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The genealogy of H1N1 flu [Jul. 22nd, 2009|08:52 am]
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You have to be a bit of a biomed geek to understand why I think this is so cool.   The New England Journal of Medicine's July 16 issue has a fascinating (to me, anyway) perspective article on the relationship of this year's pandemic flu to the 1918 pandemic virus, with a graphic that clearly shows which viral genes came from where.  For previous flu outbreaks we have only accounts of illness, but in 1918,  some hospitals saved tissue and blood samples...making it possible with the late 20th and early 21st techniques in viral genome analysis to determine exactly how closely related the two are.  

These viruses all have eight genes, and each gene can have variants.  You can think of the genes as suitcases carried on a trip from person to person and species to species: each has something in it the virus needs.  But the "wet weather clothes" suitcase need only have sufficient wet-weather clothes...the virus can drop a pair of black rain boots off in a hog farm and pick up a pair of green ones for that suitcase (so to speak.)  Viruses in general (and flu viruses in particular) are constantly changing because of this ability to swap out the contents of each suitcase (or gene).  Some swaps make the virus more capable of infecting a given species' cells--genes encoding surface proteins of the virus, for instance, that allow it to bind to and release virus into cells.  Some make it more capable of multiplying in those cells by co-opting the cells' own biochemical mechanisms, etc.  

Those surface proteins classify the viruses by H (hemagglutin, 16 possible proteins) and N (neuraminidase, 9 possible proteins), but although there are 144 possible combinations, only three (H1N1, H2N2, and H2N3) have been found in human flu strains (with human-to-human transmission, that is.)

The current H1N1 pandemic virus is a direct descendant of the 1918 pandemic virus in a fascinating roundabout way.   The 1918 human H1N1 moved across species to swine in North America, providing an H1N1 swine flu.   The progenitor gene pool for the 1918 human H1N1 (believed to be avian)  moved across species to swine also, providing Eurasian swine H1N1, whose genes were slightly different from North American H1N1 swine flu.  H1N1 could also cross-assort with H1N2 and H2N3.   So right now we're dealing with seasonal H1N1 strains, and a pandemic H1N1 strain, plus seasonal H3N2.  The seasonal H1N1 has genes all derived from the 1918 human flu (they've mellowed over the years but still kill thousands a year.  The pandemic one has genes from avian, North American swine, and Eurasian swine H1N1 genes.

I was fascinated to learn that the severe flu pandemics of 1957 and 1968 were also direct descendants of the 1918 pandemic, but H2N2 and H3N2 respectively.  I had my first flu shot for the 1957 one (I was twelve and had no choice) and either reacted to the shot or got sick with the flu anyway (it felt like flu)...so after that was reluctant to have the shot.   In 1968, having refused to take the shot, I got the flu, and the pneumonia that followed (I will say that if you do your gas-mask training in the military with your lungs full of crud, the tear gas side effects don't last as long.)   After that, I had seasonal flu a few times with much less trouble (milder strains, obviously) but when working in EMS agreed that as part of emergency services I should be available and started taking flu shots again.  No reaction, no problems.  When I got flu anyway it was usually mild and mostly I didn't. 

Anyway, there's a lot more technical stuff known about the flu virus genes, what they do, why bird flu and swine flu are cross-infective with humans, and so on. All of it interesting, even if it weren't a disease that can infect and kill us.  There's a lot more that's still not known.  Why can't an H13N4 be a viable human strain, for instance?  (I'm glad it's not, but still...) 


[User Picture]From: ramblin_phyl
2009-07-22 04:31 pm (UTC)
Good post. I can't take any flu shot because the vaccine is cultured in egg. The animal casein in that concentration shot directly into my blood stream makes me sicker than if I got the flu.

