Treatment, Prevention, & Transmission

Because influenza is often highly virulent (particularly H1N1) and can be extremely dangerous to at-risk populations,2 treatment and prevention of disease is one of the most prominent focuses of influenza study. This includes vaccine development, antiviral pharmaceuticals, and public health efforts to prevent spread of disease (though less relevant to this project).

As discussed on previous pages, the frequent genetic drift of influenza viruses makes vaccine development difficult. Currently, there are two primary types of influenza vaccines: inactivated influenza vaccine (IIV) and live attenuated influenza vaccine (LAIV). The former has been around longer, is more widely used, and is typically administered by intramuscular injection. IIV vaccines are prepared by growing the virus in embryonated chicken eggs, inactivating the virus, and then isolating the HA and NA components. These vaccines lead to systematic antibody production. Functional LAIV is newer, though interestingly, it is rooted in observations from the 1930s, shortly after isolation of the influenza virus, which demonstrated that exposure to the aerosolized virus protected from future infection in ferrets. These vaccines contain a live but weakened version of the virus, and lead primarily to mucosal antibody formation.9

Figure 1. A schematic of live attenuated influenza vaccine (LIAV) production.9 Acronyms: genes encoding polymerase protein components (PB1, PB2, PA), hemagglutinin gene (HA), neuraminidase gene (NA), nonstructural protein gene (NS), surface ion channel gene (M), and nucleoprotein (NP).

LAIV is not necessarily available or recommended every season, but it was popular in the late portion of the 2009 H1N1 pandemic. Current influenza vaccines are typically either trivalent or quadrivalent, meaning they protect against three or four different subtypes, respectively. Strains included are determined by experts prior to the start of each flu season.9

While these seasonal vaccines can provide protection from the most likely common strains in a given year, they can only be so effective, as they are designed for a “moving target” given the frequency of viral mutations.1 In cases where influenza viruses make a sudden jump from animal to human host, as with the 2009 H1N1 pandemic, seasonal vaccines offer little aid.1 There is, however, interest in creating a “universal vaccine” which could provide protection from all strains in the future.2 Some have suggested targeting the stalk of the hemagglutinin (HA) protein, as this is relatively well conserved between viral strains, but the bulky head of the HA protein precludes antibody access to this region in vivo.1 Nonetheless, many research groups continue to work towards creative solutions and a better understanding of the immune response to hopefully make this a possibility in the future.1

A variety of antiviral drugs have also been developed.3 Common antiviral agents include amantadine/rimantadine, zanamivir, and oseltamivir. The first is an M2 channel blocker, and the latter two are neuraminidase (NA) inhibitors. The M2 channel blocker can only protect from influenza A viruses, while the others are effective with both A and B.8 As discussed on previous pages (see Cellular and Molecular Basis of Infection), the M2 channel is implicated in initial viral release within the cell, and the NA protein is essential for viral budding from the cell post-replication. Both of these processes are necessary for viral proliferation.2,8 As with bacterial infections, this field also faces modern issues with drug resistance in viral strains.2

Figure 2. A graphical representation of where M2 channel blockers and neuraminidase inhibitors (NAIs) exert their antiviral properties during the influenza lifecycle.8 Acronyms: hemagglutinin (HA), neuraminidase (NA), M2 proton channel (M2).

In accordance with interest in prevention, there is also a large focus throughout the literature on mechanisms of transmission. Influenza viruses can come from a variety of animals, though the H1N1 subtype is typically found in pigs, and mechanisms of both animal-human and human-human transmission are of prominent interest in prevention of potential outbreaks.2 Human infection with animal influenza virus can occur through aerosols or contaminated water, but human to human transmission more commonly occurs from respiratory droplets or accidental exposure from contaminated surfaces.2

An issue pertaining to transmission of much more prominent biochemical focus is factors affecting virulence and pathogenesis of influenza viruses. Many of the proteins encoded in the influenza viral genome can serve as virulence factors based on their individual functions.4 The cellular availability of proteases which cleave a given HA can contribute to the virus’s ability to replicate in given tissues. Additionally, PB2 activity can affect the rate of viral synthesis by controlling transcription of viral RNA (vRNA), and the non-structural protein 1 (NS1) can interfere with the host immune response by caspase-1 inhibition, interrupting the NLRP3 inflammasome response and delaying cytokine production.4 Additionally, the PA protein can downregulate host gene expression, shuttling cellular resources towards viral replication.4

Identified molecular factors contributing to pathogenicity are complex, and there is undoubtedly lots left to uncover. The H1 protein has long been associated with the high virulence of many H1N1 outbreaks.4 An N66S substitution, as compared to conserved sequences in other influenza viruses in the PB1 protein is thought to have contributed to the pathogenicity of the 1918 H1N1 flu, because this variant reduces the production of interferons in the host cell.4 The NS1 protein on H1N1 is also known to contain a PDZ domain motif associated with higher virulence. Certain strains of Influenza A subtype H1N1 have NA proteins known to recruit plasminogen, which once converted to its active form, will cleave the HA protein even when trypsin proteases are not present. This is thought to contribute to virulence.4

