Tag Archives: swine flu

Measuring Epidemiological Contacts in Schools

I am happy to report that our paper describing the measurement of casual contacts within an American high school is finally out in the early edition of PNAS. Stanford’s great social science reporter, Adam Gorlick, has written a very nice overview of our paper for the Stanford Report (also here in the LA Times and here on Medical News Today). The lead author, and general force of nature behind this paper, is Marcel Salathé, who until recently was a post-doc here at Stanford in Marc Feldman‘s lab.  This summer, Marcel moved to the Center for Infectious Disease Dynamics at Penn State, a truly remarkable place and now all the better for having Marcel.  From the Penn State end, there is a nice video describing our results as well as well as a brief note on Marcel’s blog.  This paper has not been picked up quite like our paper on plague dynamics this summer, probably because measuring casual contacts in an American high school generally does not involve carnivorous mice.

With generous NSF funding, we were able to buy a lot of wireless sensor motes — enough to outfit every student, teacher, and staff member at a largish American high school so that we could record all of their close contacts in a single, typical day. By “close contact,” we mean any more-or-less face-to-face interaction within a radius of three meters.  As Marcel was putting together this project, we were (once again) exceptionally lucky to find ourselves at Stanford along with one of the world authorities on wireless sensor technology, Phil Levis, of Stanford’s Computer Science department.  Phil and his students, Maria and Jung Woo Lee, made this work come together in ways that I can’t even begin to fathom.  This actually leads me to a brief diversion to reflect on the nature of collaboration.  As with our plague paper or SIV mortality paper, this paper is one where collaboration between very different types of researchers (viz., Biologists, Computer Scientists, Anthropologists) is absolutely fundamental to the success of the work.  In coming up for tenure — and generally living in an anthropology department — the question of what I might call the partible paternity of papers (PPP) comes up fairly regularly. “I see you have a paper with five co-authors; I guess that means you contributed 17% to this paper, no?”  Well, no, actually.  I call this the “additive fallacy of collaboration.” When a paper is truly collaborative, then the contributions of the paper are not mutually exclusive from each other and so do not simply sum.  To use a familiar phrase, the whole is greater than the sum of the parts.  Our current paper is an example of such a truly collaborative project.  Without the contributions of all the collaborators, it’s not that the paper would be 17% less complete; it probably wouldn’t exist. I can’t speak particularly fluently to what Phil, Maria, and Jung Woo did other than by saying, “wow” (thus our collaboration), but I can say that we couldn’t have done it without them.

I’ll talk more about our actual results later.  For now, you’ll either have to read the paper (which is open access), watch the video, or read the overview in the Stanford Report.

More On Flu

There is a nice video piece at the New York Times website done by science reporter Donald G. McNeil Jr.  In it, he makes a number of important points that I have been trying to emphasize in my latest posts on the topic. McNeil is to be congratulated.  This is the kind of reporting we need now and in the coming months on swine flu.

The New Scientist also has an editorial (which I just found because I’m behind on my RSS reader) which notes the distinct possibility that H1N1 could come back with a vengeance this Fall.  Note that most of the deaths in the pandemic of 1918 occurred in September of 1918 even though the first cases were reported in March of 1918.  The pandemic of 1918 (which was really the pandemic of 1918-1920) killed 50 million people, perhaps as many as 100 million.  The world population in 1920 was 1.86 billion, which means there were around 1.78 billion or so in 1918.  The case fatality ratio for the 1918 flu was >2.5%, and perhaps as high as 5%, which means that 25-50 people died out of 1000 infected with the flu.  All in all, this means that anywhere from 0.5% to 2% of the world’s population died during the pandemic of 1918 (though if 100,000,000 people really died, then the overall world mortality rate was actually over 5%!).  The following figure (from Taubenberger and Morens 2006) shows the time series of deaths from flu for 1918-1919.  

Taubenberger and Morens (2006), Figure 1.

