed that urban baseline flu incidence lines revealed the start of epidemics 1–3 weeks earlier: among the general population in 12 cities, persons over 15 years old – in 9, children 3–6 years old – in 6 and 7–14 years old – in 5. A retrospective assessment of the effectiveness of city and federal influenza baselines (from 2009 to 2022) showed their effectiveness both in the seasons from 2009 to 2016 (before the baseline calculation period) and after. The effectiveness of urban baselines for early detection of the start of epidemics depended on the etiology of the epidemic – more with influenza A(H3N2) than with influenza A(H1N1), the level of intensity of influenza diseases and the age group of the population (more in children with low intensity and in adults with an average level).Conclusion. The results obtained on the basis of population epidemiological data on the incidence of influenza, namely, new criteria for detecting the start of an epidemic in cities, can be used in health management bodies in cities and subjects of the Russian Federation for early detection of epidemics and management decisions, timely introduction of anti-epidemic measures, creating a stock of medicines. The expected effect of the method of early epidemiological diagnosis of epidemics is a decrease in morbidity, etc.

Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance.

As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Centers (BRC) to assist researchers with their analysis of genome sequence and other omics-related data. Recently, the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD), and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs merged to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) at https://www.bv-brc.org/ . The combined BV-BRC leverages the functionality of the original resources for bacterial and viral research communities with a unified data model, enhanced web-based visualization and analysis tools, and bioinformatics services.Here we demonstrate how antimicrobial resistance data can be analyzed in the new resource.

The Mystery of Tomato Flu in India

Introduction: While the globe fights against monkeypox and the coronavirus, a new virus known as "Tomato flu" threatens. This virus's recognized target is children. In May 2022, the virus was found for the first time in Kerala, India. Due to its principal symptom, tomato-shaped blisters all over the body, the ailment was given the term "Tomato Flu." Recent reports described it as type of hand, foot and mouth disease (HFMD). It is easily diagnosed by a history and physical examination. It is an infectious condition, but there are still a lot of unanswered questions. To shed light on this topic, we decided to collect and summarize the information on this novel viral pathogen. Materials and Methods: To accomplish this, we undertook a thorough literature assessment of the Tomato Flu research that has already been done. We analyzed data from various sources such as medical journals, government reports and news articles to gain a better understanding of this emerging disease. In addition, we conducted interviews with healthcare professionals who have treated patients with Tomato Flu to gain insights into their experiences. Results: Survey of literature showed that Tomato Flu is a self-limiting disease. Children under the age of 5 and immunocompromised individuals are more susceptible to this disease. There is no diagnostic test for the disease, differential diagnosis involves typical symptoms and the absence of other known viral agents. There is no treatment, supportive care brings relief. Conclusion: Overall, this review provides a better understanding of Tomato Flu and its potential impact on public health. By shedding light on this emerging virus, we hope to contribute to ongoing efforts to prevent and treat of this infectious disease. Medicine Today 2023 Vol.35(2): 129-133

The First International Avian Influenza Summit. The University of Arkansas. October 16-17, 2023

Dear Esteemed Guests, Distinguished Speakers, Honorable Delegates, and all participants worldwide With great pleasure and excitement, we extend our warmest welcome to the First International Avian Influenza Summit, a momentous event hosted by the Center of Excellence in Poultry Science of the University of Arkansas. This groundbreaking summit, set to take place in Fayetteville, Arkansas, USA, on October 16-17, 2023, promises to be a significant milestone in the global efforts to combat Avian Influenza. Through the convergence of leading experts, innovators, and stakeholders worldwide, we aim to forge new frontiers in research, policy, and industry collaboration. The unique free hybrid format of this event, blending both in-person and virtual participation (a total of 1,842 participants from all over the world, see Figure 1), ensures that knowledge exchange and networking opportunities are accessible to a diverse and global audience. Whether you join us in Fayetteville or connect remotely, you will be crucial in advancing our collective understanding and response to this critical challenge. Over the course of two days, the summit will feature a dynamic program encompassing keynote addresses, panel discussions, workshops, and interactive sessions. Together, we will explore the latest advancements in avian influenza research, surveillance strategies, vaccination initiatives, and emergency response protocols. Moreover, this summit provides a vital platform for fostering collaborations between academia, industry, government agencies, and non-governmental organizations. By harnessing all stakeholders’ collective expertise and resources, we can catalyze innovation and drive solutions that protect both avian and human populations. In the spirit of unity and shared purpose, we look forward to the stimulating conversations, valuable insights, and lasting connections that will emerge from this summit. Together, we can profoundly impact the global fight against Avian Influenza. Once again, welcome to the First International Avian Influenza Summit. We are honored to have you with us, and we are confident that your contributions will help pave the way for a safer and more resilient future.

