Effect Measure

Swine flu: what did you expect?

Usually “What did you expect?” is a rhetorical question, but we have a more serious point to make. Let’s start with the familiar and move on to the less familiar. Many of you are coming here to find the latest news about swine flu. It’s an imprecise term that covers two different things: what has happened that is new, in the sense of surprising and we didn’t already know it would happen; and what is the current situation. Overnight (in the US) Europe (Spain) registered its first confirmed case. That’s additional data but not surprising. We know this virus is seeded out there and we shouldn’t be too surprised when we find it if we look hard enough in the days and weeks ahead. The other sense of news is about the current situation. The growing list of US states, and now countries, is relevant to understanding where we are at the moment. Similarly, the growing list of suspected cases will grow, probably very quickly. You should expect it. Those of you follow the H5N1 (“bird flu”) story will recognize what is happening here. Flu of any kind has very non specific symptoms (cough, sore throat, fever, etc.) that are caused by numerous respiratory viruses (adenovirus, metapneumovirus, respiratory syncytial virus, parainfluenza, influenza B, etc). They are all circulating at this time of year. Some of them can cause severe disease, although mostly they just produce “spring” (or “summer”) colds or flu (most of which isn’t flu in the strict sense). In the context of this outbreak each of these respiratory virus cases has the potential to become a “suspect” case. Mexico City has 1614 “cases” and 103 deaths. Not all, or even most, of the cases have been confirmed by laboratory. They are really suspect cases. Some have been confirmed, most not. Confused? Expect that, too. In the opening days and weeks of an outbreak, everyone is confused. That’s why we pool our information and try to sort it out.

Now to the less familiar parts of “what did you expect?” If there is normally so much respiratory disease around, why is this an outbreak or even an epidemic? It’s a more difficult question than it appears, and it relates to “what did you expect?” An epidemic is an increase in the number of new cases beyond what you would expect. Four or five cases of human rabies in an area in the US would be an outbreak or even an epidemic. Hundreds of colds or even serious pneumonias in an urban area is normal. It’s not an epidemic. What makes the swine flu an outbreak is that it is an infection with a virus we haven’t seen before and which we believe may be new. Hence these cases are not what we expect and it is an outbreak. If it turned out that there had been the same number of cases in Mexico but from many different known viruses we might look for another explanation, for example, a change in insurance that changed care seeking behavior so cases were counted that weren’t counted before.

Another thing that most people and probably most clinicians expect is that we know a lot about influenza. Perhaps because of the increased scientific interest since bird flu (an increased interest which will pay off handsomely in this outbreak, by the way) we do know quite a bit, but we also now know many of the things we thought we knew about flu, like the main ways it is transmitted from person to person, we don’t really know. For example, how likely is it that you can get flu by touching a door knob or arm rest that someone with the flu just touched? Or that you can get the flu by sitting in the same emergency department waiting room (but not next to) other flu cases? These are open questions (see some of our many posts on this here, here, here, here). Why is flu seasonal? We don’t know. We’ll try to get to some more of these questions in the days ahead, since we have many new readers, but one big thing to know was emphasized by Acting CDC Director Richard Besser at the White House briefing yesterday: the influenza virus is highly unpredictable and our certain knowledge of it very scant. If you’ve seen one flu pandemic, you’ve seen one flu pandemic.

If this outbreak becomes a sustained worldwide one — the definition of a pandemic — you should not expect it to be the same as any other pandemic. It might be like 1918, 1957, 1968 or just a bad flu season. Or not.

But what did you expect?


  1. #1 Tom DVM
    April 27, 2009

    Thanks Revere for an excellent piece of writing and your works over the weekend when you probably had better things to do.

    It has been very informative.

  2. #2 woodpuppy
    April 27, 2009

    The US and the world intends to fight the swine flu with Tamiflu… the new virus is partly composed of H1N1 which is resistant to Tamiflu… has any organization or gov’t confirmed that Tamiflu is even effective???

  3. #3 DebP
    April 27, 2009

    We know that tamiflu interferes with the testing of H5N1. Do you know if it interferes with this test also? I heard that the boys in New York recieved doses of tamiflu, do you think they would not have had mild cases if they did not recieve it?

  4. #4 Robin
    April 27, 2009

    Have all the US cases received Tamiflu and if so is it possible this is responsible for the mildness of the symptoms being reported here? If this is the case, then we are SOL; because we all know there is definitely not enough tamiflu to go around.

  5. #5 Phillip Huggan
    April 27, 2009

    “Why is flu seasonal? We don’t know”

    We didn’t know in 05/2007. We know now. A February PNAS paper says it is the dry air in winter. They think water droplets impact flu’s protein surfaces or something.

    “If you’ve seen one flu pandemic, you’ve seen one flu pandemic.”

    A solid gold nugget of info. This is why we come to this site.

  6. #6 Mike Dunford
    April 27, 2009

    H1N1 doesn’t refer to a single virus. It’s a category that includes a number of different strains that share certain characteristics. The current swine flu isn’t “partly composed of” H1N1. It is an H1N1 strain.

