Author
Correspondence author
International Journal of Super Species Research, 2024, Vol. 14, No. 2
Received: 19 Feb., 2024 Accepted: 28 Mar., 2024 Published: 10 Apr., 2024
The influenza virus, particularly influenza A virus, exhibits a high degree of variability and evolves continuously through antigenic drift and antigenic shift, leading to seasonal influenza outbreaks and occasional pandemics on a global scale. This study provides an in-depth understanding of how the influenza virus evades detection by the immune system during its evolution and explores the impact of these evolutionary mechanisms on vaccine development and public health strategies. The results show that the influenza virus rapidly mutates and reassorts its genes, producing new strains that can evade host immunity and spread across different species, thereby increasing the challenges of controlling influenza. The evolution of the influenza virus not only challenges existing vaccines and antiviral treatment strategies but also underscores the importance of continuous global surveillance and research to better predict and respond to future influenza outbreaks. This study provides scientific evidence for the development of more effective vaccines and influenza control strategies, thereby enhancing global public health response capabilities.
1 Introduction
Influenza is a highly contagious respiratory disease caused by influenza A, B, and C viruses, with influenza A being the most significant in terms of public health impact. The World Health Organization (WHO) estimates that annual influenza epidemics result in approximately 1 billion infections, 3~5 million cases of severe illness, and 300 000~500 000 deaths globally (Krammer et al., 2018). Influenza A viruses, in particular, have been responsible for several pandemics, including the devastating 1918 pandemic which resulted in over 40 million deaths worldwide. These viruses can cause zoonotic infections, adapting from animal hosts to humans, leading to sustained transmission and the emergence of novel viruses (Taubenberger and Kash, 2010). The rapid mutation rates of influenza viruses challenge the efficacy of vaccines and antiviral treatments, making influenza a persistent threat to global health (Shao et al., 2017; Asha et al., 2023).
Understanding the mechanisms of viral evolution and immune evasion is crucial for developing effective strategies to combat influenza. Influenza viruses evolve through antigenic drift and shift, which involve mutations and re-assortment of viral genomes, respectively (Shao et al., 2017). These evolutionary processes enable the virus to evade the host immune system, leading to recurrent seasonal epidemics and occasional pandemics (Taubenberger and Kash, 2010; Shao et al., 2017). The rapid genetic changes in influenza viruses can result in the emergence of drug-resistant strains, further complicating treatment efforts (Smyk et al., 2022). Additionally, the virus's ability to adapt to new hosts and overcome species barriers underscores the importance of continuous surveillance and research to anticipate and mitigate future outbreaks (Taubenberger and Kash, 2010; Jansen et al., 2019).
This study systematically elucidates the mechanisms by which the influenza virus evolves to evade the immune system. By analyzing the genetic changes and adaptive strategies of the virus, it provides a comprehensive understanding of its evolutionary dynamics. These findings are expected to offer important insights for the development of more effective vaccines and antiviral therapies, thereby enhancing public health responses to influenza outbreaks. Additionally, the study underscores the critical role of continuous monitoring and in-depth study in predicting and preventing future pandemics. Through a detailed analysis of viral evolution and immune evasion, this study is committed to supporting global efforts to control and ultimately eliminate influenza as a major public health threat.
2 Biology of the Influenza Virus
2.1 Structure and genetic makeup of the influenza virus
The influenza virus is an RNA virus belonging to the Orthomyxoviridae family. It has a segmented genome consisting of eight single-stranded RNA segments, which encode for various viral proteins essential for the virus's lifecycle. The virus is enveloped, with a lipid bilayer derived from the host cell membrane, and it contains two major surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA). These glycoproteins play crucial roles in the virus's ability to infect host cells and in the immune response elicited by the host (Malik and Zhou, 2020; Liang, 2023).
2.2 Types of influenza viruses
Influenza viruses are classified into four types: A, B, C, and D. Influenza A and B are the most significant in terms of human disease. Influenza A viruses (IAVs) are known for their high genetic variability and ability to cause pandemics. They are further subtyped based on the HA and NA proteins, with notable subtypes including H1N1 and H3N2 (Luo et al., 2020). Influenza B viruses (IBVs) are less variable and are divided into two lineages: Victoria and Yamagata. Influenza C viruses cause mild respiratory illness and are less studied, while Influenza D viruses primarily affect cattle and are not known to infect humans (Valesano et al., 2019; Liang, 2023).
2.3 Mechanisms of infection and replication in host cells
The infection process of influenza viruses begins with the binding of the HA glycoprotein to sialic acid receptors on the surface of host cells. This binding facilitates the entry of the virus into the cell via endocytosis. Once inside, the viral RNA segments are transported to the nucleus, where they are transcribed and replicated (Malik and Zhou, 2020). This nuclear replication is unique among RNA viruses and allows the influenza virus to utilize the host's nuclear machinery. The newly synthesized viral RNA and proteins are then assembled into new virions, which bud off from the host cell, acquiring a portion of the host cell membrane as their envelope. This process is facilitated by the NA protein, which cleaves sialic acid residues to prevent the aggregation of new virions at the cell surface (Smyk et al., 2022).
Influenza viruses have evolved various mechanisms to evade the host immune response, including antigenic drift and shift, which lead to the emergence of new viral strains that can escape pre-existing immunity. These mechanisms, along with the virus's ability to reassort its segmented genome, contribute to the ongoing challenge of controlling influenza through vaccination and antiviral treatments (Peacock et al., 2018; Liang, 2023).
