A review into the influenza virus, its spread, drug resistance and the steps taken to reduce outbreaks


Humans have made remarkable progress, and even today they are at the stage of controlling and managing certain aspects of human biology by extending lifespan and gene cloning. Although scientific research has precluded the expansion of multiple diseases in retrospect, a virus remains to be the greatest prospective threat to global health. This research on the influenza virus was conducted because the pathological illnesses that have had a devastating effect on mankind so far were the more common ones. Every year, worldwide flu epidemics arise from the influenza virus. The virus can mutate, which makes vaccine development challenging. This study reviews the viral outbreaks, their prevention, potential cures, and drug resistance. The points regarding how the influenza virus integrates itself within the living cells, the mechanisms behind antiviral medicines, how the influenza virus becomes resistant to drugs, and some discussions that address potential solutions to said problem are also explicated.
Keywords: influenza virus, epidemics, mutation, vaccine, viral outbreaks, drug resistance, antiviral

1.0 Introduction

Viruses are microscopic parasites which cannot reproduce without a host [1]. Outside the host cell, they exist as a protein capsid, sometimes enclosed inside a membrane. The capsid encloses the genetic material of the virus in the form of DNA or RNA [2]. Once in contact with a host cell, the viral genetic material is inserted into the host cell and it takes over the functioning of the cell, producing more viral protein and genetic material that are repackaged and leave the host cell to affect new host cells [3-4]. Viruses cause a lot of diseases in humans and animals such as influenza, smallpox, chickenpox, rabies, herpes, Ebola, AIDS [5], and in animals such as African horse sickness (AHS) and Classical swine fever [6].
The influenza virus is a major pathogen that causes influenza, a contagious respiratory infection in some mammals and birds [7]. It is transmitted as an aerosol and brings about severe health problems among the young, elderly, and individuals with compromised immune systems. There are four major types of influenza; A, B, C, and D. Influenza A and B are responsible for the seasonal flu epidemic every year. Influenza C causes mild symptoms while Influenza D affects cattle. Influenza A, being the common type to affect humans, causes a pandemic when a new strain of influenza A affects people [8]. Influenza A is subcategorized based on the surface proteins it possesses, which are proteins that are attached to the cell membrane and determine how the cell interacts with the external environment. If the surface protein haemagglutinin is present, it is called H while if the surface protein neuraminidase is present, it is called N. There are 18 different types of haemagglutinin (H) and 11 different types of neuraminidase (N). Therefore the N types are N1 to N11 and the H types are H1 to H18. The influenza A viruses found in people are influenza A (H1N1) and influenza A (H3N2). Influenza A (H1N1) and influenza A (H3N2) are included in each year’s influenza vaccine, along with one or two influenza B. These vaccines are not able to protect humans against influenza C and any other kind of influenza that may arise [9].
Across the world, there are various influenza outbreaks and pandemics. A major known influenza
pandemic includes the Spanish flu, from 1918 to 1920 [10]. This was the first pandemic caused by the H1N1 influenza virus, and it is described as the greatest medical holocaust in history. This pandemic registered 40 to 50 million deaths worldwide. Furthermore, between 1957-1958, the Asian flu, recorded 1 to 2 million deaths worldwide. The Hong-Kong flu from 1968 to 1970 killed 0.5 to 2 million people worldwide [11].
According to the World Health Organization (WHO), there are seasonal outbreaks of influenza virus in various regions[12]. It is estimated 1 billion infection cases annually, with 3 to 5 million cases of severe illness and 300,000 to 500,000 influenza-related deaths. People infected with the influenza virus develop antibodies that can get rid of the virus when it arises again in the body [13]. However, the ability of the influenza virus to reinvent itself over time enables it to escape from the immune system that makes people more prone to infection. Annual influenza vaccination programs that alternate in the Northern and Southern hemispheres are used as major tools in the prevention or control of seasonal influenza epidemics. However, the emergence of antiviral drug resistance in the influenza virus is a major concern because it could lead to catastrophe as mutations occur in the features of the virus such that antiviral drugs could no longer tackle the virus [14-15].