    There are some H1N1 strains that are at least somewhat resistant to Tamiflu, but this isn’t one of them. Both Tamiflu and amantadine have been tested for effectiveness against this strain. It’s resistant to amantadine, but not to Tamiflu.

  7. #7 Lisa in Ontario, Canada
    April 27, 2009

    I posted this on yesterday’s post where it seemed more relevant, but it seems everyone has moved on….

    Re: the differences between the “Mexican strain” and others

    Has anyone considered the genetic differences in the population as a basis for the greater lethality of the disease in Mexico? There is a large indigenous population in Mexico, which has interbred with the European population to a much greater degree than in the rest of North America.

    Given that the indigenous populations here were isolated for the first 10,000 years of human history, and did not live in close proximity to farm animals as the Eurasian populations did, they may not have developed the same level of genetic immunity through repeated exposures to pandemics over thousands of years.

    Perhaps that explains the differences in outcomes.

  8. #8 Speechless
    April 27, 2009

    Yes indeed what were we expecting? Overcrowding and over development lead to unsanitary conditions where disease breeds. I know its not scientific to say this without numbers and charts to back it up. Still for thousands of years its been recognized that when human populations get out of balance, war,famine, pestilence and plague follow after.

    I just read on a website called Grist that Smithfield Farms, the worlds largest producer of pork products, has an unhygienic, overcrowded farm facility in Vera Cruz, Mexico. The poor hygiene practices of other US in Mexico and Mexican farms have led to some of the dreadful food borne illnesses of the past decade (remember the spinach scallions, strawberries which were all implicated for disease in the last 5 years?)

    When profit motives far outweigh concern for the common good, disease seems to follow too quickly.

  9. #9 revere
    April 27, 2009

    Philip: The PNAS paper was a guinea pig experiment and implicated humidity. Unfortunately it is only a hypothesis and not consonant with all the data. As noted in another post the peak of the flu season in a tropical climate (Nicaragua) was July, the hottest and rainiest time. For flu scientists this remains an open question.

    Lisa: Host genetic differences are quite unlikely. This would have to be a much more powerful effect than anyone thinks plausible. More likely explanations are a biased difference in ascertainment (Mexicans looking only at serious cases, US looking mainly at outpatient non serious ones) or some co-factor (like combination with another virus) prevalent in Mexico but not here. We don’t know yet. Let’s wait for data.

    Tamiflu: Mike Dunford has it exactly right. This virus is sensitive to Tamiflu and Relenza (so far). As far as I know only one US patient received any of these drugs, so that’s not the explanation.

  10. #10 Snowy Owl
    April 27, 2009

    U.S. monitors border for swine flu
    Last Updated: 27th April 2009, 9:28am

    Richard Besser, acting head of the U.S. Centers for Disease Control and Prevention, revealed that American authorities were undertaking “passive screening” at its borders and reiterated the government’s call for people to remain calm. Besser said that U.S. officials at border checkpoints were “asking people about fever and illness, looking for people who are ill.”

    Besser discussed the problem on morning news shows as President Barack Obama prepared to address it later Monday morning in remarks to a meeting of the country’s top scientists.

    Besser travelled the morning news-show circuit Monday, telling interviewers the U.S. government was being “extremely aggressive” and saying he wouldn’t personally recommend travelling to parts of Mexico where the new virus has taken hold. But he noted that the issue of a travel ban was under discussion and that nothing had been decided.

    Besser said he was not reassured by the fact that so far in the U.S., no one has died from the disease.

    “From what we understand in Mexico, I think people need to be ready for the idea that we could see more severe cases in this country and possibly deaths,” he said. “That’s something people have to be ready for and we’re looking for that. So far, thankfully, we haven’t seen that. But we’re very concerned and that’s why we’re taking very aggressive measures.”


  11. #11 Mark
    April 27, 2009

    I should confess I had the same thought as Lisa. I don’t think it’s impossible that people of European, African and Asian descent would have greater resistence to a pathogen than people of indigenous American descent. There is historical precedent in the great die-off that occurred among native Americans when Europeans landed.

    Of course this is total speculation, but so are the other explanations. I don’t see what makes one explanation more likely than another, at this point.

  12. #12 Alf Refsum
    April 27, 2009

    I would like to see more information about the timeline of this “proto-pandemic”. Cases now coming to light in Europe are people that returned from either somewhere in Mexico or the US up to week ago. That should tell something about the disease and something about the current potential spread. It has been there for a while (weeks ?) and it is a “slow” developer.

  13. #13 Phillip Huggan
    April 27, 2009

    Thx Revere. I thought the Feb paper settled the issue. If your link paper only accounts for two years that is anecdotal. Does Nicaragua’s flu season regularly peak in summer? If it indeed does it might be because of the traditional winter peak explanation; maybe people stay inside cooped up during their rainy season?

  14. #14 Tom
    April 27, 2009


    Thanks again for your splendid work!

    Othen, family and friends ask even those of us who unlike you work more in social epidemiology and decision analysis rather than medical epidemiology for practical advice in preparing for, preventing and getting apt treatment for suspected swine flu. Could you, this early in the outbreak, give us advice to pass on to lay persons?