3 Mechanisms of Immune Evasion
3.1 Antigenic drift: gradual mutations in hemagglutinin (HA) and neuraminidase (NA)
Antigenic drift refers to the gradual accumulation of mutations in the hemagglutinin (HA) and neuraminidase (NA) proteins of the influenza virus, which can lead to decreased vaccine efficacy and the emergence of new viral variants. For example, a study on the H1N1 influenza virus in Saudi Arabia found that multiple amino acid mutations occurred at antigenic sites in the hemagglutinin (HA) and neuraminidase (NA) genes of the H1N1 virus, leading to increased genetic diversity. Specifically, mutations at key antigenic sites in the HA protein, such as S101N, S179N, and I233T, may have resulted in antigenic drift, giving rise to new variants distinct from the vaccine strains (Figure 1) (Naeem et al., 2020).
Similarly, research on swine influenza A viruses revealed a high level of genetic and antigenic differences within the same lineage, with the majority of mutations occurring in the globular head of the HA protein, driven by positive selection (Ryt-Hansen et al., 2020). Another study highlighted the role of specific amino acid substitutions in the HA protein of Eurasian avian-like H1N1 swine influenza viruses, which resulted in escape from neutralizing monoclonal antibodies and contributed to antigenic drift (Xu et al., 2022).
3.2 Antigenic shift: reassortment of gene segments leading to new viral strains
Antigenic shift is a more abrupt process compared to antigenic drift, involving the reassortment of gene segments between different influenza virus strains, leading to the creation of new viral strains with novel antigenic properties. This mechanism is responsible for the emergence of pandemic influenza viruses, which can cause widespread outbreaks due to the lack of pre-existing immunity in the human population.
For example, the 2009 H1N1 pandemic virus emerged through antigenic shift, combining gene segments from North American and Eurasian swine influenza viruses (Chen et al., 2022). The study generated different mutant strains by mutating the amino acid residues of the NA 370-loop in the 2009 H1N1 virus and evaluated the impact of these mutations on NA enzyme activity, hemagglutination titers, mouse virulence, and immunogenicity. The results showed that the I365T/S366N and I365E/S366D mutations enhanced NA activity and were also associated with higher hemagglutination titers, suggesting a possible interaction between HA and NA functions that could influence viral fitness. Despite the differences in enzyme activity and titers, all mutant strains exhibited reduced virulence in mice, indicating a complex relationship between these factors and pathogenicity. The unpredictability of antigenic shift poses significant challenges for vaccine formulation and pandemic preparedness, as highlighted by the need for universal influenza vaccines that can provide broad and long-lasting immunity against diverse viral strains (Nachbagauer et al., 2020).
3.3 Escape from host immune response: avoiding neutralizing antibodies and cellular immunity
Influenza viruses have evolved various strategies to escape the host immune response, including the evasion of neutralizing antibodies and cellular immunity. One study demonstrated that specific mutations in the HA protein of influenza viruses can lead to escape from neutralizing antibodies, thereby allowing the virus to persist and spread within the host population (Xu et al., 2022). Additionally, the introduction or removal of glycans on the HA protein can alter the immunodominance of viral epitopes, focusing the immune response on subdominant but broadly protective epitopes (Bajic et al., 2019).
Another study found that neuraminidase (NA) mutations can affect the enzyme activity and immunogenicity of the virus, further contributing to immune evasion (Chen et al., 2022). The interplay between HA and NA mutations and their impact on immune escape underscores the complexity of influenza virus evolution and the ongoing challenge of developing effective vaccines (Daulagala et al., 2023; Fox, 2023). By understanding these mechanisms of immune evasion, researchers can better anticipate the evolutionary trajectories of influenza viruses and develop more effective strategies for disease control and prevention.
4 The Role of Host Factors in Influenza Evolution
4.1 Host immune pressure and its influence on viral mutations
Host immune pressure plays a significant role in driving the evolution of influenza viruses. The immune system exerts selective pressure on the virus, leading to the emergence of mutations that allow the virus to escape immune recognition. This process, known as antigenic drift, involves changes in the viral genome that alter antigenic sites, enabling the virus to evade detection by pre-existing antibodies.
Studies have shown that the distribution of immune memory cells in the host population creates a dynamic fitness landscape for circulating strains, driving antigenic escape and increasing the rate of viral evolution (Rouzine and Rozhnova, 2018; Xue and Bloom, 2019). Within-host evolution is also influenced by factors such as antigenic selection and antiviral treatment, which can affect the genetic diversity of the virus and its ability to adapt to immune responses (Xue et al., 2018; Xue and Bloom, 2019).
4.2 The role of human behavior, such as vaccination practices, in shaping viral evolution
Human behavior, particularly vaccination practices, significantly impacts the evolution of influenza viruses. Vaccination exerts selective pressure on the virus, promoting the emergence of strains that can escape vaccine-induced immunity. The effectiveness of vaccination in reducing overall escape pressure depends on the relative contribution of vaccinated and unvaccinated hosts to antigenic escape. If vaccinated hosts contribute significantly more to escape pressure, intermediate levels of vaccination may maximize escape pressure, whereas high levels of vaccination generally reduce it (Gutierrez and Gog, 2022).
Additionally, the efficacy of vaccines against transmission and infection plays a crucial role in shaping the evolutionary dynamics of the virus. The annual evaluation and update of influenza vaccine formulations are necessary to keep pace with the rapid antigenic evolution of the virus (Valesano et al., 2019).
