Fit to Fight the Flu

Influenza virus, the causative agent of flu, has a genome composed of segmented, single-stranded, negative sense RNA.  This combination leads to challenges for your immune system because this virus can evolve through occasional genetic shift and continuous genetic drift.  Let me explain.

To cause a genetic shift, two different strains of influenza infect the same animal (and, importantly, the same cell within the animal) simultaneously.  The outcome can be that the segments from the two strains of influenza mix and match to form a novel virus (aka a reassortant virus).  For illustration purposes, I have drawn a cell that is infected with one virus (all red genome) and a second virus (all yellow genome).  The result is virus progeny that have red and yellow genome segment combinations called reassortments.  The new virus may be a human influenza virus and an animal virus, so the progeny would be a new form of influenza that would be a novel threat to everyone in the world.  If you hear about pandemic flu viruses, these viral reassortants would be the culprits.

Reassortant virus

Genetic drift, the accumulation of variant genomes, is also a problem for our immune systems due to new virus mutants that result from errors made by RNA polymerases.  Vaccines developed for the northern hemisphere’s winter are designed to “teach” the immune system about new variants dominating in the southern hemisphere’s during their “winter” (aka summer in the northern hemisphere).  You see, unlike polymerases that read DNA to make RNA, polymerases that read RNA to make RNA lack proofreading mechanisms where, upon making a mistake, the polymerase backs up in a 3’ to 5’ direction and fixes the error (1).  In summary, the genetic drift that occurs annually in the southern hemisphere are the mutations northern hemisphere populations need to be ready to detect.

When vaccines miss the mark regarding the most likely variants of flu coming to the northern hemisphere, the innate immune system has increased importance in protection against severe disease.  This branch of the immune system responds to general microbial molecules, such as a bacterium’s cell wall, rather than to specific, genome-encoded molecules such as proteins.  Regardless of which strain of flu virus causes an infection, the innate immune system is ready to resist the uncontrolled replication of the virus.

This brings us to the article we are going to discuss, “IFITM3 restricts the morbidity and mortality associated with influenza”, that was published in the journal, Nature, in 2012 (2).  Being in a high-tiered journal, one of my first questions usually is, “Why was this study published in _______?”  In this particular case, I believe it is because the story presented in this manuscript works its way from animal models, to clinical genetic and epidemiological data, and finishes with human cell cultures that support the mouse and human findings.

IFITM3 was known to be involved in innate immunity responses and, specifically, was highlighted in a previous study that used a genomic screen to identify proteins that function to restrict virus replication (3).  Not only did this original study show that IFITM3 restricts the replication of influenza (family Orthomyxoviridae), but also protects against a couple of flaviviruses (Dengue and West Nile).

Mice aren’t always a great model for influenza infections because they are resistant to many influenza strains.  Certain strains such as “PR/8” are virulent in mice because these strains were selected for virulence as they went through many rounds of infection in mice.  The authors of the study showed that even virus strains that are typically nonlethal in mice cause such extreme sickness that the mice unable to make IFITM3 lost over 20% of their weight (an indication that the mice needed to be euthanized to prevent unnecessary suffering).  The disease severity was not associated with a difference in viral replication in the first two days, but instead, the IFITM3 mutant mice were not able to restrict virus replication as well in the third and fourth day of the infection.  This is consistent with the idea that IFITM3 acts within the innate branch of the immune system since adaptive immune responses would take effect later in the infection.

When the lungs of the infected mice were examined, traces of the virus was found throughout the lungs.  Moreover, the pathology of the lungs of IFITM3-lacking mice included edema and bleeding with an infiltration of an innate immune cell knowns as neutrophils (aka polymorphonuclear cells).  None of these observations was too surprising as severe influenza infections are often associated with this type of pathology.

While many studies would be expected to end with the mechanism of the protein in question being discovered.  For IFITM3, the mechanism(s) of protection against influenza virus does not appear to be settled and has been the topic of more recent research.  Instead, this study ends with a look at IFITM3 mutants in the human population.

Through sequencing many human genomes, scientists have been able to identify specific base pair mutations within the human populations.  Technically, these mutations are known as single nucleotide polymorphisms (SNPs).  At the time of the publication, 28 IFITM3 SNPs were known.  Interestingly, the authors went on to sequence the IFITM3 gene for 53 individuals that had been hospitalized by either the 2009 H1N1 pandemic flu or the seasonal flu from that year.  Incredibly, the SNP that caused the loss of a portion of the IFITM3 protein was found far more frequently in these hospitalized patients than in the population as a whole.

With a likely important SNP in hand, the authors conjured up some human cell lines that had the “normal” IFITM3 protein or the shortened IFITM3 protein caused by the SNP in question.  Consistent with their mouse and human data, the mutant IFITM3 cells supported higher levels of influenza infection that their normal counterparts.

A question to ponder after reading this paper is, “Why does the shortened IFITM3 mutant exist in the population?”  Some answers include:

  • Evolutionary pressure hasn’t caused this mutant to be lost in the population yet.
  • The shortened form of IFITM3 has a beneficial quality…just not in the case of viral infections.
  • The selective pressure from the viral infections has not been strong enough to counteract genetic drift of this human genotype.


  1. Steinhauer, D. A., Domingo, E., and Holland, J. J. (1992) Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene. 122, 281–288
  2. Everitt, A. R., Clare, S., Pertel, T., John, S. P., Wash, R. S., Smith, S. E., Chin, C. R., Feeley, E. M., Sims, J. S., Adams, D. J., Wise, H. M., Kane, L., Goulding, D., Digard, P., Anttila, V., Baillie, J. K., Walsh, T. S., Hume, D. A., Palotie, A., Xue, Y., Colonna, V., Tyler-Smith, C., Dunning, J., Gordon, S. B., Smyth, R. L., Openshaw, P. J., Dougan, G., Brass, A. L., and Kellam, P. (2012) IFITM3 restricts the morbidity and mortality associated with influenza. Nature. 484, 519–523
  3. Brass, A. L., Huang, I. C., Benita, Y., John, S. P., Krishnan, M. N., Feeley, E. M., Ryan, B. J., Weyer, J. L., van der Weyden, L., Fikrig, E., Adams, D. J., Xavier, R. J., Farzan, M., and Elledge, S. J. (2009) The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus. Cell. 139, 1243–1254

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