    Alternatively would you please provide helpful urls (perhaps to specific items in Effect Measure) , to us to help respond to these very practical questions.

    If your reply is seen as complex by even college-educated laypersons, I will be happy to cast your reply and/or url(s) into a decision aid such as a concept map, etc. and send it to you for an accuracy check. Only if/when the decision aid meets your approval, would I disseminate the decision aid in any manner. . As the more information becomes known, the decision aid could be updated, checked for accuracy, and disseminated.

    Also, Revere, if you believe it might help nudge policy makers towards acting more rationally in responding to this outbreak, I will be happy to cast your judgement into separate decision aids for policy makers, if you provide me with the needed information. Again, I realize that it may premature to attempt this step. And of course, I full recognize that even the best information cast into the simplest to understand form does not guarantee rational action. But it may help…



    p.s. I leave it entirely to you to decided if my comment is best handled off-line or as a Effect Measure comment.

    pps. I leave for another day, the question of the relative merits of different decision aids
    for different audiences and different phases of medical crises. E.g., the best use of highly focused decision aids such as flow charts or expert systems vs. aids which facilitate broader understanding to increase motivation to act such as concept maps.

  15. #15 engstudent
    April 27, 2009

    Thanks for all of the writings over the weekend – I’ve been following this developing situation and your writings have added some clarity to the noise.

  16. #16 Houston
    April 27, 2009

    To g336
    I don’t want to clutter this list,but what a wonderful post,
    and many thanks to revere for all the hard work.

  17. #17 Habebe
    April 27, 2009

    “Tamiflu: Mike Dunford has it exactly right. This virus is sensitive to Tamiflu and Relenza (so far). As far as I know only one US patient received any of these drugs, so that’s not the explanation.”

    @revere – apparently last night on FoxNews a NY phycisian attending the St.Francis students said more serious cases had been given Tamiflu. Unfortunately, I cannot find a video file of that interview, so that’s just hearsey at the moment.

  18. #18 Snowy Owl
    April 27, 2009

    With nations across the globe trying to contain an outbreak of deadly swine flu, President Obama addressed the National Academy of Sciences and talked about the outbreak of the virus. Scroll down for the text of his speech as prepared for delivery.

    For more information on swine flu visit HuffPost’s Swine Flu BigNews Page.

    President Obama’s speech:

    It is my privilege to address the distinguished members of the National Academy of Sciences, as well as the leaders of the National Academy of Engineering and the Institute of Medicine who have gathered here this morning.

    I’d like to begin today with a story of a previous visitor who also addressed this august body.

    In April of 1921, Albert Einstein visited the United States for the first time. His international celebrity was growing as scientists around the world began to understand and accept the vast implications of his theories of special and general relativity. He attended this annual meeting, and after sitting through a series of long speeches by others, he reportedly said, “I have just got a new theory of eternity.” I’ll do my best to heed this cautionary tale.

    The very founding of this institution stands as a testament to the restless curiosity and boundless hope so essential not just to the scientific enterprise, but to this experiment we call America.

    A few months after a devastating defeat at Fredericksburg, before Gettysburg would be won and Richmond would fall, before the fate of the Union would be at all certain, President Lincoln signed into law an act creating the National Academy of Sciences.

    Lincoln refused to accept that our nation’s sole purpose was merely to survive. He created this academy, founded the land grant colleges, and began the work of the transcontinental railroad, believing that we must add “the fuel of interest to the fire of genius in the discovery… of new and useful things.”

    This is America’s story. Even in the hardest times, and against the toughest odds, we have never given in to pessimism; we have never surrendered our fates to chance; we have endured; we have worked hard; we have sought out new frontiers.

    Today, of course, we face more complex set of challenges than we ever have before: a medical system that holds the promise of unlocking new cures and treatments – attached to a health care system that holds the potential to bankrupt families and businesses. A system of energy that powers our economy – but also endangers our planet. Threats to our security that seek to exploit the very interconnectedness and openness so essential to our prosperity. And challenges in a global marketplace which links the derivative trader on Wall Street to the homeowner on Main Street, the office worker in America to the factory worker in China – a marketplace in which we all share in opportunity, but also in crisis.

    At such a difficult moment, there are those who say we cannot afford to invest in science. That support for research is somehow a luxury at a moment defined by necessities. I fundamentally disagree. Science is more essential for our prosperity, our security, our health, our environment, and our quality of life than it has ever been. And if there was ever a day that reminded us of our shared stake in science and research, it’s today.

    We are closely monitoring the emerging cases of swine flu in the United States. This is obviously a cause for concern and requires a heightened state of alert. But it is not a cause for alarm. The Department of Health and Human Services has declared a Public Health Emergency as a precautionary tool to ensure that we have the resources we need at our disposal to respond quickly and effectively. I’m getting regular updates on the situation from the responsible agencies, and the Department of Health and Human Services as well as the Centers for Disease Control will be offering regular updates to the American people so that they know what steps are being taken and what steps they may need to take. But one thing is clear – our capacity to deal with a public health challenge of this sort rests heavily on the work of our scientific and medical community. And this is one more example of why we cannot allow our nation to fall behind.