4.3 Cross-species transmission and its impact on viral evolution
Cross-species transmission is a critical factor in the evolution of influenza viruses. Influenza A viruses, in particular, have the ability to jump from animal reservoirs, such as birds, to humans, leading to the emergence of novel strains with pandemic potential. The interaction between viral and host factors, such as the PB2 subunit of the influenza virus RNA polymerase and host ANP32 protein, facilitates the adaptation of the virus to new hosts (Zhang et al., 2021).
The host range of influenza A viruses is determined by species-specific interactions that enable the virus to bind, enter, and replicate within host cells, as well as evade host immune responses (Long et al., 2018). Understanding these molecular events and the factors involved in breaking the cross-species barrier is crucial for surveillance and prevention of potential influenza outbreaks (Long et al., 2018; Zhang et al., 2021). The rapid evolution of the virus through mutation and reassortment further complicates efforts to predict and control cross-species transmission (Liang, 2023). By examining the role of host factors in influenza evolution, we gain insights into the complex interplay between the virus and its host, which drives the continuous adaptation and emergence of new viral strains.
5 Global Surveillance of Influenza Strains
5.1 The importance of continuous monitoring and surveillance of circulating strains
Continuous monitoring and surveillance of circulating influenza strains are crucial due to the virus's rapid evolution and genetic variability. Influenza viruses, particularly Influenza A, are known for their high mutation rates, which can lead to significant changes in their biological properties, including virulence and host adaptation (Smyk et al., 2022). This genetic instability complicates the implementation of effective prophylactic programs, such as vaccinations, and can result in resistance to antiviral drugs. Therefore, ongoing surveillance is essential to detect these changes early and adjust public health strategies accordingly (Owuor et al., 2022; Smyk et al., 2022).
5.2 Role of WHO and global health organizations in tracking influenza evolution
The World Health Organization (WHO) and other global health organizations play a pivotal role in tracking the evolution of influenza viruses. The WHO established a global influenza surveillance network in the 1950s, which now includes institutions in 122 member states. This network monitors circulating influenza strains in both human and animal reservoirs, aiming to detect strains with pandemic potential (Harrington et al., 2021).
Laboratories contributing to the WHO Global Influenza Surveillance and Response System (GISRS) continuously monitor the antigenic phenotypes of circulating viruses, providing critical data for vaccine strain selection (Agor and Özaltın, 2018). These efforts are complemented by pandemic risk assessment tools developed by the WHO and the United States Centers for Disease Control and Prevention (CDC), which evaluate emerging strains to prioritize research and funding (Harrington et al., 2021).
5.3 Challenges in predicting the dominant strains for seasonal vaccines
Predicting the dominant strains for seasonal influenza vaccines is fraught with challenges due to the virus's rapid and unpredictable evolution. The genetic and antigenic variability of influenza viruses means that the strains circulating in one season can differ significantly from those in the next (Nyang'au et al., 2020; Owuor et al., 2022). This variability often leads to mismatches between the vaccine strains and the predominant circulating strains, reducing vaccine effectiveness (Agor and Özaltın, 2018).
Additionally, the limited predictability of amino acid substitutions in the virus's surface proteins further complicates accurate predictions (Barrat-Charlaix et al., 2020). Despite advances in modeling and prediction methodologies, the dynamic nature of influenza virus evolution necessitates continuous improvement in surveillance and vaccine strain selection processes (Agor and Özaltın, 2018; Barrat-Charlaix et al., 2020). By maintaining robust global surveillance systems and leveraging advanced predictive models, health organizations can better anticipate and respond to the ever-changing landscape of influenza virus evolution, ultimately improving public health outcomes.
6 Recent Case Study: The Emergence of the H3N2 Variant
6.1 Background on the H3N2 subtype and its significance
The H3N2 subtype of the influenza A virus has been a significant contributor to seasonal influenza epidemics since its introduction to the human population in 1968. This subtype is known for its rapid genetic and antigenic evolution, which allows it to evade host immune responses and complicates vaccine design and effectiveness. H3N2 viruses have been associated with severe influenza seasons, often resulting in higher morbidity and mortality rates compared to other influenza subtypes (Allen and Ross, 2018; Belongia and McLean, 2019). The hemagglutinin (HA) protein of H3N2 is particularly prone to mutations, which can lead to antigenic drift and the emergence of new variants that escape pre-existing immunity (Allen and Ross, 2018; Aw et al., 2022).
6.2 Evolutionary changes observed in the H3N2 variant during the 2021-2023
During the 2021-2023 influenza seasons, the H3N2 variant exhibited several notable evolutionary changes. These changes were primarily driven by mutations in the HA protein, which is the main target of the host immune response (Dudin et al., 2023). Key mutations included the addition of N-linked glycans to the HA, which can shield antigenic sites from antibody binding, and changes in receptor binding preferences (Allen and Ross, 2018; Belongia and McLean, 2019). The emergence of these mutations has been linked to the virus's ability to escape immune detection and maintain its circulation in the human population.
Studies have shown that the H3N2 variant during this period also acquired mutations that affected its replication efficiency and antigenic properties. Genetic sequencing and phylogenetic analysis revealed multiple amino acid substitutions in the HA and NA genes. For instance, in Riyadh, Saudi Arabia, twelve and nine amino acid substitutions were identified in the HA and NA genes, respectively, which were absent in the current vaccine strains (Dudin et al., 2023). Additionally, serial passaging studies revealed that the passage of H3N2 influenza virus in MDCK-SIAT1 cells resulted in specific mutations in genes such as HA, NA, and PB1, particularly the D457G mutation in the HA2 subunit, which is associated with increased virus plaque size and enhanced viral infectivity (Figure 2) (Aw et al., 2022). These mutations highlight the virus's ability to adapt and evolve rapidly, posing challenges for vaccine efficacy and public health responses.