2. Influenza pathogenesis and immunology

2.1 Structure of the influenza virus

The influenza virus is a roughly spherical enveloped virus with an outer lipid membrane [16]. It contains glycoproteins, which protrude out of the membrane. They are linked to sugars called hemagglutinin (HA) and neuraminidase (NA) on which the categorization of influenza viruses is based. Antiviral drugs target the NA as well as the M2 (ion channel) protein. The protein M1, also called matrix protein, gives rigidity and strength to the lipid envelope. The interior parts of the virus contain RNAs [17].

Figure 2. An exterior and interior structure of the influenza virus

2.2 How the virus enters the body

The flu viral transmission is most commonly transmitted from person to person as aerosol droplets that enter the body through the mucous membranes of the nose, eyes, or mouth [18]. Once one of these areas is touched, the virus can be transferred and infection can happen.


Figure 3. The pathway of influenza virus infection through the respiratory system

2.3 Action in the human body

The pathogenicity of the virus depends on both the virus and the host cell [19]. The target receptors of a cell and its suitable enzymes that can aid the viral replication makes the cell more vulnerable to viral infection. Additionally, the virus\’s ability to bind to host cells and viral shedding increases the pathogenicity.
The preliminaries of an infection predominantly involve the epithelial cells of the respiratory tract. The epithelial cells are susceptible to attack if they possess the right receptor for viral binding. Influenza binds to viral haemagglutinin (HA), which is a prerequisite to bind to the galactose bound sialic acid on the surface of the host cell. The virus attaches to the target cell, and penetrates. Inside the host cell, it releases nucleic acids which contain viral genes. These integrate into the host cell genome with the help of integrase. Viral proteins are produced and the viral components assemble. They are released as viral buds, which can then infect other cells [20].

2.4 Patterns of influenza occurrence

Seasonal infections in the Northern hemisphere increase from November to March, in the Southern hemisphere from April to September. In said regions, seasonality can be driven by mutations as well as viral preference for cold, dry weather conditions. In the tropics, infections can occur all year round. According to the WHO report for October 2019, influenza activity remained inter-seasonal in most countries of the northern hemisphere, while in Arabian Peninsula nations, it continued to rise.
In Central American countries, influenza activity increased mainly in El Salvador and Nicaragua. The influenza activity was uniformly low in the Caribbean and tropical South American countries, as well as regions like Southern Asia. While the temperate zones of the southern hemisphere also reported generally low cases of influenza activity, Chile continuously reported the detection of influenza B virus. In tropical Africa, Western Africa showed a rise in influenza activity. Meanwhile, in Southeast Asia and the Philippines there was a rise in Lao People\’s Democratic Republic. In general, the vast majority of the cases across the world were caused by the influenza A virus, although the ratio of influenza B occurrences grew recently [21].

Figure 4. The trend of influenza occurrence showing number of influenza cases reported throughout different months from 2014 to 2019 and the average number of notifications

2.5 Prevention of influenza

According to the WHO’s Global Influenza Strategy 2019-2030, a lot of effort is to be put in preventing seasonal influenza, controlling its spread from animals to humans and also preparing for the next pandemic. Vaccination is the most effective way of preventing influenza [22]. Many safe and effective vaccines are available for use; vaccines with inactivated influenza are commonly used. However, since the immunity from vaccines weakens with time, annual vaccination is strongly recommended by the WHO for vulnerable people like pregnant women at any stage of pregnancy, children between 6 months to 5 years, the elderly above 65 years of age, individuals with chronic medical conditions as well as health care workers. There is also a Global Influenza Surveillance and Response System (GISRS) to continuously monitor the influenza viruses circulating in humans [23]. Based on the results from the monitoring system, updates are made to the influenza vaccine twice per year.