    Unfortunately, that is exactly what has happened.

    Federal funding in the physical sciences as a portion of our gross domestic product has fallen by nearly half over the past quarter century. Time and again we’ve allowed the research and experimentation tax credit, which helps businesses grow and innovate, to lapse.

    Our schools continue to trail. Our students are outperformed in math and science by their peers in Singapore, Japan, England, the Netherlands, Hong Kong, and Korea, among others. Another assessment shows American fifteen year olds ranked 25th in math and 21st in science when compared to nations around the world.

    And we have watched as scientific integrity has been undermined and scientific research politicized in an effort to advance predetermined ideological agendas.

    We know that our country is better than this.

    A half century ago, this nation made a commitment to lead the world in scientific and technological innovation; to invest in education, in research, in engineering; to set a goal of reaching space and engaging every citizen in that historic mission. That was the high water mark of America’s investment in research and development. Since then our investments have steadily declined as a share of our national income – our GDP. As a result, other countries are now beginning to pull ahead in the pursuit of this generation’s great discoveries.

    I believe it is not in our American character to follow – but to lead. And it is time for us to lead once again. I am here today to set this goal: we will devote more than three percent of our GDP to research and development. We will not just meet, but we will exceed the level achieved at the height of the Space Race, through policies that invest in basic and applied research, create new incentives for private innovation, promote breakthroughs in energy and medicine, and improve education in math and science. This represents the largest commitment to scientific research and innovation in American history.

    Just think what this will allow us to accomplish: solar cells as cheap as paint, and green buildings that produce all of the energy they consume; learning software as effective as a personal tutor; prosthetics so advanced that you could play the piano again; an expansion of the frontiers of human knowledge about ourselves and world the around us. We can do this.

    The pursuit of discovery half a century ago fueled our prosperity and our success as a nation in the half century that followed. The commitment I am making today will fuel our success for another fifty years. That is how we will ensure that our children and their children will look back on this generation’s work as that which defined the progress and delivered the prosperity of the 21st century.

    This work begins with an historic commitment to basic science and applied research, from the labs of renowned universities to the proving grounds of innovative companies.

    Through the American Recovery and Reinvestment Act and with the support of Congress, my administration is already providing the largest single boost to investment in basic research in American history.

    This is important right now, as public and private colleges and universities across the country reckon with shrinking endowments and tightening budgets. But this is also incredibly important for our future. As Vannevar Bush, who served as scientific advisor to President Franklin Roosevelt, famously said: “Basic scientific research is scientific capital.”

    The fact is, an investigation into a particular physical, chemical, or biological process might not pay off for a year, or a decade, or at all. And when it does, the rewards are often broadly shared, enjoyed by those who bore its costs but also by those who did not.

    That’s why the private sector under-invests in basic science – and why the public sector must invest in this kind of research. Because while the risks may be large, so are the rewards for our economy and our society.

    No one can predict what new applications will be born of basic research: new treatments in our hospitals; new sources of efficient energy; new building materials; new kinds of crops more resistant to heat and drought.

    It was basic research in the photoelectric effect that would one day lead to solar panels. It was basic research in physics that would eventually produce the CAT scan. The calculations of today’s GPS satellites are based on the equations that Einstein put to paper more than a century ago.

    In addition to the investments in the Recovery Act, the budget I’ve proposed – and versions have now passed both the House and Senate – builds on the historic investments in research contained in the recovery plan.

    We double the budget of key agencies, including the National Science Foundation, a primary source of funding for academic research, and the National Institute of Standards and Technology, which supports a wide range of pursuits – from improving health information technology to measuring carbon pollution, from testing “smart grid” designs to developing advanced manufacturing processes. And my budget doubles funding for the Department of Energy’s Office of Science which builds and operates accelerators, colliders, supercomputers, high-energy light sources, and facilities for making nano-materials. Because we know that a nation’s potential for scientific discovery is defined by the tools it makes available to its researchers.

    But the renewed commitment of our nation will not be driven by government investment alone. It is a commitment that extends from the laboratory to the marketplace.

    That is why my budget makes the research and experimentation tax credit permanent. This is a tax credit that returns two dollars to the economy for every dollar we spend, by helping companies afford the often high costs of developing new ideas, new technologies, and new products. Yet at times we’ve allowed it to lapse or only renewed it year to year. I’ve heard this time and again from entrepreneurs across this country: by making this credit permanent, we make it possible for businesses to plan the kinds of projects that create jobs and economic growth.

    Second, in no area will innovation be more important than in the development of new technologies to produce, use, and save energy – which is why my administration has made an unprecedented commitment to developing a 21st century clean energy economy.

    Our future on this planet depends upon our willingness to address the challenge posed by carbon pollution. And our future as a nation depends upon our willingness to embrace this challenge as an opportunity to lead the world in pursuit of new discovery.

