Flu

We have been sick with Influenza A, apparently of the lineage from the H1N1 pandemic of 2009. The flu vaccine is not effective against it.  The vaccine did work against Influenza B that was circulating in December, only unvaccinated people got sick with that one, but B is milder than A. 

The most common comment from people who had A this year is that they understand how people die of it.  Ali says she knows now how she will die, not cancer or stroke (her old fears) but just a simple flu.  We both got antivirals and maybe they shortened the duration, but they provide no relief for days. 

The first day you just feel weird, tired, have a slight fever and think you "might" have the flu.  The next day is worse and you have a fever all day and can't eat.  Extreme lethargy sets in.  That night is the worst, fever above 103 and you hallucinate and want to die.  Acetaminophen does nothing for it, but aspirin does help a bit.  On the 3rd day you feel better and can eat a bit, but are easily exhausted.  That night you sweat again all night and now the phlegm gets bad and you wake coughing.  Cough medicine does nothing, but a combination of decongestant and expectant and something to knock you out (antihistamine) lets you rest.  The 4th day is much like the 3rd, and you live in fear of nightime.
You might try to go to work, and you'll get dressed and eat breakfast in a daze, then send in for more PTO and go straight back to bed.  On the 5th day you'll make it in to work and check emails, tell everyone you're not contagious because you haven't had a fever in 24 hours and you washed all your clothes, then get a headache and feel brain dead and go home early.

Its mostly just staring at a wall, watching star trek and trying not to think about anything.  The body has taken over and is going through its reboot sequence and the mind is totally superfluous. The body doesn't want the mind to do anything, but the mind feels it has something its supposed to do, it just can't remember what.  Eventually it realizes the body knows best and the mind finally relaxes, gives up on whatever complicated socially-determined pressures it had programmed itself to believe in, and goes along for the ride.

Why I Plan to Get the Seasonal Flu Vaccine Next Year

Introducing The Virus

Image of flu virus with antigen proteins on phospholipid(?) surface and RNA in the middle. From. http://www.cdc.gov/flu/professionals/laboratory/antigenic.htm. Tamiflu works by binding the purple neurominadse proteins. Tamiflu was developed from shikimic acid, which was originally available only as an extract of Chinese star anise but by 2006 30% of the supply was manufactured recombinantly in E. coli.[54][55]

Vaccine viruses are chosen (i.e., February for the Northern Hemisphere flu vaccine) because it takes 6-8 months to grow them in chicken eggs. Health officials would like to grow them in human(?) cell culture, but that it not currently allowed. Eggs are problematic because viruses may adapt to the egg.

"As a result, Immunologically naïve ferrets) are the most sensitive method available for detecting antigenic differences between influenza viruses."(from http://www.cdc.gov/flu/professionals/laboratory/antigenic.htm)

Evolution and Types of Virus

H3N2 (swine) flu and H1N1 (avian) flu are main lineages. Major outbreaks occur suddenly and unpredictably through transmission of new varieties from animal hosts. Seasonal (common) flus are derived from the same lineage, but generally evolve slowly and predictably. Each year, novel viruses make the leap from animal to human. For example, during the 2013–14 influenza season, one case of human infection with an new strain of H3N2v virus occurred in a child from Iowa with known direct exposure to swine. Birds seem to have co-evolved with the flu virus and do not mount an immune response to it. Therefore (luckily!) it appears to evolve much more slowly in resevoir species than in humans. This has important implications for the dynamics of seasonal and epidemic flu outbreaks.


Influenza A is the most common. It is highly likely that of all the seasonal influenza strains circulating at the present, one of them will multiply and give rise to the entire seasonal influenza populations in around 5 years. The descendants of all other viruses will most likely be extinct.


For example, the 2014–15 influenza vaccines used in the United States have the same antigenic composition as those used in 2013–14. The trivalent vaccines should contain an A/California/7/2009-like (2009 H1N1) virus, an A/Texas/50/2012-like (H3N2) virus, and a B/Massachusetts/2/2012-like (B/Yamagata lineage) virus. (http://www.medscape.com/viewarticle/826572_6)

The lineage of evolutionarily successful viruses is usually termed the trunk of H3N2 influenza’s evolutionary treea:




The tree is based on hemagluttin protein sequence evolution, colored according to estimated geographic location, indicating high permanence of the trunk in China and Southeast Asia. The genetic changes occur on the neuroamidase and hemoagglutin virus surface proteins, causing antigenic drift. The truck of the H3N3 tree with a single dominant lineage contrasts with more branching trees of other flu types where different varieties often co-circulate, such as H1N1, and Influenza B and C. This graph and these findings are complicated by whole-genome sequencing: a new graph shows overall viral genome evolution in The evolution of epidemic influenza by Martha I. Nelson and Edward C. Holmes Nature Reviews.
Figure courtesy of Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, et al. http://theglobalscientist.com/2014/11/03/what-can-data-science-tell-us-about-influenza/


Current Trends - CDC FluNet


http://www.cdc.gov/flu/weekly/


Is flu increasing...

This chart is from the same page....http://www.cdc.gov/flu/weekly/. The periodicity of flu seasons and epidemics is still being studied. Peaks occur during the winter in northern latitudes at ~2–5 year intervals, usually during H3N2-dominant seasons, since the 1968 pandemic. Recent phylogenetic analysis of viruses from single populations has shown that the virus does not ‘over-summer’, but dies out at the end of each seasonal epidemic, and that subsequent seasonal viral re-emergence is ignited by imported genetic variation.

Or decreasing?

Weekly Map

http://www.cdc.gov/flu/weekly/usmap.htm