The most striking feature of this figure is the pronounced spike in mortality in the Fall of 1918.  We are currently a month before this time series starts in our current potential pandemic. Note that the death rate in June of 1918 was not too dissimilar from the mortality rate estimated from Mexican outbreak data by Fraser et al. (2009).

The New Scientist also reports that a flu vaccine incorporating the new A(H1N1) is unlikely to be available by the Fall of next year.  This is, of course, distressing news.  So, what can we do?

It seems to me that the best plan is to follow D.G. Margaret Chan‘s call for international solidarity.  She has rightly noted that the people likely to be hardest hit by the an H1N1 pandemic (or any other infectious disease for that matter) are the citizens of the world’s poor countries.  They are the ones who bear 85% of the infectious disease burden, after all.  So, why should we in the developed north care about this other half (homage to Yogi Berra intended)?

For the time-being the strain of A(H1N1) is relatively benign (just as it was in 1918 at this point), but influenza has an incredible capacity to mutate, recombine with other co-circulating flu strains, and respond to selection (the part that you don’t typically hear about in news reports). Let us not forget that there is currently another highly pathogenic strain of flu out there. Highly pathogenic Influenza A(H5N1) — remember bird flu? — has an overall mortality rate of approximately 60%. Yes, that’s an order of magnitude greater than the high-ball estimate for the 1918 flu.  Of course, this variant of influenza has only infected a total of 424 people in the world since 2003.  141 of those have been in Indonesia (where 115 have died for a case fataility ratio of 81.5%).  We have gotten very lucky so far with H5N1 because it is not efficiently transmitted from person-to-person.  The emergent H1N1, however, is.  It’s basic reproduction ratio is substantially greater than that of seasonal flu, which indicates it is very efficiently transmitted. God help us if a recombinant strain with the pathogenicity of bird flu and the transmissibility of swine flu were to evolve.

This suggests to me that a little bit of financial and technical assistance from the north to the countries of the south might be a very good investment at this point. Let’s help developing countries entering their flu season control swine flu to the absolute best degree we can manage. Minimizing the number of cases also minimizes the evolutionary potential of the virus — fewer infections, fewer opportunities for mutation and subsequent selection. I realize that we are in the throes of a major economic crisis, the likes of which we haven’t seen since 1929.  But, do you have any idea what losing 5% of the world’s population would do to the economy?

Keep Washing Your Hands

As the potential pandemic fades into the obscurity of a couple weeks’ worth of the 24-hour news cycle, cases continue to mount.  New York City reported its first swine-flu death, an assistant principal in a NYC public school. As with most of the other deaths so far, this particular victim had medical complications that contributed to his especially severe illness.  This is typical for influenza and other serious respiratory illnesses like SARS.  One of the greatest risk factors for dying of SARS during the outbreak of 2003 was being a diabetic (Chan et al. 2003).   Flu is dangerous.  As noted by Thomas R. Frieden, New York City’s health commissioner and Obama appointee to head CDC, “We should not forget that the flu that comes every year kills about 1,000 New Yorkers.”  As I noted in a previous post, analysis of the outbreak data from Mexico suggests that the current influenza A(H1N1) has a case fatality ratio a little bit higher than the usual seasonal flu, so we should expect it to kill more people, though not dramatically more.

The number of cases continues to rise in Japan, another northern hemisphere country with high-functioning public health infrastructure, despite how late in the season it is. The Japanese government has closed over a thousand schools around the western cities of Kobe and Osaka in an attempt to curtail transmission.  So far, there does not appear to be sustained community transmission, but again, it is remarkable that there is any  transmission to speak of this late in the flu season.  One other troubling part of this particular outbreak is that the school cluster around Kobe and Osaka is not associated with overseas travel as clusters in the United States and Europe have been.