    When the Soviet Union launched Sputnik a little more than a half century ago, Americans were stunned: the Russians had beaten us to space. We had a choice to make: we could accept defeat – or we could accept the challenge. And as always, we chose to accept the challenge.

    President Eisenhower signed legislation to create NASA and to invest in science and math education, from grade school to graduate school. And just a few years later, a month after his address to the 1961 Annual Meeting of the National Academy of Sciences, President Kennedy boldly declared before a joint session of Congress that the United States would send a man to the moon and return him safely to the earth.

    The scientific community rallied behind this goal and set about achieving it. And it would lead not just to those first steps on the moon, but also to giant leaps in our understanding here at home. The Apollo program itself produced technologies that have improved kidney dialysis and water purification systems; sensors to test for hazardous gasses; energy-saving building materials; and fire-resistant fabrics used by firefighters and soldiers. And, more broadly, the enormous investment of that era – in science and technology, in education and research funding – produced a great outpouring of curiosity and creativity, the benefits of which have been incalculable.

    The fact is, there will be no single Sputnik moment for this generation’s challenge to break our dependence on fossil fuels. In many ways, this makes the challenge even tougher to solve – and makes it all the more important to keep our eyes fixed on the work ahead.

    That is why I have set as a goal for our nation that we will reduce our carbon pollution by more than 80 percent by 2050. And that is why I am pursuing, in concert with Congress, the policies that will help us meet this goal.

    My recovery plan provides the incentives to double our nation’s capacity to generate renewable energy over the next few years – extending the production tax credit, providing loan guarantees, and offering grants to spur investment. For example, federally funded research and development has dropped the cost of solar panels by ten-fold over the last three decades. Our renewed efforts will ensure that solar and other clean energy technologies will be competitive.

    My budget includes $150 billion over ten years to invest in sources of renewable energy as well as energy efficiency; it supports efforts at NASA, recommended as a priority by the National Research Council, to develop new space-based capabilities to help us better understand our changing climate.

    And today, I am also announcing that for the first time, we are funding an initiative – recommended by this organization – called the Advanced Research Projects Agency for Energy, or ARPA-E.

    This is based on the Defense Advanced Research Projects Agency, known as DARPA, which was created during the Eisenhower administration in response to Sputnik. It has been charged throughout its history with conducting high-risk, high-reward research. The precursor to the internet, known as ARPANET, stealth technology, and the Global Positioning System all owe a debt to the work of DARPA.

    ARPA-E seeks to do this same kind of high-risk, high-reward research. My administration will also pursue comprehensive legislation to place a market-based cap on carbon emissions. We will make renewable energy the profitable kind of energy in America. And I am confident that we will find a wellspring of creativity just waiting to be tapped by researchers in this room and entrepreneurs across our country.

    The nation that leads the world in 21st century clean energy will be the nation that leads in the 21st century global economy. America can and must be that nation.

    Third, in order to lead in the global economy – and ensure that our businesses can grow and innovate, and our families can thrive – we must address the shortcomings of our health care system.

    The Recovery Act will support the long overdue step of computerizing America’s medical records, to reduce the duplication, waste, and errors that cost billions of dollars and thousands of lives.

    But it’s important to note: these records also hold the potential of offering patients the chance to be more active participants in prevention and treatment. We must maintain patient control over these records and respect their privacy. At the same time, however, we have the opportunity to offer billions and billions of anonymous data points to medical researchers who may find in this information evidence that can help us better understand disease.

    History also teaches us the greatest advances in medicine have come from scientific breakthroughs: the discovery of antibiotics; improved public health practices; vaccines for smallpox, polio, and many other infectious diseases; anti-retroviral drugs that can return AIDS patients to productive lives; pills that can control certain types of blood cancers; and so many others.

    And because of recent progress – not just in biology, genetics and medicine, but also in physics, chemistry, computer science, and engineering – we have the potential to make enormous progress against diseases in the coming decades. That is why my Administration is committed to increasing funding for the National Institutes of Health, including $6 billion to support cancer research, part of a sustained, multi-year plan to double cancer research in our country.

    Fourth, we are restoring science to its rightful place.

    On March 9th, I signed an executive memorandum with a clear message: Under my administration, the days of science taking a back seat to ideology are over. Our progress as a nation – and our values as a nation – are rooted in free and open inquiry. To undermine scientific integrity is to undermine our democracy.

    That is why I have charged the White House Office of Science and Technology Policy with leading a new effort to ensure that federal policies are based on the best and most unbiased scientific information. I want to be sure that facts are driving scientific decisions – and not the other way around.

    As part of this effort, we’ve already launched a website that allows individuals to not only make recommendations to achieve this goal, but to collaborate on those recommendations; it is a small step, but one that is creating a more transparent, participatory and democratic government.

    We also need to engage the scientific community directly in the work of public policy. That is why, today, I am announcing the appointment of the President’s Council of Advisors on Science and Technology, known as PCAST, with which I plan to work closely.