The Influenza B Virus Victoria and Yamagata Lineages Display Distinct Cell Tropism and Infection-Induced Host Gene Expression in Human Nasal Epithelial Cell Cultures.

Understanding Influenza B virus infections is of critical importance in our efforts to control severe influenza and influenza-related diseases. Until 2020, two genetic lineages of influenza B virus-Yamagata and Victoria-circulated in the population. These lineages are antigenically distinct, but the differences in virus replication or the induction of host cell responses after infection have not been carefully studied. Recent IBV clinical isolates of both lineages were obtained from influenza surveillance efforts of the Johns Hopkins Center of Excellence in Influenza Research and Response and characterized in vitro. B/Victoria and B/Yamagata clinical isolates were recognized less efficiently by serum from influenza-vaccinated individuals in comparison to the vaccine strains. B/Victoria lineages formed smaller plaques on MDCK cells compared to B/Yamagata, but infectious virus production in primary human nasal epithelial cell (hNEC) cultures showed no differences. While ciliated epithelial cells were the dominant cell type infected by both lineages, B/Victoria lineages had a slight preference for MUC5AC-positive cells, and B/Yamagata lineages infected more basal cells. Finally, while both lineages induced a strong interferon response 48 h after infection of hNEC cultures, the B/Victoria lineages showed a much stronger induction of interferon-related signaling pathways compared to B/Yamagata. This demonstrates that the two influenza B virus lineages differ not only in their antigenic structure but also in their ability to induce host innate immune responses.

Development of B-cell response during immunization with inactivated influenza vaccines "Grippol plus", "Sovigripp" and "Ultrix"

The worldwide circulating influenza viruses annually lead to serious medical and socio-economic consequences. It is generally recognized that vaccination is the most effective and safe strategy for preventing influenza and its complications. In order to reduce side effects when using live viruses, split and subunit influenza vaccines are widely used. To date, the characteristics of B cell response after immunization with influenza vaccines remain insufficiently studied. The aim of our study was to compare the effects of immunization with different influenza vaccines, i.e., “Sovigripp”, “Grippol plus” and “Ultrix”, on the B cell response. The study was conducted on the base of Clinical Department at the A.Smorodintsev Influenza Research Institute during the epidemic flu season of 2018-2019. For clinical studies, venous blood samples were obtained from 39 volunteers before vaccination, on the 7th and 21st days after vaccination. The subpopulations of B cells were analyzed by flow cytometry using fluorescently labeled antibodies to CD3, CD19, CD20, CD27, CD38, IgD, IgA surface antigens (BioLegend, USA). Cryopreserved mononuclear cells (1 × 106 cells/sample) were used for analysis. The processing of flow cytometry data was carried out with special software (H., Cytexpert, Beckman Coulter, Inc., USA) and Kaluza 2.0 (Beckman Coulter, Inc., USA). The differences with pre-vaccination data were evaluated using the Mann–Whitney U-test and being considered significant at p &lt; 0.05. As a result of the studies, the following subpopulations of B lymphocytes (CD3-CD19+) were specified: naive B cells (CD20+CD27-IgD+), non-switched memory B cells (CD20+CD27+IgD+), switched memory B cells (CD20+CD27+IgD-), effector memory B cells (CD20+CD27-IgD-), plasmablasts (CD20-CD38hiCD27hi). Activation of the B cell immune response was assessed by measuring the relative content of CD38+B cells belonging to subpopulations of naive, effector B lymphocytes, switched and non-switched memory B cells. The analysis of B cell response showed an increase in both the total number of B lymphocytes and their subpopulations including plasmablasts and activated switched memory B cells after immunization. With adjuvant vaccines “Grippol plus” and “Sovigripp”, as compared with the split “Ultrix” vaccine, an early increase in relative counts of plasmablasts was shown on the 7th day of the study. At the same time, all three vaccines equally contributed to an increase in the number of activated memory B cells with a switched antibody isotype. Thus, the assessment of B cell response revealed significant changes in contents of peripheral blood B cell subpopulations in response to vaccination with “Grippol plus”, “Sovigripp”, or “Ultrix”.

Multiple Vaccines and Strategies for Pandemic Preparedness of Avian Influenza Virus.