More recently, a number of residues largely unique to pathogenic influenza subtypes and strains have been identified, though current understanding for some appears to be more a matter of correlation than causation. These residues were identified as common variants from the avian consensus sequence for major viral proteins. They include A199S (PB2), L475M (PB2), D567N (PB2), E627K (PB2), D55N (PA), E382D (PA), T552S (PA), and others. Notably, the A199S residue is implicated in the PB1 binding site, and the L475M residue is associated with nuclear localization.  The K627 of PA is known to be associated with pathogenicity in H5N1, and is known to be important for host adaptation in H1N1. Some amino acids identified for PB1 are associated with cRNA and vRNA binding, but all other amino acids identified, across all three proteins, serve unknown functions.6 As discussed briefly above, the avian-derived PB1 protein is highly conserved among virulent strains, including the 1918 H1N1, and it is thought that acquiring this protein by reassortment may be of benefit to influenza viruses.6 

It should also be noted, though, that the ability of a virus to cause disease is a function of not only the molecular factors encoded by the virus, but by the host’s ability to fight that infection. It is thought that H1N1, responsible for multiple notable epidemics, may have had such success in years such as 1918 in part due to a lack of herd immunity among the human population.2 The host response can also affect the course of the disease when it is too strong – an aggressive immune reaction, sometimes called a cytokine storm, can result in harm to the human host.5 Conversely, those with weakened immune systems or pre-existing health conditions which weaken the body may have a more difficult time fighting the infection, allowing it to spread further through the respiratory tract, leading to increased chance of complications like pneumonia and acute respiratory distress syndrome (ARDS).2 Ease of human to human transmission is also important. H5N1, for example, is thought to be highly pathogenic and deadly, but cases of human to human contact are extremely rare, precluding true epidemics of this virus thus far.2

Ultimately, a better understanding of factors affecting virulence and pathogenicity will be essential to developing improved treatments and preventative measures in the future. 

Summary of Major Scientific Innovations: 

  • 1918 – Early attempts at vaccine development, but targeting the “bacillus of influenza,” rather than the virus itself
  • 1933 – Serum from recovered animal is shown to protect others from influenza infection7 
  • 1937 – Intranasal administration of the live virus following serial passage in ferrets is shown to protect from influenza infection9
  • 1945 – First influenza vaccine developed and implemented for civilian inoculation2 
  • 1960s – Amantadine, an M2 channel blocker, begins clinical use. This is one of the first truly effective antivirals8
  • 1990 – Reverse genetics technologies to generate desired recombinant influenza enhances vaccine development efforts2
  • Present day – efforts into developing a universal influenza vaccine are underway 2

Works Cited

  1. Eisenstein, M. Towards a universal flu vaccine. Nature Outlook. 2019
  2. Krammer, F.; Smith, G. J. D.; Fouchier, R. A. M.; Peiris, M.; Kedzierska, K.; Doherty, P. C.; Palese, P.; Shaw, M. L.; Treanor, J.; Webster, R. G.; et al. Influenza. Nat. Rev. Dis. Primer 2018, 4 (1), 1–21.
  3. CDC. “Flu” (Accessed 10 April 2020).
  4. Schrauwen, E.J.A.; de Graaf, M.; Herfst, S.; Rimmelzwaan, G.F.; Osterhaus, A.; and Fouchier, R.A.M. Determinants of virulence of influenza A virus. Eur J Clin Microbiol Infect Dis. 2014, 33(4): 479-490. 
  5. Teijaro, J.R.; Walsh, K.B.; Rice, S.; Rosen, H.; and Micahel, B.A. Mapping the innate signaling cascade essential for cytokine storm during influenza virus infection. PNAS 2014, 111(10): 3799-3804. 
  6. Taubenberger, J.K.; Reid, A.H.; Lourens, R.M.; Wang, R.; Jin, G.; and Fanning, T.G. Characterization of the 1918 influenza virus polymerase genes. Nature 2005, 4437, 889-893. 
  7. Smith, W., Andrewes, C.H., and Laidlaw, P.P. [Reviewed] Timbury, M.C. A Virus obtained from influenza Patients. Reviews in Medical Virology. 1995* (1933), 5:187-191
  8. Stiver, G. The treatment of influenza with antiviral drugs. CMAJ. 2003, 168(1): 49-57.
  9. Treanor, J. History of Live, Attenuated Influenza Vaccine. Journal of the Pediatric Infectious Disease Society. 2020, 9(S1):S3-S9.

For more information and resources, see Annotated Bibliography.

2 Replies to “Treatment, Prevention, & Transmission”

  1. Hey Miranda! Your blog is a joy to read, and I especially liked learning about the “flu shot” I receive yearly but have never thought twice about! In your description of the types of vaccinations available, you mentioned that LAIV is not recommended or available every season, but it became popular in 2009. Could you explain why LAIV is not always recommended? Does the presence of the live-version of the virus have a greater potential for adverse effects, especially for more at-risk populations? Or perhaps is it more cost-effective to produce trivalent or quadrivalent IIV vaccines? Thanks so much!

    1. Hey Em! Thank you! First, I should clarify that while LAIV has been used relatively rarely in the US, it is more common in other countries (particularly in Europe). LAIV has some advantages to IIV, as it elicits a much more broad immune response. However, for reasons not entirely understood, it has not proven very effective with H1N1 or H2N3, the most common subtypes affecting the US population, and has therefore not been recommended recently in the United States (though it has been approved since 2003). In a typical season, some studies suggest that there is no significant difference between LAIV versus IIV, at least in children. Additionally, as you suggest in your comment, LIAV is contraindicated in young children and at-risk populations. While I am not entirely sure what the relative cost of the two methods is, I would not be surprised if it is preferable to administer the tri- or quadrivalent vaccine in that regard. This situation is currently evolving, and is complicated by conflicting data coming out of the US and Europe on this matter. It seems to me that this matter will develop significantly once there is a more concrete biochemical understanding of these issues.

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