Given that last fall I wrote a four-part series on influenza and the human immune system, you can probably guess that this is a topic that fascinates me.  (If you would like to go back and read it, here are the links, Part I, Part II, Part III, and Part IV.)  I had not planned to revisit the topic this year, but it turns out there is a part of the story I did not cover last year, a part that may explain why the 2012-2013 flu season may be the worst since 2009.  But first, as always, the science.
The flu virus infects cells in your nose, throat, and lungs, then hijacks control of their inner workings such that the infected cells make replicas of the virus – a lot of replicas.  The replicated viruses then infect new cells and the process is repeated.  The immediate threat posed by influenza is damage to the lung tissue.  In addition, as your body fights off the virus, fluid can accumulate in your lungs which can provide fertile ground for a bacterial infection (pneumonia).  During influenza epidemics which predated the development of antibiotics, deaths from pneumonia outnumbered deaths from the virus itself.  Even now, in the age of antibiotics, influenza continues to be a major health threat, causing over 30,000 deaths in the U.S. and up to half a million around the world each year.
As soon as you are infected by the flu, your immune system works rapidly to “study” the structure of the virus and to “learn” to generate immunities which stop the spread of the virus and eliminate it from your body.  Once you have successfully fended off a virus, you will be immune to future infections from that particular virus.  Vaccinations are given to allow your body to learn how to generate immunities against the virus without you having to endure the actual illness.  However, the strength and persistence of your immune response to an actual episode of the disease is stronger and longer compared to just receiving the vaccine.
There are many viruses such as tetanus, measles, and chicken pox for which you only need a vaccine once in your life or once a decade to remain immune.  However, to protect yourself from the flu, you need get the vaccine every year.  The need to be re-vaccinated annually stems from the fact that the influenza virus exists in many different strains which change rapidly through two types of mutation.  There is a slow form of mutation, called genetic drift, in which the virus undergoes small changes from year to year.  As long as the structure of the new virus is similar to ones that you have been exposed to in the past, either by infection or vaccination, your immune system will have at least a limited defense against the new strain.  The other type of mutation, called genetic rearrangement, is more dramatic and occurs when a single cell is infected with two different strains of influenza viruses which swap DNA segments.  This process of genetic rearrangement can create a novel strain of virus for which the human population has no residual immunity and can result in a pandemic.  The genetic rearrangement can occur within a human or within other animals which are also susceptible to influenza, commonly birds or pigs.  Our ability to share the flu with pigs and birds provides the basis for calling different strains of flu virus swine or bird flus.  The most recent global pandemic occurred in 2009 with the creation of a new H1N1 (bird) virus. 
Every year a group within the World Health Organization (WHO), called the Global Influenza Surveillance Network, monitors which strains of flu are circulating among the population.  They use this information to decide which three strains of virus will be included in the flu vaccine for that year.  Depending on their observations, the vaccine for the southern and northern hemispheres may or may not be the same in a given year. 
Due to genetic drift or rearrangement, the viruses which are addressed by the vaccine usually change from year to year.  Regardless of changes in the types of flu circulating around the globe, health authorities encourage you to get a flu shot every year.  To promote annual vaccination, they engage in a bit of a “white lie” by telling the public that the vaccine is only effective for one year.  The truth is a bit more nuanced that this.  It is certainly true that in the year when you get your flu vaccine your immunity is the highest, but most people retain a measurable, but diminishing, amount of immunity for up to three years. 
Let me pause to say that I am a zealous advocate for getting your flu shot every year.  (I’ve gotten mine for this year already.  Have you?) In addition to ensuring that you maximize your immunity against the strains currently circulating, the vaccine also gives you some degree of cross-immunity against strains of the virus similar to those specifically targeted by the vaccine. 
The graph at the top of the page is updated by the Centers for Disease Control (CDC) for percentage of outpatient visits for flu-like cases in the U.S. every week.  The dashed horizontal line, at approximately 2.3%, represents the long-term average.  You can see that in 2009-2010, the advent of the novel H1N1 virus for which there was no immunity among the population, there were significantly more cases of the flu than in an average year. 
For the 2010-2011 flu season, the vaccine included the new H1N1 strain and two others called A/Perth/16/2009 and B/Brisbane/60/2008.  As you see from the graph, the 2010-2011 flu season was a normal sort of flu season with few cases in the summer months and more in the winter, roughly evening out to the average of 2.3% outpatient visits for the full year.  The return to normal resulted, at least in part, from the growth in immunity to H1N1 in the U.S. population among people who either had been previously infected or had received the vaccine for 2010-2011 which included it.
Then in 2011-2012 something somewhat usual happened.   When the Global Influenza Surveillance Network looked at the strains of influenza circulating they saw that they were exactly the same as the year before.  Therefore, the vaccine for 2011-2012 was exactly the same as the year before.   As a result, for the 2011-2012 flu season, the population in the U.S. had built up a larger than usual degree of  immunity for all three viruses within everyone who had previously either contracted one of these three strains or been vaccinated in either that season or the one prior.   As you can clearly see in the graph, this high level of immunity within the populace resulted in a mild flu season.
For this season (2012-2013), things have returned to normal status.  While this year’s vaccine still includes the H1N1 strain from the 2009 pandemic, two new strains have been included (A/Victoria/361/2011 and B/Wisconsin/1/2010).  Since these two strains have not been circulating during the last several years, the U.S. population will be more susceptible to the flu than we were last year.  So head out and get your flu shot.  And if you do get sick, stay home, take care of yourself and don’t spread it around.
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