6.3 Impact on vaccine effectiveness and public health responses
The evolutionary changes observed in the H3N2 variant during the 2021-2023 seasons had a significant impact on vaccine effectiveness. The antigenic drift resulting from these mutations often led to a mismatch between the circulating strains and the vaccine strains, reducing the overall protective efficacy of the vaccines (Belongia and McLean, 2019; Byrd-Leotis et al., 2019). For example, the egg passage adaptation of vaccine viruses introduced mutations that altered glycosylation patterns, impairing the neutralizing antibody response and further compromising vaccine effectiveness (Belongia and McLean, 2019).
Public health responses to the emergence of the H3N2 variant included increased surveillance and molecular characterization of circulating strains to inform vaccine strain selection. The development of alternative approaches, such as high content imaging-based neutralization tests (HINT), was also explored to improve the accuracy of antigenic characterization and vaccine strain selection (Jorquera et al., 2019). Despite these efforts, the rapid evolution of the H3N2 variant posed ongoing challenges for maintaining effective vaccination strategies and highlighted the need for continued research and innovation in influenza vaccine development.
The emergence of the H3N2 variant during the 2021-2023 seasons underscores the dynamic nature of influenza virus evolution and its implications for public health. The observed evolutionary changes in the H3N2 variant have significant consequences for vaccine effectiveness and necessitate ongoing surveillance and adaptation of vaccination strategies to mitigate the impact of seasonal influenza epidemics.
7 Implications for Influenza Vaccination Strategies
7.1 Challenges in designing effective vaccines due to rapid viral evolution
The rapid evolution of the influenza virus poses significant challenges in designing effective vaccines. The virus undergoes frequent antigenic drift and shift, leading to the emergence of new strains that can evade immunity elicited by previous infections or vaccinations. This necessitates the annual reformulation of seasonal vaccines to match the circulating strains, which is a time-consuming and often imperfect process (Sangesland and Lingwood, 2021; Tripp, 2023). The hemagglutinin (HA) protein, particularly its head domain, is highly variable and the primary target of current vaccines, which limits their efficacy and necessitates frequent updates (Nachbagauer et al., 2020). Additionally, the virus's ability to mutate and escape immune responses further complicates vaccine design, as it requires a continuous effort to predict and counteract these changes (Zost et al., 2019; Knight et al., 2020).
7.2 The role of universal influenza vaccines and their potential to overcome immune evasion
Universal influenza vaccines aim to provide broad and long-lasting protection against diverse influenza strains by targeting conserved regions of the virus, such as the HA stalk domain, nucleoprotein (NP), and matrix 2 (M2) proteins (Nachbagauer et al., 2020; Misplon et al., 2023). These vaccines are designed to elicit immune responses that are less susceptible to antigenic drift and shift, thereby overcoming the limitations of strain-specific vaccines.
For instance, chimeric hemagglutinin-based vaccines have shown promise in inducing broadly cross-reactive antibodies against the HA stalk domain, which is less variable than the head domain (Nachbagauer et al., 2020). Recombinant adenovirus-based vaccines expressing conserved influenza antigens have also demonstrated long-lasting protection and reduced lung inflammation upon viral challenge, highlighting their potential as universal vaccines (Lo et al., 2021; Misplon et al., 2023). By focusing on these conserved sites, universal vaccines could provide more consistent and reliable protection against both seasonal and pandemic influenza strains (Sangesland and Lingwood, 2021; Tripp, 2023).
7.3 Analysis of vaccine mismatch and its consequences
Vaccine mismatches occur when the strains included in the seasonal influenza vaccine do not match the circulating strains, leading to reduced vaccine efficacy and increased incidence of influenza-related illness. For example, during the 2014-2015 influenza season, the H3N2 component of the vaccine was mismatched with the circulating strain, resulting in significantly lower vaccine effectiveness and higher rates of influenza-associated hospitalizations and deaths (Rajão and Pérez, 2018; Tripp, 2023). Such mismatches underscore the need for improved vaccine design and prediction methods. The development of universal vaccines could mitigate the impact of these mismatches by providing broader protection against a wider range of influenza strains, thereby reducing the reliance on accurate strain prediction and annual vaccine reformulation (Nachbagauer et al., 2020; Lo et al., 2021).
8 Impact of Influenza Evolution on Public Health
8.1 Increased severity and transmissibility of new influenza strains
The rapid evolution of the influenza virus, particularly Influenza A, poses significant challenges to public health due to its ability to mutate and recombine, leading to the emergence of new strains with increased virulence and transmissibility. The genetic instability of the virus allows it to adapt to new hosts and environments, potentially resulting in pandemics with severe health impacts (Hsu, 2018; Smyk et al., 2022). Historical data, such as the 1918 influenza pandemic, highlight the devastating potential of highly virulent strains, which can cause millions of deaths worldwide (Hsu, 2018). Additionally, the virus's ability to evade the host immune response through antigenic drift and shift further complicates efforts to control its spread and severity (Lyons and Lauring, 2018; Smyk et al., 2022).