    This council represents leaders from many scientific disciplines who will bring a diversity of experiences and views. I will charge PCAST with advising me about national strategies to nurture and sustain a culture of scientific innovation. It will be co-chaired by John Holdren, my top science advisor; Eric Lander, one of the principal leaders of the Human Genome Project; and Harold Varmus, former head of the National Institutes of Health and a Nobel laureate.

    In biomedicine, for example, this will include harnessing the historic convergence between life sciences and physical sciences that is underway today; undertaking public projects – in the spirit of the Human Genome Project – to create data and capabilities that fuel discoveries in tens of thousands of laboratories; and identifying and overcoming scientific and bureaucratic barriers to rapidly translating scientific breakthroughs into diagnostics and therapeutics that serve patients.

    In environmental science, it will require strengthening our weather forecasting, our earth observation from space, the management of our nation’s land, water and forests, and the stewardship of our coastal zones and ocean fisheries.

    We also need to work with our friends around the world. Science, technology, and innovation proceed more rapidly and more cost-effectively when insights, costs, and risks are shared; and so many of the challenges that science and technology will help us meet are global in character. This is true of our dependence on oil, the consequences of climate change, the threat of epidemic disease, and the spread of nuclear weapons, among other examples.

    That is why my administration is ramping up participation in – and our commitment to – international science and technology cooperation across the many areas where it is clearly in our interest to do so. In fact, this week, my administration is gathering the leaders of the world’s major economies to begin the work of addressing our common energy challenges together.

    Fifth, since we know that the progress and prosperity of future generations will depend on what we do now to educate the next generation, today I am announcing a renewed commitment to education in mathematics and science.

    Through this commitment, American students will move from the middle to the top of the pack in science and math over the next decade. For we know that the nation that out-educates us today – will out-compete us tomorrow.

    We cannot start soon enough. We know that the quality of math and science teachers is the most influential single factor in determining whether or a student will succeed or fail in these subjects. Yet, in high school, more than twenty percent of students in math and more than sixty percent of students in chemistry and physics are taught by teachers without expertise in these fields. And this problem is only going to get worse; there is a projected shortfall of more than 280,000 math and science teachers across the country by 2015.

    That is why I am announcing today that states making strong commitments and progress in math and science education will be eligible to compete later this fall for additional funds under the Secretary of Education’s $5 billion Race to the Top program.

    I am challenging states to dramatically improve achievement in math and science by raising standards, modernizing science labs, upgrading curriculum, and forging partnerships to improve the use of science and technology in our classrooms. And I am challenging states to enhance teacher preparation and training, and to attract new and qualified math and science teachers to better engage students and reinvigorate these subjects in our schools.

    In this endeavor, and others, we will work to support inventive approaches. Let’s create systems that retain and reward effective teachers, and let’s create new pathways for experienced professionals to enter the classroom. There are, right now, chemists who could teach chemistry; physicists who could teach physics; statisticians who could teach mathematics. But we need to create a way to bring the expertise and the enthusiasm of these folks – folks like you – into the classroom.

    There are states, for example, doing innovative work. I am pleased to announce that Governor Ed Rendell will lead an effort with the National Governors Association to increase the number of states that are making science, technology, engineering and mathematics education a top priority. Six states are currently participating in the initiative, including Pennsylvania, which has launched an effective program to ensure that his state has the skilled workforce in place to draw the jobs of the 21st century. I’d want every state participate.

    But our work does not end with a high school diploma. For decades, we led the world in educational attainment, and as a consequence we led the world in economic growth. The G.I. Bill, for example, helped send a generation to college. But in this new economy, we’ve come to trail other nations in graduation rates, in educational achievement, and in the production of scientists and engineers.

    That’s why my administration has set a goal that will greatly enhance our ability to compete for the high-wage, high-tech jobs of the 21st century – and to foster the next generation of scientists and engineers. In the next decade – by 2020 – America will once again have the highest proportion of college graduates in the world. And we’ve provided tax credits and grants to make a college education more affordable.

    My budget also triples the number of National Science Foundation graduate research fellowships. This program was created as part of the Space Race five decades ago. In the decades since, it’s remained largely the same size – even as the numbers of students who seek these fellowships has skyrocketed. We ought to be supporting these young people who are pursuing scientific careers, not putting obstacles in their path.

    This is how we will lead the world in new discoveries in this new century. But it will take far more than the work of government. It will take all of us. It will take all of you.

    And so today I want to challenge you to use your love and knowledge of science to spark the same sense of wonder and excitement in a new generation.

    America’s young people will rise to the challenge if given the opportunity – if called upon to join a cause larger than themselves. And we’ve got evidence. The average age in NASA’s mission control during the Apollo 17 mission was just 26. I know that young people today are ready to tackle the grand challenges of this century

    So I want to persuade you to spend time in the classroom, talking – and showing -young people what it is that your work can mean, and what it means to you. Encourage your university to participate in programs to allow students to get a degree in scientific fields and a teaching certificate at the same time. Think about new and creative ways to engage young people in science and engineering, like science festivals, robotics competitions, and fairs that encourage young people to create, build, and invent – to be makers of things.

    And I want you to know that I’m going to be working along side you. I’m going to participate in a public awareness and outreach campaign to encourage students to consider careers in science, mathematics, and engineering – because our future depends on it.