Avian influenza viruses (AIV) are a continuous cause of concern due to their pandemic potential and devasting effects on poultry, birds, and human health. The low pathogenic avian influenza virus has the potential to evolve into a highly pathogenic avian influenza virus, resulting in its rapid spread and significant outbreaks in poultry. Over the years, a wide array of traditional and novel strategies has been implemented to prevent the transmission of AIV in poultry. Mass vaccination is still an economical and effective approach to establish immune protection against clinical virus infection. At present, some AIV vaccines have been licensed for large-scale production and use in the poultry industry; however, other new types of AIV vaccines are currently under research and development. In this review, we assess the recent progress surrounding the various types of AIV vaccines, which are based on the classical and next-generation platforms. Additionally, the delivery systems for nucleic acid vaccines are discussed, since these vaccines have attracted significant attention following their significant role in the fight against COVID-19. We also provide a general introduction to the dendritic targeting strategy, which can be used to enhance the immune efficiency of AIV vaccines. This review may be beneficial for the avian influenza research community, providing ideas for the design and development of new AIV vaccines.

Misclassified: identification of zoonotic transition biomarker candidates for influenza A viruses using deep neural network.

Introduction: Zoonotic transition of Influenza A viruses is the cause of epidemics with high rates of morbidity and mortality. Predicting which viral strains are likely to transition from their genetic sequence could help in the prevention and response against these zoonotic strains. We hypothesized that features predictive of viral hosts could be leveraged to identify biomarkers of zoonotic viral transition. Methods: We trained deep learning models to predict viral hosts based on the virus mRNA or protein sequences. Our multi-host dataset contained 848,630 unique nucleotide sequences obtained from the NCBI Influenza Virus and Influenza Research Databases. Each sequence, representing one gene from one viral strain, was classified into one of the three host categories: Avian, Human, and Swine. Trained models were analyzed using various neural network interpretation methods to identify interesting candidates for zoonotic transition biomarkers. Results: Using mRNA sequences as input led to higher prediction accuracies than amino acids, suggesting that the codon sequence contains information relevant to viral hosts that is lost during protein translation. UMAP visualization of the latent space of our classifiers showed that viral sequences clustered according to their host of origin. Interestingly, sequences from pandemic zoonotic viral strains localized at the margins between hosts, while zoonotic sequences incapable of Human-to-Human transmission localized with non-zoonotic viruses from the same host. In addition, host prediction for pandemic zoonotic sequences had low prediction accuracy, which was not the case for the other zoonotic strains. This supports our hypothesis that ambiguously predicted viral sequences bear features associated with cross-species infectivity. Finally, we compared misclassified sequences to well-classified ones to extract interesting candidates for zoonotic transition biomarkers. While features varied significantly between pairs of species and viral genes, several codons were conserved in Swine-to-Human and Avian-to-Human misclassified sequences, and in particular in the NA, HA, and NP genes, suggesting their importance for zoonosis in Humans. Discussion: Analysis of viral sequences using neural network interpretation approaches revealed important genetic differences between zoonotic viruses with pandemic potential, compared to non-zoonotic viral strains or zoonotic viruses incapable of Human-to-Human transmission.

Protein sequence features of H1N1 swine influenza A viruses detected on commercial swine farms in Serbia.

Swine influenza A viruses (swIAVs) are characterised by high mutation rates and zoonotic and pandemic potential. In order to draw conclusions about virulence in swine and pathogenicity to humans, we examined the existence of molecular markers and accessory proteins, cross-reactivity with vaccine strains, and resistance to antiviral drugs in five strains of H1N1 swIAVs. Amino acid (AA) sequences of five previously genetically characterised swIAVs were analysed in MEGA 7.0 software and the Influenza Research Database. Amino acid analysis revealed three virus strains with 590S/591R polymorphism and T271A substitution within basic polymerase 2 (PB2) AA chains, which cause enhanced virus replication in mammalian cells. The other two strains possessed D701N and R251K substitutions within PB2 and synthesised PB1-F2 protein, which are the factors of increased polymerase activity and virulence in swine. All strains synthesised PB1-N40, PA-N155, PA-N182, and PA-X proteins responsible for enhanced replication in mammalian cells and downregulation of the immune response of the host. Mutations detected within haemagglutinin antigenic sites imply the antigenic drift of the five analysed viruses in relation to the vaccine strains. All viruses show susceptibility to neuraminidase inhibitors and baloxavir marboxil, which is important in situations of incidental human infections. The detection of virulence markers and accessory proteins in the analysed viruses suggests their higher propensity for replication in mammalian cells, increased virulence, and potential for transmission to humans, and implies compromised efficacy of influenza vaccines.