8.2 Economic and societal burden of influenza outbreaks
Influenza outbreaks impose a substantial economic and societal burden. The direct costs include healthcare expenses for treating infected individuals and the indirect costs encompass lost productivity due to illness and absenteeism. The frequent need for updated vaccines and antiviral drugs, driven by the virus's rapid evolution, adds to the financial strain on healthcare systems (Honce and Schultz‐Cherry, 2019; Smyk et al., 2022). Moreover, the impact of influenza is exacerbated in vulnerable populations, such as the elderly, children, and individuals with underlying health conditions, leading to increased morbidity and mortality rates (Ranjeva et al., 2018). The 2009 H1N1 pandemic, for instance, highlighted the significant economic and societal disruptions caused by widespread influenza outbreaks (Honce and Schultz‐Cherry, 2019).
8.3 Strategies for mitigating the impact of rapidly evolving influenza viruses
To mitigate the impact of rapidly evolving influenza viruses, several strategies are essential. Continuous monitoring and surveillance of influenza strains are crucial for early detection and response to emerging variants (Smyk et al., 2022). Developing universal vaccines that target conserved viral epitopes could provide broader and longer-lasting protection against multiple strains, reducing the need for frequent vaccine updates (Sangesland and Lingwood, 2021).
Additionally, novel therapeutic interventions that demonstrate high specificity and cross-reactivity against various influenza subtypes are needed to enhance treatment efficacy and reduce the development of drug resistance (Hsu, 2018). Public health measures, such as promoting vaccination, improving antiviral drug use, and implementing effective infection control practices, are also vital in managing the spread and impact of influenza (Hsu, 2018; Sangesland and Lingwood, 2021; Smyk et al., 2022). By understanding the mechanisms of influenza virus evolution and implementing comprehensive strategies, we can better prepare for and mitigate the public health challenges posed by this continually emerging infectious threat.
9 Future Directions in Influenza Research and Control
9.1 Advances in genomics and molecular biology for studying viral evolution
The continuous evolution of influenza viruses poses significant challenges for vaccine development and antiviral treatments. Advances in genomics and molecular biology are crucial for understanding the mechanisms behind viral evolution. High-throughput sequencing technologies have enabled detailed analysis of viral genetic diversity within hosts, providing insights into how mutations arise and spread (Rouzine and Rozhnova, 2018).
Additionally, the development of in vitro models, such as the human lung airway-on-a-chip, allows for the study of viral evolution and drug resistance in a controlled environment, which can inform the design of more effective vaccines and therapeutics (Si et al., 2021). These advancements highlight the importance of integrating genomic data with molecular biology techniques to predict and counteract the rapid evolution of influenza viruses.
9.2 The role of artificial intelligence and modeling in predicting viral evolution
Artificial intelligence (AI) and computational modeling have become indispensable tools in predicting the evolution of influenza viruses. Machine learning algorithms can analyze large datasets to identify patterns and predict phenotypic traits from genomic data, aiding in the selection of vaccine strains (Borkenhagen et al., 2021). For instance, predictive models that focus on site-wise mutation dynamics have shown promise in forecasting representative viral strains for upcoming seasons, thereby facilitating timely vaccine updates (Lou et al., 2023). Moreover, natural language processing techniques have been adapted to predict viral escape mutations, which can help in understanding how viruses evade the immune system (Hie et al., 2020). These AI-driven approaches are essential for improving the accuracy of predictions and enhancing the effectiveness of influenza control measures.
9.3 Recommendations for global collaboration in influenza research and vaccine development
Global collaboration is vital for advancing influenza research and developing effective vaccines. The World Health Organization's Global Influenza Surveillance and Response System (GISRS) exemplifies the importance of international cooperation in monitoring circulating virus strains and informing vaccine composition (Agor and Özaltın, 2018). To further enhance global efforts, it is recommended that research centers worldwide share genomic and phenotypic data, as well as collaborate on the development and validation of predictive models. Continuous monitoring of antiviral drug resistance across different regions is also crucial to ensure the effectiveness of treatment options (Smyk et al., 2022). By fostering a collaborative environment, the global scientific community can better anticipate and respond to the evolving threat of influenza, ultimately improving public health outcomes.
10 Concluding Remarks
Influenza viruses are adept at evading immunity through mechanisms such as antigenic drift and shift. Antigenic drift involves gradual mutations in the virus's surface proteins, particularly hemagglutinin (HA) and neuraminidase, which allow the virus to escape recognition by the host's immune system. Antigenic shift, on the other hand, involves more abrupt changes, often resulting from the reassortment of genetic material between different influenza strains, leading to the emergence of novel viruses capable of causing pandemics. The HA head domain is particularly prone to mutations, which facilitates the virus's ability to evade immunity elicited by prior infections or vaccinations. Despite these challenges, the HA stalk domain remains relatively conserved, presenting a promising target for universal vaccine development.
The continuous evolution of influenza viruses necessitates frequent updates to seasonal vaccines, which are often strain-specific and may not provide broad protection against diverse or novel strains. The development of universal influenza vaccines that target conserved regions of the virus, such as the HA stalk domain, holds promise for providing broader and more durable protection. Additionally, understanding the host immune response, including the role of immunological memory and the impact of previous exposures, can guide the design of more effective vaccines. Public health strategies should also focus on enhancing natural immunity and improving vaccine production technologies to respond rapidly to emerging strains.