    And the Department of Energy and the National Science Foundation will be launching a joint initiative to inspire tens of thousands of American students to pursue careers in science, engineering and entrepreneurship related to clean energy.

    It will support an educational campaign to capture the imagination of young people who can help us meet the energy challenge. It will create research opportunities for undergraduates and educational opportunities for women and minorities who too often have been underrepresented in scientific and technological fields – but are no less capable of inventing the solutions that will help us grow our economy and save our planet. And it will support fellowships, interdisciplinary graduate programs, and partnerships between academic institutions and innovative companies to prepare a generation of Americans to meet this generational challenge.

    For we must always remember that somewhere in America there’s an entrepreneur seeking a loan to start a business that could transform an industry – but she hasn’t secured it yet. There’s a researcher with an idea for an experiment that might offer a new cancer treatment – but he hasn’t found the funding yet. There is a child with an inquisitive mind staring up at the night sky. Maybe she has the potential to change our world – but she just doesn’t know it yet.

    As you know, scientific discovery takes far more than the occasional flash of brilliance – as important as that can be. Usually, it takes time, hard work, patience; it takes training; often, it requires the support of a nation.

    But it holds a promise like no other area of human endeavor.

    In 1968, a year defined by loss and conflict, Apollo 8 carried into space the first human beings ever to slip beyond the earth’s gravity. The ship would circle the moon ten times before returning home. But on its fourth orbit, the capsule rotated and for the first time earth became visible through the windows.

    Bill Anders, one of the astronauts aboard Apollo 8, could not believe what he saw. He scrambled for a camera. He took a photo that showed the earth coming up over the moon’s horizon. It was the first ever taken from so distant a vantage point, soon to become known as “Earthrise.”

    Anders would say that the moment forever changed him, to see our world – this pale blue sphere – without borders, without divisions, at once so tranquil and beautiful and alone.

    “We came all this way to explore the moon,” he said, “and the most important thing is that we discovered the Earth.”

    Yes, scientific innovation offers us the chance to achieve prosperity. It has offered us benefits that have improved our health and our lives – often improvements we take too easily for granted. But it also gives us something more.

    At root, science forces us to reckon with the truth as best as we can ascertain it. Some truths fill us with awe. Others force us to question long held views. Science cannot answer every question; indeed, it seems at times the more we plumb the mysteries of the physical world, the more humble we must be. Science cannot supplant our ethics, our values, our principles, or our faith, but science can inform those things, and help put these values, these moral sentiments, that faith, to work – to feed a child, to heal the sick, to be good stewards of this earth.

    We are reminded that with each new discovery and the new power it brings, comes new responsibility; that the fragility and the sheer specialness of life requires us to move past our differences, to address our common problems, to endure and continue humanity’s strivings for a better world.

    As President Kennedy said when he addressed the National Academy of Sciences more than 45 years ago: “The challenge, in short, may be our salvation.”

    Thank you all for your past, present, and future discoveries. God bless you and may God bless the United States of America.

    P.S. Can you reformat it I have to post it to other countries.

    Thank you again

  19. #19 George Leach
    April 27, 2009

    In Mexico the deaths have been predominantly in the 20-40 age group. In the US most, or perhaps all, of the known cases have been mild and outside this age group. Of course there may be other reasons for the different mortality rates, but perhaps might age be a factor? It would be more reassuring if there were lots of non-Mexican 20-40 year olds presenting with mild symptoms and no sign of the ‘cytokine storm’ that appears to have characterised deaths in the Spanish Flu pandemic in 1918. I guess it’s still too soon for any conclusions.

  20. #20 bryan
    April 27, 2009

    It’s George’s point that troubles me: Have we seen any U.S. cases in the 20-45 range?

  21. #21 Chris
    April 27, 2009

    George, Bryan:
    50% of deaths from the 1918 strain occurred in the 20-40 age group. That means another 50% killed people above 40 and below 20- so we should have seen a death in the US by now. There may still be reason for optimism.

  22. #22 woodpuppy
    April 27, 2009

    Mike Dunford:

    Thanks for your response… I appreciate the clarification on the H1N1 strain…

  23. #23 anon
    April 27, 2009

    I expect 10M deaths worldwide
    (subjective expectation value)

  24. #24 Paul
    April 27, 2009

    I’ll ask it more briefly this time, but I received no answer because of the rapid flow of info burying earlier posts.

    Can someone reassure me that this is improbable, because if it’s not I see this as being a much more worrisome possibility. Simply put: This new H1N1 has new elements, including AVIAN FLU!!! I DO think it will prove to have facilitated H2H transmissibility. My worry is that when it reaches Egypt or Indonesia, where humans are not infrequently infected with H5N1, there will occur reassortment within one of these individuals who becomes host to both H5N1, and this new breed of H1N1.

    What are the chances for reassortment occuring in such a situation, rendering H5N1 much more capable of H2H transmission…thus, THE PANDEMIC that everyone already knows to fear?

