Musings: Influenza (Swine flu)

This is a supplementary page, consolidating multiple posts on influenza. Initial posts were focused on the new swine flu, now called H1N1 2009. Over time, the name for that flu varied, and the topic more broadly became the new flu in general. Posts are in chronological order, oldest first.

The item titles are not very helpful here; all posts are on the same general topic.
My original post (April 28, 2009)
A reply (April 30, 2009)
Swine flu (May 2, 2009)

The new flu (October 21, 2009)
The new flu: your questions (October 28, 2009)

There are other flu posts that are not on this page. Some are on more general flu or vaccine issues; also, I have experimented with how pages should be organized.
Flu vaccine -- some good news (July 29, 2008)
Progress toward a flu vaccine with broader specificity (March 30, 2009)
Google tracks the flu (April 30, 2009)
A flu shot for Santa Claus? (December 5, 2009)
A better way to deliver a vaccine? (July 25, 2010)
A modified chicken that cannot transmit bird flu (March 26, 2011)
* International relations: sharing flu viruses (May 28, 2011)
* Predicting vaccine responses (August 22, 2011)
* Who gets sick from the flu? (September 20, 2011). This and the post just above are an interesting pair. One deals with the variability of infection responses between individuals. One deals with variability of vaccine responses between individuals. The approach is similar for the two papers. Is there any actual connection between what is being studied? Interesting question. I don't think we can tell at this point.
* Little yellow-shouldered bats -- and the Guatemalan bat flu (March 30, 2012). A new flu.
* What about the H5N1 flu? (August 21, 2012). Q&A for some perspective.
* Face masks and flu virus transmission on airplanes: an analysis of a flight (August 27, 2013).
* Google tracks the flu -- follow-up (April 11, 2014).
* Transparency of clinical trials -- Is the flu drug Tamiflu worthless? (May 4, 2014).
* Why vaccine effectiveness may vary: role of gut microbiome? (February 27, 2015).
* Tamiflu revisited (March 22, 2015).
* What's the connection: Narcolepsy and the flu vaccine (or getting the flu)? (October 3, 2015).
* Added September 24, 2016. A quick-response system for making new vaccines (September 24, 2016).
* Added November 21, 2016. Guaico Culex virus: the first example of an animal virus that packages segments of its genome in different particles (November 21, 2016).
* Added March 6, 2017. Is it worthwhile to require flu vaccination for health care workers? (March 6, 2017).

Other new diseases...
* Schmallenberg virus (January 20, 2012).
* A new SARS-related virus seems to be emerging -- and an "ethics" story (February 4, 2013).


My original post

April 28, 2009

From ASM (American Society for Microbiology). (Links have been updated.)

"The ASM is closely following the swine flu outbreak and wants to make you aware of current information and educational resources that you may find helpful. For general information please go to CDC site on the new flu. The CDC site contains information in print, podcast and Spanish translation for your use. In all infectious disease outbreaks, handwashing is one of the first and most important lines of defense against disease spread. The ASM has long been a leader in increasing awareness of the importance of handwashing and also has public education resources on handwashing for download and distribution at Don't Get Caught Dirty Handed."

Things are moving fast, and much is unclear. I may write some more about this, but it is hard to keep up. I think the ASM info above is a good start.

One of the things that will be confusing and perhaps of concern... It is important that our institutions treat this as potentially serious. On the other hand, it may or may not turn out to be. Certainly in the short term, it probably has little impact for most people. So, we will likely get annoyed at the government seeming to overplay it. Yet we would be even more annoyed if they underplayed it and it turned out to be serious. I think we just need to be conscious of this issue.

I do have a web page on the flu. It focuses on the bird flu, but frankly many of the issues are about the same. That page is: Biotechnology in the News (BITN): Influenza (Bird flu).

(Let me know of questions; it may help me put together something.)



A reply

April 30, 2009

It's a double-edged sword you touch on here that is a major factor. A colleague of mine spent some time with me yesterday heatedly commenting on the "extreme" reaction people and organizations are having to this flu. She pointed out that there are thousands of deaths due to flus each year and yet the news is focusing in on 9 (or so was the count I believe. Earlier reports said over 100, but now others are saying they are not related?). She spent quite some time studying pathobiology and just found the coverage frustrating because, at least where she was concerned, she felt that strains within the Avian Flu were more likely to turn into a pandemic than this swine flu.

As annoying as it may be to many already, the point still remains that, well, if no one paid this flu much attention in its early stages, what could be the likely outcome?

Do you get the feeling that the media is overplaying or under-playing the severity of the issue? I would imagine that the best way to go about it is to objectively tell the public of the cases that have actually occurred specifically with this strain and what circumstances were likely to lead to the recent deaths. I believe, for example, there was one case that the individual had waited so long to get treatment that regardless of what flu strain, it would have been difficult to treat him. Isn't more productive to just tell people to be cautious, wash their hands, and seek medical attention if symptoms occur than focusing on each possible case with every news story?