WHO Director General Margaret Chan announced at the recent meeting of the World Health Assembly that the apparent quiescence of flu activity now — even as WHO has kept its pandemic alert at level 5 — could still be “just the calm before the storm.”  She urged countries to work together to continue to control the current outbreak of A(H1N1), noting that those most vulnerable remain the poorest of the world’s citizens. As quoted in the NY TImes, “I strongly urge the international community to use this grace period wisely. I strongly urge you to look closely at anything and everything we can do, collectively, to protect developing countries from, once again, bearing the brunt of a global contagion.”

Just to highlight the fact that, despite the media silence, the swine flu outbreak continues to grow globally, I will post an updated plot of the WHO case counts for today.

Yes, cases continue to rise.  Let’s continue to take reasonable personal precautions, help with the battle against flu in countries of the southern hemisphere, and prepare for the next flu season here.  It never hurt anyone to wash their hands a couple more times a day.

On Swine Flu

A lot has happened in the last week.  I was frantically preparing for a big talk that I had to give at the end of the week when the news about swine flu started heating up.  As of the most recent posting from the Pan-American Health Organization, there are 1118 confirmed cases and 27 deaths in 18 countries worldwide. The United States has had 279 laboratory-confirmed cases and one death.  As I write, it sounds like the epidemiological situation is much better than it could have been.

But last Monday things were looking like they were going to get very serious. While I should have been preparing for my talk, I spent the day working out the details for an internet-based survey on people’s knowledge, attitudes, and behavior regarding the emerging H1N1 (a.k.a. “swine”) flu. Marcel Salathé and I realized that we had an historic opportunity to field a survey and learn something about people’s responses as the public health emergency unfolded.  Our survey has been online since the morning of Wednesday, April 29th (and is available here for anyone interested in taking it — it’s only 16 questions long and takes less than five minutes to complete) and we have gotten well over 5,000 responses so far. Vijoy Abraham at the Institute for Research in the Social Sciences was amazingly helpful in helping us get the survey online in a hurry, and IRiSS very kindly hosted the survey.

Marcel posted a nice blog piece on the survey and it was later picked up by Carl Zimmer on his blog, and then the big-time: we got written about on boing boing.  This idea clearly resonates with people.  Stanford put out a press release and now Marcel and I have done a number of interviews for various local and international media outlets (links forthcoming).  All this before we’ve even done any analysis!

We will keep the survey online as long as it is relevant, though we will begin doing some exploratory data analysis shortly. The thing about flu is that, even though it seems like it is fizzling out already, it could actually kick around for months. I was speaking with a prominent disease ecologist this past week who predicted that this particular outbreak would fizzle in the northern hemisphere for the time-being. You see, by May, we are pretty well past flu season in the north.  For whatever reason, flu shows marked seasonality in transmission.  Jeff Shaman at Oregon State has shown pretty convincingly that this seasonality is a matter of absolute humidity, which is lowest in the winter in temperate regions and is presumably more conducive for influenza transmission and virus survival. The disease ecologist who made the prediction for northern-hemisphere fizzle also suggested that the southern hemisphere might be in for a hard flu season during the austral winter.  Extensive and sustained transmission could be bad news for those of us who feel like we’ve dodged a bullet here in the north because when flu season rolls back around here, we might get slammed on the rebound.  A very interesting paper by Cécile Viboud and colleagues shows that it was the second influenza season that had the higher mortality rates during the last influenza pandemic of 1968.  The moderator on ProMED-mail wrote “Even if the present A/H1N1 has pandemic potential it is therefore highly likely that the outbreak will fade out within the next 2 to 3 weeks, but it will reappear in the autumn.”  Time to get cracking on getting this H1N1 strain incorporated into the next flu vaccine, I’d say.

This means that we will probably need to keep our survey up for a while to come.  It will be interesting — and hopefully informative — to see how people’s anxieties and knowledge about swine flu wax and wane as this system evolves. 

That’s all for now though I suspect this won’t be the last post I write about swine flu. Oh, and the talk turned out fine; thanks for asking…