Continued research is essential to fully understand the mechanisms of influenza virus evolution and immune evasion. This includes studying the evolutionary dynamics of the virus at both the global and within-host levels to identify potential targets for intervention. Innovation in vaccine design, such as the development of chimeric hemagglutinin-based vaccines, should be prioritized to achieve broad and long-lasting immunity. Furthermore, public health initiatives must emphasize the importance of annual vaccination and the need for global surveillance to detect and respond to emerging influenza strains promptly. Collaborative efforts between researchers, healthcare providers, and policymakers are crucial to advancing influenza control and preventing future pandemics.
Acknowledgments
The authors extend their sincere gratitude to the two anonymous peer reviewers for their contributions during the evaluation of this manuscript.
Conflict of Interest Disclosure
The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.
References
Agor J., and Özaltın O., 2018, Models for predicting the evolution of influenza to inform vaccine strain selection, Human Vaccines & Immunotherapeutics, 14: 678-683.
https://doi.org/10.1080/21645515.2017.1423152
Allen J., and Ross T., 2018, H3N2 influenza viruses in humans: Viral mechanisms, evolution, and evaluation, Human Vaccines & Immunotherapeutics, 14: 1840-1847.
https://doi.org/10.1080/21645515.2018.1462639
Asha K., Meseko C., and Kumar B., 2023, Editorial: Influenza and related viruses: Epidemiology, pathogenesis, and therapeutics, Frontiers in Molecular Biosciences, 385: 96-105.
https://doi.org/10.3389/fmolb.2022.1117067
Aw D., Heng K., Heok J., Kong X., Chen H., Zhang T., Zhai W., and Chow V., 2022, Serial passaging of seasonal H3N2 influenza A/Singapore/G2-31.1/2014 virus in MDCK-SIAT1 cells and primary chick embryo cells generates HA D457G mutation and other variants in HA, NA, PB1, PB1-F2, and NS1, International Journal of Molecular Sciences, 23(20): 12408.
https://doi.org/10.3390/ijms232012408
Bajic G., Maron M., Adachi Y., Onodera T., McCarthy K., McGee C., Sempowski G., Takahashi Y., Kelsoe G., Kuraoka M., and Schmidt A., 2019, Influenza antigen engineering focuses immune responses to a subdominant but broadly protective viral epitope, Cell Host & Microbe, 25(6): 827-835.e6.
https://doi.org/10.1016/j.chom.2019.04.003
Barrat-Charlaix P., Huddleston J., Bedford T., and Neher R., 2020, Limited predictability of amino acid substitutions in seasonal influenza viruses, Molecular Biology and Evolution, 38: 2767-2777.
https://doi.org/10.1093/molbev/msab065
Belongia E., and McLean H., 2019, Influenza vaccine effectiveness: Defining the H3N2 problem, Clinical Infectious Diseases, 69(10): 1817-1823.
https://doi.org/10.1093/cid/ciz411
Borkenhagen L., Allen M., and Runstadler J., 2021, Influenza virus genotype to phenotype predictions through machine learning: A systematic review, Emerging Microbes & Infections, 10: 1896-1907.
https://doi.org/10.1080/22221751.2021.1978824
Byrd-Leotis L., Gao C., Jia N., Mehta A., Trost J., Cummings S., Heimburg-Molinaro J., Cummings R., and Steinhauer D., 2019, Antigenic pressure on H3N2 influenza virus drift strains imposes constraints on binding to sialylated receptors but not phosphorylated glycans, Journal of Virology, 93(22): e01178-19.
https://doi.org/10.1128/JVI.01178-19
Chen T., Chen C., and Wu S., 2022, Neuraminidase (NA) 370-loop mutations of the 2009 pandemic H1N1 viruses affect NA enzyme activity, hemagglutination titer, mouse virulence, and inactivated-virus immunogenicity, Viruses, 14(6): 1304.
https://doi.org/10.3390/v14061304
Daulagala P., Mann B., Leung K., Lau E., Yung L., Lei R., Nizami S., Wu J., Chiu S., Daniels R., Wu N., Wentworth D., Peiris M., and Yen H., 2023, Imprinted anti-hemagglutinin and anti-neuraminidase antibody responses after childhood infections of A(H1N1) and A(H1N1)pdm09 influenza viruses, mBio, 14(3): e00084-23.
https://doi.org/10.1128/mbio.00084-23
Dudin G., Aziz I., Alzayed R., Ahmed A., Hussain T., Somily A., Alsaadi M., and Almajhdi F., 2023, Genetic diversity and evolutionary kinetics of influenza A virus H3N2 subtypes circulating in Riyadh, Saudi Arabia, Vaccines, 11(3): 702.
https://doi.org/10.3390/vaccines11030702
Fall A., Han L., Yunker M., Gong Y., Li T., Norton J., Abdullah O., Rothman R., Fenstermacher K., Morris C., Pekosz A., Klein E., and Mostafa H., 2023, Evolution of influenza A(H3N2) viruses in two consecutive seasons of genomic surveillance, 2021–2023, Open Forum Infectious Diseases, 10(12): ofad577.
https://doi.org/10.1093/ofid/ofad577
Fox A., 2023, Drift and shape—new insights into human immunity against influenza virus neuraminidase, mBio, 14: e01654-23.
https://doi.org/10.1128/mbio.01654-23
Gutierrez M., and Gog J., 2022, The importance of vaccinated individuals to population-level evolution of pathogens, Journal of Theoretical Biology, 567: 111493.
https://doi.org/10.1101/2022.11.29.22282822
Harrington W., Kackos C., and Webby R., 2021, The evolution and future of influenza pandemic preparedness, Experimental & Molecular Medicine, 53: 737-749.