Again, I'm torn. I think disease prevention is a serious issue and people should be aware of how quickly pathogens can transfer, but at the same time I get the feeling that there may be too much hype going on here. (Perhaps a welcomed distraction from other common news? I hate to sound condescending, so I hope it doesn't come across that way.)



Swine flu

May 2, 2009

See page Swine flu [pdf file; link opens in new window] for my overview of swine flu.

General comment. Swine flu is a rapidly developing story. "Facts" have been changing day by day, and it is hard to keep track. However, there are important general issues here. How do we react to an imminent threat or an actual disaster? Remember BSE and SARS, as well as the lurking H5N1 bird flu. And Katrina and the tsunami from the Indonesian earthquake a few years back. Most of you should relate to some of those, and perhaps to others. Each of these involves a story of how our society reacted to a situation. For the most part, they are not very satisfying stories. (I remember one of you telling me about a relative pulling in bodies of dead children off the beach in southern India after the tsunami. The quake was not preventable; the tsunami was not preventable. But the human tragedy was entirely preventable -- at least as far away as India.)

There has been much effort trying to prepare for a possible bird flu problem. Even those who felt that this bird flu was unlikely to develop into a human pandemic understood that preparing for it was good, simply because it was a good example of preparing for such a disaster. The current swine flu incident is an exercise in disaster preparedness. If this swine flu turns out to be of little consequence (entirely possible, with some recent data even suggesting that is the likely outcome), we will still want to evaluate the response in the larger context.

Recommended book, on the broad topic of emerging diseases: Dorothy H Crawford, Deadly Companions - How microbes shaped our history (2007). The book discusses many examples through history of microbes jumping from other animals to humans, and causing problems. It starts with a rather detailed discussion of SARS. See my page Book suggestions for more on this book.


Further contributions on this topic are welcomed. We can discuss flu virus or we can discuss disaster preparedness. Both are important; neither is simple. I'll leave names off. Do remember that the "facts" (what we know -- or at least, what we think we know) are changing, so each person's comment reflects what they know as of that moment.



The new flu

October 21, 2009

We had some discussion of the new flu strain that emerged last spring. I have made no attempt to keep up with all the flu events since then; there have been too many, and they are often confusing. But now it is the new flu season (in the Northern Hemisphere), and perhaps time to take stock.

The new strain, which we will call 2009 H1N1, is back; a vaccine for it (or is the vaccine against it?) is just coming out, and we are learning some things about the new flu.

An important characteristic of any flu virus strain is the type of disease it causes. This is reflected in its mortality (how many die from it), and in the age distribution of its victims. The common flu is something of a killer -- about 35,000 in the US each year. Its victims are largely the aged, and many die from secondary infections.

The 2009 H1N1 flu is showing a different pattern. It is particularly dangerous to young adults. The reason is not clear, but this is a pattern that has been seen with occasional flu strains, including the famous 1918 "Spanish flu" (which did not come from Spain).

* A news story that summarizes some recent findings, as recently published in JAMA: Most Critical And Fatal Cases Of 2009 Influenza A(H1N1) Initial Outbreak Were Healthy Adolescents And Young Adults. (Medical News Today, October 13, 2009.)
* The JAMA papers seem to be freely available. An editorial, with a general overview: Preparing for the Sickest Patients With 2009 Influenza A(H1N1). (D B White & D C Angus, JAMA 302:1905, 11/4/09.) At the bottom, this page links to "related articles" -- the three detailed reports. The editorial might be a good place to start; the articles themselves are rather technical. (If you have any trouble with access to these, let me know.)


Take home lesson. The most important lesson is that we must not assume that the 2009 H1N1 flu is like other flu that we have known. At this point, it seems that young adults are particularly susceptible to getting serious disease from the 2009 H1N1 flu; these people would probably be advised to check with a doctor upon getting the flu, because early treatment can be critical.

Remember, there are some simple things you can do to minimize getting the flu -- and other respiratory infections. For example... Wash your hands frequently, and keep hands out of your face.

There is a follow-up post, responding to some questions. It is immediately below, dated 10/28/09.



The new flu: your questions

October 28, 2009

The flu item posted last week generated some questions. Here are a couple of the questions, with some responses (indented).

Last week's post is immediately above, dated 10/21/09.

* * * * *

Question. I don't really understand your fascination with flu. That is just a virus that likes to mutate, and sometimes has fatal consequences. Colon cancer or coronary diseases are much bigger killers, but there is not a fraction of publicity on them as on flu. Probably due to the fact that there isn't a pill ready that takes away negative effects of bad eating habits.

Interesting issue. Several points...