2.6 Common influenza drugs and drug resistance

Adamantanes (M2 ion channel) inhibitors e.g., amantadine & rimantadine and neuraminidase inhibitors (NAIs) e.g., oseltamivir, peramivir, zanamivir & laninamivir are used in influenza drugs [24]. Antiviral drugs commonly target portions called active sites that the virus uses to enter into normal cells [25]. If the virus changes its active sites, then the antiviral drug might be rendered ineffective.
Adamantanes act at the beginning of the replication cycle by blocking the M2 ion channel to prevent viral uncoating [26]. This is an effective method because it prevents the start of the replication cycle. Neuraminidase inhibitors on the other hand act at the end of the replication cycle by blocking the action of neuraminidase protein which removes sialic acids from oligosaccharides binding to newly produced viruses to the surface of the cell [27]. This prevents the formation of new virions and prevents further infection. Table 1 shows the different stages of the viral life cycle where various inhibitors can be used to prevent viral entry, integration into the host cell DNA, production of viral proteins, assembly, and release from the host cell [28].

Viral replication cycle Cycle stage Antiviral drug
Fusion with host cell During attachment Attachment inhibitors
During penetration Fusion inhibitors
Uncoating Release of nucleic acids Uncoating inhibitors (e.g., rimantadine)
Replication of the viral genome Reverse transcription Reverse transcriptase inhibitors
DNA integration by integrase enzyme Integrase inhibitors
Nucleic acid synthesis by DNA polymerase Viral DNA polymerase inhibitors
Protein synthesis and assembly of viral components Protein synthesis (transcription and translation) Transcription and translation inhibitors
Proteolytic processing by protease Protease inhibitors
Release of new viruses from the host cell Viral budding Neuraminidase inhibitors eg oseltamivir, peramivir and zanamivir

Figure 5. Viral replication methods of the influenza virus, the cycle stage and the mechanism of the antiviral drugs

The table shows different ways the influenza virus replicate themselves, the cycle stage in which the replication occurs and how antiviral drugs tackle each replication method.
Most circulating influenza viruses have become resistant to M2 ion channel inhibitors. Therefore, most currently used anti influenza drugs use NAIs inhibitors. Some viruses have acquired resistance against the neuraminidase (NA) inhibitors and this threatens the ability to treat influenza. Combination therapy focuses on efforts to limit drug resistance, involving two or more different classes of antiviral agents.
The influenza can develop resistance to a single antiviral agent quickly, but it takes longer to develop resistance to both drugs simultaneously. As such, with the use of two drugs, nearly all viruses produced during infection are susceptible to one or more drugs. Therefore, these viruses will not replicate and the infection will be suppressed.

2.7 Mutation of the influenza virus

When the influenza virus changes the active site where the antiviral drug works, the virus increases its ability to survive despite the presence of antiviral drugs. These changes are constantly monitored in order to overcome antiviral drug resistance. Oseltamivir, which is commonly prescribed for the recommended antiviral drugs; binds to NA proteins of an influenza virus and inhibits the enzymatic activity of these proteins. It prevents influenza viruses from spreading from infected cells to healthy cells. If the NA proteins of influenza virus changes, oseltamivir may lose its ability to bind to the virus’s NA proteins and inhibit its function. This results in \”oseltamivir resistance\”.
Vaccination involves the introduction of small amounts of inactivated or weakened antigenic substances to stimulate the host\’s immune system. The immune system then reacts by developing leukocytes specifically to fight against the introduced pathogens; this results in adaptive immunity. The host immune system causes the pathogen to undergo what is called an antigenic drift and an antigenic shift, which are both evolution of the surface antigens (HA and NA). These evolutions make it difficult to tackle IAV. Antigenic drift is caused by polymerase substitution, giving rise to small mutations in the surface antigen epitope which enables the virus to reinfect the same host; and this is most apparent in seasonal IAVs. On the other hand, antigenic shift, a combination of multiple viral strains creating a new subtype, is responsible for triggering IAV pandemics.
Influenza viruses are constantly changing. As the influenza virus replicates, its genetic makeup changes. This causes a change to its structures mainly with the two primary surface proteins: neuraminidase (NA) and hemagglutinin (HA). This makes the virus less likely to get affected by one or more antiviral drugs used to treat or prevent influenza.
Influenza can change in two different ways, the first means being an Antigenic Drift [29]. Small mutations in the genes of the viruses can lead to changes in the surface proteins of the virus: HA and NA. The immune system can recognize these surface antigens, therefore triggering immune responses such as producing antibodies, and thus blocking the infection. Antigen drift occurs over the course of time during the replication process of a virus. While most flu shots target the HA surface antigens of a virus only, the Nasal Spray Flu Vaccine (LAIV) tackles both the HA and NA surface antigens. These small changes lead to formation of closely related viruses. This can be illustrated by their close location in the phylogenetic tree. Our immune system is designed to develop antibodies as a response when it recognizes an influenza virus. Also, due to \’cross-reactivity\’, the antibodies are also likely to respond to multiple different types of influenza viruses with similar antigenic properties. However as the small antigenic drift-related variations accumulate over time, it will result in antigenically different virus mutations that are further away on the phylogenetic tree. Even a single variation in the location of an important HA could cause an antigenic drift. When this occurs immune system productivity diminishes, as it is unable to recognize and neutralize the new mutated influenza virus. Thus, it cannot respond to the virus, making the person vulnerable to flu infection again. Antigenic drift is the root cause of people getting the flu more than once; therefore in order to keep abreast of the evolving influenza virus, revision of the flu vaccine composition and an annual update on it is necessary.