https://doi.org/10.1038/s12276-021-00603-0
Hie B., Zhong E., Berger B., and Bryson B., 2020, Learning the language of viral evolution and escape, Science, 371: 284-288.
https://doi.org/10.1126/science.abd7331
Honce R., and Schultz‐Cherry S., 2019, Impact of obesity on influenza A virus pathogenesis, immune response, and evolution, Frontiers in Immunology, 10: 1071.
https://doi.org/10.3389/fimmu.2019.01071
Hsu A., 2018, Influenza virus: A master tactician in innate immune evasion and novel therapeutic interventions, Frontiers in Immunology, 9: 743.
https://doi.org/10.3389/fimmu.2018.00743
Jansen J., Gerlach T., Elbahesh H., Rimmelzwaan G., and Saletti G., 2019, Influenza virus-specific CD4+ and CD8+ T cell-mediated immunity induced by infection and vaccination, Journal of Clinical Virology, 119: 44-52.
https://doi.org/10.1016/j.jcv.2019.08.009
Jorquera P., Mishin V., Chesnokov A., Nguyen H., Mann B., Garten R., Barnes J., Hodges E., Cruz J., Xu X., Katz J., Wentworth D., and Gubareva L., 2019, Insights into the antigenic advancement of influenza A(H3N2) viruses, 2011–2018, Scientific Reports, 9: 2676.
https://doi.org/10.1038/s41598-019-39276-1
Knight M., Changrob S., Li L., and Wilson P., 2020, Imprinting, immunodominance, and other impediments to generating broad influenza immunity, Immunological Reviews, 296: 191-204.
https://doi.org/10.1111/imr.12900
Krammer F., Smith G., Fouchier R., Peiris M., Kedzierska K., Doherty P., Palese P., Shaw M., Treanor J., Webster R., and García-Sastre A., 2018, Influenza, Nature Reviews Disease Primers, 4: 3.
https://doi.org/10.1038/s41572-018-0002-y
Liang Y., 2023, Pathogenicity and virulence of influenza, Virulence, 14(1): 2223057.
https://doi.org/10.1080/21505594.2023.2223057
Lo C., Misplon J., Li X., Price G., Ye Z., and Epstein S., 2021, Universal influenza vaccine based on conserved antigens provides long-term durability of immune responses and durable broad protection against diverse challenge virus strains in mice, Vaccine, 39(33): 4628-4640.
https://doi.org/10.1016/j.vaccine.2021.06.072
Long J., Mistry B., Haslam S., and Barclay W., 2018, Host and viral determinants of influenza A virus species specificity, Nature Reviews Microbiology, 17: 67-81.
https://doi.org/10.1038/s41579-018-0115-z
Lou J., Liang W., Cao L., Zhao S., Chen Z., Chan R., Cheung P., Zheng H., Liu C., Li Q., Chong M., Zhang Y., Yeoh E., Chan P., Zee B., Mok C., and Wang M., 2023, Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations, Nature Communications, 15(1): 2546.
https://doi.org/10.1101/2023.08.23.554557
Luo W., Tian L., Gan Y., Chen E., Shen X., Pan J., Irwin D., Chen R., and Shen Y., 2020, The fit of codon usage of human-isolated avian influenza A viruses to human, Genetics and Evolution, 81: 104181.
https://doi.org/10.1016/j.meegid.2020.104181
Lyons D., and Lauring A., 2018, Mutation and epistasis in influenza virus evolution, Viruses, 10(8): 407.
https://doi.org/10.3390/v10080407
Malik G., and Zhou Y., 2020, Innate immune sensing of influenza A virus, Viruses, 12(7): 755.
https://doi.org/10.3390/v12070755
Misplon J., Lo C., Crabbs T., Price G., and Epstein S., 2023, Adenoviral-vectored universal influenza vaccines administered intranasally reduce lung inflammatory responses upon viral challenge 15 months post-vaccination, Journal of Virology, 97: e00674-23.
https://doi.org/10.1128/jvi.00674-23
Nachbagauer R., Feser J., Naficy A., Bernstein D., Guptill J., Walter E., Berlanda-Scorza F., Stadlbauer D., Wilson P., Aydillo T., Behzadi M., Bhavsar D., Bliss C., Capuano C., Carreño J., Chromikova V., Claeys C., Coughlan L., Freyn A., Gast C., Javier A., Jiang K., Mariottini C., McMahon M., McNeal M., Solórzano A., Strohmeier S., Sun W., Wielen M., Innis B., García-Sastre A., Palese P., and Krammer F., 2020, A chimeric hemagglutinin-based universal influenza virus vaccine approach induces broad and long-lasting immunity in a randomized, placebo-controlled phase I trial, Nature Medicine, 27: 106-114.
https://doi.org/10.1038/s41591-020-1118-7
Naeem A., Yameen M., Ahmad M., and Imran M., 2020, Structural insights into non-synonymous mutations of neuraminidase protein involved in antiviral drug resistance in influenza A (H1N1) virus, Microbial Pathogenesis, 143: 104127.
https://doi.org/10.1016/j.micpath.2020.104127
Nakowitsch S., Waltenberger A., Zaderer V., Bauer L., and Stoiber H., 2021, How influenza A viruses manipulate innate immunity -A review, Microorganisms, 9(7): 1420.
https://doi.org/10.3390/microorganisms9071420
Nelson M., and Holmes E., 2007, The evolution of epidemic influenza, Nature Reviews Genetics, 8(3): 196-205.
https://doi.org/10.1038/nrg2053
Neumann G., and Kawaoka Y., 2019, Predictive analysis of viral mutations to mitigate pandemics, Cell Host & Microbe, 26(6): 713-717.