So I stay home a lot when these things rage, wash my hands frequently, and I use the sanitary wipes on grocery carts etc.
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[User Picture]From: e_moon60
2009-07-22 05:13 pm (UTC)
Also...don't touch your face (esp. eyes, nose, mouth, something that I have a really hard time with...) except right after handwashing. If you must be in close quarters with people who are sneezing (or who might--I got a terrific cold from a little girl on a city transit in Australia, who sneezed right in my face; her mother was appalled, but it was too late) and if there's flu in your town, consider a surgical mask for those trips to the grocery. Disposable ones are one-use only, and aren't perfect, but they confer some protection. Discard and immediately wash hands (the outside will be the side contaminated with other peoples' germs. And stocking up on supplies so you don't need to go to the grocery, etc. as often also helps. Fewer trips, fewer exposures.

Social isolation really works, but it's a psychological bummer...I'm wondering if our online society helps with that. (Considering how fast I went from talking on the phone with people to exchanging emails, probably it will help a lot. Until the power goes out. Boy, do I feel isolated these days if the power goes out.)

Since we have both flu season and hurricane season approaching, I'm doing my usual summer (less expensive) pantry supply runs. We could use some good heavy rains (understatement!) but the real reason for the hurricane-stocking-up is a) having grown up in a hurricane prone area, and b) experience with how crowded and sometimes understocked the area groceries are when a big hurricane sends a wave of refugees inland.
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[User Picture]From: pyg_klb
2009-07-23 02:51 pm (UTC)

Oddly enough...

...the egg washing machine I use on my farm is from a company that was bought by guys who had a laying flock used for vaccine production (talk about clean-room chickens!), and needed a machine to wash and sterilize the shells. I've seen a new version of our venerable Aqua-Magic, and outside of being build from stainless steel (sterilizing bleach being hard on anything else), it is very much like my 40-year-old "egg car wash."
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[User Picture]From: e_moon60
2009-07-22 06:15 pm (UTC)
I'm even going to get the pneumonia vaccine this year. I'm in the age range where it's recommended, and while it doesn't protect against viral pneumonias, I don't want to be dealing with the Old Original pneumococcal one. Last year's pneumonia convinced me...I'd planned to wait until I was 65 at least, but...no.

But yeah, this whole flu re-aggregation and shifting stuff is amazing. The relationship between host resistance and viral virulence...both host populations and virus populations thumbing through their repertoire of attacks/defenses. This current pandemic one wasn't in the U.S. a month before it had pulled "resistance to flu drugs" out of its tool kit (I read another article, maybe a month ago, on that.) Our immune defenses drive the shifts in population of the virus...it's a chameleon, but which colors/patterns survive to reproduce depend on where our defenses are open--and we (the human race, and the swine, and the birds) then shift immune response to plug that hole. Which, when plugged, ensures that a different viral gene combo will find another one.

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[User Picture]From: countrycousin
2009-07-22 06:31 pm (UTC)
I'll agree on the "good post" assessment. :-)

Above history summary:
First flu shot - significant, unpleasant reaction.
First flu case - significant, unpleasant reaction.
Subsequent shots and cases - milder reactions.

Alternative interpretation to milder strain hypothesis:
Better educated/trained immune system. Or some combination of both.

I don't remember all of my history and was much older at the time of my first shot, but the severity and frequency of my reactions to colds and flus has been decreasing over the years. (Also, however, my children are grown and scattered and I'm retired, but I still get out and about and to public meetings. Less contact might explain the reduced frequency, but not the reduced reaction.)
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[User Picture]From: liz_gregory
2009-07-24 01:24 am (UTC)
Working in public education, I've gotten the flu shot every year for the past 8. I've never had a reaction to it, and never gotten the flu, either. Not even when I was younger, or at least within the past 25 years.

Good immune system? Lucky? The same type of biological weirdness that causes "non-drowsy" sudafed to completely knock me out, caffeine to do nothing for my wakefulness, and tylenol and vicodin to have absolutely no effect on headaches or other pain?

I enjoy geeking out to your biologically related posts, they make me happy to see others like me out there. :)
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[User Picture]From: e_moon60
2009-07-25 02:13 am (UTC)
We're all individuals, however inconvenient it is...Sudafed neither makes me drowsy nor keeps me awake; too much dark chocolate eaten after 10 pm will keep me awake another hour. Ibu works better on my muscle/joint pain than Execedrin, but Excedrin works better on the headaches.

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