Figure 6. The antigenic drift; how mutation in the HA gene of the influenza virus causes the HA antigen to change its shape

The ‘second’ type of change is called \”antigenic shift.\” Antigenic shift refers to a sudden and major alteration that only occurs in influenza A virus. It creates new HA or HA/NA proteins that can infect humans. Antigenic shift can create a new subtype of influenza A virus. Unlike antigenic drift that takes place constantly, antigenic shifts take place less frequently. An emergence of a new subtype of IAV from animals with an ability to infect humans could be an example of a shift. When the shift happens, the majority of humans are not immune to it since the combination of HA/NA antigen of animal-origin viruses greatly differ from that of virus subtype in humans (e.g., novel virus). Such an event happened in 2009 where the H1N1 virus emerged from North American Swine, Eurasian Swine, humans and birds, and quickly spread among humans, resulting in a pandemic. However, influenza pandemics occur very rarely; in the past century, there have only been four pandemics.

Figure 7. The antigenic shift; three main ways that the genes from different influenza viruses coming from different animal species mix together, forming a new influenz

3. Discussion

3.1 Limitations in execution of experimentation

Pathology studies of Influenza virus infections : Virus-related experiments have limitations that execution of experimentation and host for the test are limited. As one of the solutions, it is important to conduct future pathology studies on autopsies of patients with influenza infections by endemic, seasonal or animal strains [30]. Analysis considering the pathological aspects combined with biological and immunological analysis will contribute to our understanding of influenza viruses, and thus help in prediction.

3.2 Prediction – mathematical model to find optimal combination therapy

Investigating different mechanisms of combination therapy: As combination therapy appreciates in an effort to extend the coverage, and optimize in predictions, mathematical models can help in the effort to find optimal combinations [31-32]. Mathematical models of influenza have been frequently utilized to investigate multiple aspects of antiviral treatment, such as deriving drug efficacy parameters. Research regarding the extent to which machine learning could help in prediction of fast mutation of Influenza virus should be conducted.

4. Conclusion and recommendation

4.1 Influenza viruses are still a threat for both endemic and epidemic forms

Influenza viruses are difficult to develop vaccine strategies and pandemic plans due to their unique, fast, continuous and unpredictable nature. Therefore it is still a threat for both endemic and epidemic forms.

4.2 Prevention of drug resistance

The key to control and suppress viral pathogens may not be on a single method, but on continuous efforts and ongoing research in comprehensive approaches along with vaccines, antiviral drugs and surveillance [31].


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About the Author

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Seohyun Baek is a Year 12 student at Korea International Institute. She is particularly interested in how an influenza virus could result in a global pandemic and possible ways to prevent it. 

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