Actually, colon cancer and flu are about equal in deaths (US data). Further, colon cancer is on the decline (a gradual decline), whereas flu deaths vary a lot -- and could be much larger. More on this below.

Flu is indeed big in the news. Why?

Flu is infectious, uncertain, and fast. (Colon cancer is none of those.)

As noted, flu kills about the same as colon cancer, but it varies; we fear it will kill 10x that. Maybe much more. That variation is quite a mystery to us; it may happen unexpectedly and fast.

The 1918 flu serves as a baseline for the fear. It killed tens of millions worldwide -- out of a much lower population.

Look at the current H5N1 bird flu in Asia -- which seems to have similar mortality (as 1918 flu). It is scary. It is this flu that has stimulated the development of pandemic plans.

The current H1N1 came along as a surprise. If nothing else, it provides something of a test of the pandemic plans.

But look... several months along, and we are just learning what it really does, just getting a vaccine. (OTOH, one can marvel at how much we have learned about it in a few months.) With luck... Or maybe ... The point is that the course of a flu strain is so fast that we need to prepare for it before we know how serious it is.

Flu is infectious and contagious. Very contagious. It is a social disease. We can affect our chances of getting flu by simple measures. We can do that some for the other diseases you bring up, but much more for flu. 100% protection, maybe. And some of this is just good hygiene.

The vaccine is an issue, of public interest. One aspect is public uncertainty about it. More about the vaccine in the next question.


For any of you, some questions about this... One is whether you disagree with any of the specific points (or want to comment on them further). One is what you would add. And one is how you would weigh them.

In addressing the question, I've focused largely on why flu is interesting or fascinating or important. This is not to minimize the other diseases that were mentioned. Happy to post items about them, as things come up. We have already had a post about heart disease.

* * * * *

Question. So would you recommend taking a flu shot this year? I was always reluctant towards flu shots thinking that I'd resist most viruses as long as I'm in a good shape.

I was afraid someone would ask that.

First, I don't give medical advice, so take this just as thinking, not a conclusion. We may discuss some issues about the vaccine here, but it is not for me to decide what you should do.

An important point about "the flu vaccine": The H1N1 vaccine is a different shot than the regular one (which seems to be called the "seasonal" flu vaccine). So you have two choices to make this year, and it is reasonable to think about them, in part, separately. In fact, availability of the H1N1 vaccine is still very limited. (Why is the vaccine for the new strain separate? Because the new strain came along too late to be included in the regular vaccine.)

If the point you made above is a key consideration, then it would seem that the H1N1 case deserves a re-think. This new flu (like the H5N1 bird flu) may be of greatest concern to young healthy people. (It may act by over-stimulating the immune system -- resulting in the so-called cytokine storm.)

If nothing else, the point should prompt you to at least consider it, and look into it more than you might have.

Think about your other risk factors -- and whether you tend to get the flu. Those in dense places have more chance. Day care centers are awful, and schools are pretty bad.

A cop-out is to suggest you ask your doctor. See what your doc says, and how s/he responds to your questions about it. The CDC site is also a good source of basic, mainstream information. If you are not comfortable at that point with what the doctor or CDC suggests, it helps if you at least have a defined concern. If you are concerned about a specific issue, you can learn more about that issue. OTOH, if you simply have a nebulous skepticism, it is hard to address it.


Pregnant women are considered very high risk for this flu. Check CDC recommendation; I think you will find that pregnant women (or those planning...) are among the top priority.

Contagion. I noted above that the flu is a social disease. Let's expand on that in the vaccine context. The vaccine serves two purposes: it protects you, but it also protects those around you. An important issue with many vaccines (for contagious diseases) is vaccinating a high enough percentage of the population to greatly reduce the general level of the virus, thus breaking its transmission. Think about that day care center.

Mandates. The previous point leads to the issue of "mandates" -- of requiring vaccination. One of you brought this up. Philosophically, I am not a fan of such mandates. I'd rather we persuade than require. Mandates always have the possibility of abuse -- or at least the perception of abuse. On the other hand, I'm sure they do lead to higher level of vaccination, thus help reduce transmission -- especially among school children. (With most mandates, you can decline. If you are under a mandate and it concerns you, ask.)


Personal behavior. Regardless of vaccine... If you think you are getting the flu... then do see a doctor. (At least, call the doc and ask.) This is particularly important for the "healthy young people" -- who may be at greatest risk this time around. Depending on the situation, they may test what kind (or may just assume it is the new flu). They may give you a drug, which tends to be very effective if given early. Everything about the flu is fast.

Further, if you think you are getting the flu, stay home! You are likely to be able to transmit the virus even while you feel ok. By reducing your contact with others, you help to break the transmission of the virus.

And remember, you can do much to reduce your chances of getting the flu by good personal hygiene. Go wash your hands.



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