https://doi.org/10.1016/j.chom.2019.11.009
Neumann G., Noda T., and Kawaoka Y., 2009, Emergence and pandemic potential of swine-origin H1N1 influenza virus, Nature, 459: 931-939.
https://doi.org/10.1038/nature08157
Oh D., and Hurt A., 2016, A review of the antiviral susceptibility of human and avian influenza viruses over the last decade, Scientific Reports, 6: 28999.
https://doi.org/10.1038/srep28999
Paules C., and Subbarao K., 2017, Influenza, Lancet, 390(10095): 697-708.
https://doi.org/10.1016/S0140-6736(17)30129-0
Petrova V., and Russell C., 2018, The evolution of seasonal influenza viruses, Nature Reviews Microbiology, 16(1): 47-60.
https://doi.org/10.1038/nrmicro.2017.118
Pleguezuelos O., James E., Fernandez A., Lopes V., Rosas L., Cervantes-Medina A., Cleath J., Edwards M., Gonzalez E., Jabbar T., Gray J., and Thomas D., 2020, Efficacy of FLU-v, a broad-spectrum influenza vaccine, in a randomized phase IIb human challenge study, npj Vaccines, 5: 22.
https://doi.org/10.1038/s41541-020-0161-1
Reed C., Chaves S., Kirley P., Emerson R., Aragon D., Hancock E., Butler L., Baumbach J., Hollick G., Bennett N., Laidler M., Thomas A., Meltzer M., and Finelli L., 2015, Estimating influenza disease burden from population-based surveillance data in the United States, PLoS One, 10(3): e0118369.
https://doi.org/10.1371/journal.pone.0118369
Russell C., 2010, The global circulation of seasonal influenza A (H3N2) viruses, Science, 320(5874): 340-346.
https://doi.org/10.1126/science.1154137
Sandbulte M., Westgeest K., Gao J., Xu X., Klimov A., Russell C., Burke D., Smith D., Fouchier R., and Eichelberger M., 2011, Discordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses, Proceedings of the National Academy of Sciences of the United States of America, 108(51): 20748-20753.
https://doi.org/10.1073/pnas.1113801108
Sasaki S., He X., Holmes T., Dekker C., Kemble G., and Arvin A., 2008, Influence of prior influenza vaccination on antibody and B-cell responses, PLoS One, 3(8): e2975.
https://doi.org/10.1371/journal.pone.0002975
Shu Y., and McCauley J., 2017, GISAID: Global initiative on sharing all influenza data – from vision to reality, Eurosurveillance, 22(13): 30494.
https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494
Skehel J., and Wiley D., 2000, Receptor binding and membrane fusion in virus entry: The influenza hemagglutinin, Annual Review of Biochemistry, 69: 531-569.
https://doi.org/10.1146/annurev.biochem.69.1.531
Smith D., Lapedes A., Jong J., Bestebroer T., Rimmelzwaan G., Osterhaus A., and Fouchier R., 2004, Mapping the antigenic and genetic evolution of influenza virus, Science, 305(5682): 371-376.
https://doi.org/10.1126/science.1097211
Taubenberger J., and Morens D., 2008, The pathology of influenza virus infections, Annual Review of Pathology: Mechanisms of Disease, 3: 499-522.
https://doi.org/10.1146/annurev.pathmechdis.3.121806.154316
Tong S., Zhu X., Li Y., Shi M., Zhang J., Bourgeois M., Yang H., Chen X., Recuenco S., Gomez J., Chen L., Johnson A., Tao Y., Dreyfus C., Yu W., McBride R., Carney P., Gilbert A., Chang J., Guo Z., Fan J., and Shu Y., 2013, New world bats harbor diverse influenza A viruses, PLoS Pathogens, 9(10): e1003657.
https://doi.org/10.1371/journal.ppat.1003657
Webster R., Bean W., Gorman O., Chambers T., and Kawaoka Y., 1992, Evolution and ecology of influenza A viruses, Microbiological Reviews, 56(1): 152-179.
https://doi.org/10.1128/mr.56.1.152-179.1992
Wu N., Liang M., Ge H., and Zhou S., 2023, Evolutionary dynamics of influenza viruses under selective pressure, Virology Journal, 20: 105.
https://doi.org/10.1186/s12985-023-02069-1
Xu R., Ekiert D., Krause J., Hai R., Crowe J., and Wilson I., 2010, Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus, Science, 328(5976): 357-360.
https://doi.org/10.1126/science.1186430
Zeng H., and Golding H., 2022, Immune correlates of protection against influenza, Frontiers in Immunology, 13: 928185.
https://doi.org/10.3389/fimmu.2022.928185
Zhou B., Li Y., Halpin R., Hine E., Spiro D., and Wentworth D., 2009, PB2 residue 627 contributes to pathogenicity of avian influenza viruses in mice, Journal of Virology, 83(1): 13-18.
https://doi.org/10.1128/JVI.01774-08
Zhou P., Yang X., Wang X., Hu B., Zhang L., Zhang W., Si H., Zhu Y., Li B., Huang C., Chen H., Chen J., Luo Y., Guo H., Jiang R., Liu M., Chen Y., Shen X., Wang X., Zheng X., Zhao K., Chen Q., Deng F., Liu L., Yan B., Zhan F., Wang Y., Xiao G., and Shi Z., 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 579: 270-273.
https://doi.org/10.1038/s41586-020-2012-7

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