  25. #25 George Leach
    April 27, 2009

    You are right Chris about the other 50%, and thank you for your comment, but the Spanish Flu mortality by age group graph had a W shape: in other words, the very young and very old were indeed affected, as happens with non-pandemic seasonal flu. I don’t know if I am right about this, but I believe the ‘cytokine storm’ theory is relevant for the 20-40’s only, i.e. the middle spike of the ‘W’. The very young and very old who died may have died of other complications – e.g. bacterial pneumonias – that would now be treatable. I don’t know the exact ages of all the known non-Mexican cases, but I am believe them to all be at the two low points of the ‘W’. So although I take your point that by now we would probably have seen some infants or elderly with severe illness, they seem to be absent from the data altogether. So I am holding off on the optimism for a while!

  26. #26 Rock
    April 27, 2009

    “so we should have seen a death in the US by now. There may still be reason for optimism.”

    No, I don’t think that’s accurate. The sample space of people infected in the US is very small and variation from the CFR in Mexico can be easily explained as a sampling fluke.

    At this point, there is no reason to think the CFR in the US will be any different than that in Mexico (although it is possible that the US might be able to provide better medical care). Besser essentially told everyone this when he said the US should prepare fro severe cases and deaths.

  27. #27 revere
    April 27, 2009

    Paul: Avian influenza is an infection. This strain does not “contain” avian flu. It has a segment of avian origin. All H1N1 has segments originally avian we think. The question is not transmissibility. It is clearly transmissible The question now is the virulence.

  28. #28 Dizzy
    April 27, 2009

    You have some old readers returning to the flock too Revere.

    On the Guardian website (http://www.guardian.co.uk/news/blog/2009/apr/27/swine-flu?)
    “3.55pm: The World Health Organisation says the number of confirmed cases in the US has doubled to 40, according to AP”

    Note there’s a lot of rubbish posted in the comments, one or two decent ones but swamped by those who don’t quite seem to get it.

    One of those decent comments contains the following:
    Jimmy Wales, who founded Wikipedia, has started a Flu wiki at http://flu.wikia.com/ where international information is being collated.

    I checked it out, at the moment it doesn’t contain a lot but might become a good central information point as this plays out.

    I had my doubts regarding H5N1 going pandemic on a scary scale a while back when we saw near panic on this site and others, although initially I scared myself half to death but then calmed down. This looks quite different but I’m strangely calm…

  29. #29 charles
    April 27, 2009

    Non-scientist here with a very basic question-

    Why do we still hear of about 20 “confirmed” cases in Mexico, now, three days later? I gather there are about 100 deaths, and three days ago there were about 60…

    I understand some of our CDC folks are there with test gear. Is there some reason we don’t see an updated number of confirmed cases?


  30. #30 revere
    April 27, 2009

    George, Bryan, Rock: Rock is completely correct. We will see deaths from this and there have almost certainly already been some we haven’t recognized. That’s the way it is. Be prepared for it. The apparent difference in death rates may be only apparent. We don’t know that yet. It is the $64K question.

  31. #31 Doc Holiday
    April 27, 2009

    This is interesting stuff:

    Planting orchards next to pig farms allows for efficient access to swine manure for fertilizer, but may also result in porcine exposure to flying fox saliva from partially eaten fruit or urine, from both of which the novel paramyxovirus was isolated (Chua et al. 2002b). Though remaining harmless to fruit bats, the Nipah virus acquired the capacity to cause a severe neurological and respiratory syndrome in young pigs characterized by a loud, nonproductive,“barking” cough (Mohd et al. 2000). Displaying an unusual host promiscuity, the virus caused respiratory distress in other animals proximate to the pig farm—goats, sheep, dogs, cats, and horses (Uppal 2000). The subsequent trucking of infected pigs to five states in Malaysia and into Singapore resulted in 229 human cases, nearly half of which (48%) ended in fatality (CDC 1999). A cull of more than 1 million pigs in affected areas effectively ended the outbreak (Lam 2003).
    Long-distance live animal transport has also been blamed for the spread of swine influenza viruses in the United States,where livestock may travel an average of 1,000 miles (Wilsonet al. 2000). Throughout much of the 20th century, influenza viruses had established a stable H1N1 lineage within U.S. pigs, becoming one of the most common causes of respiratory diseaseon North American pig farms (Zhou et al. 1999). That seemed to have changed in August 1998 when thousands of breeding sows fell ill on a North Carolina pig farm. An aggressive H3N2 virus was recovered, bearing the H3 and N2 antigens of the human influenza strain circulating since 1968. Not only was this highly unusual, but, upon sequencing of the viral genome, researchers found that it was not just a double reassortment (a hybrid of human and pig viruses, for example), but a never-before-described triple reassortment of human, avian, and porcine influenza virus gene segments (Zhou et al. 1999), which raised concerns about further mammalian adaptation of influenza virus (Wuethrich2003b).
    The continuous cycle of U.S. mass animal movement, involving inter-auction movements and intra-auction mixing, may provide a built-in dispersal mechanism for potentially zoonotic diease agents (Shields and Matthews 2003). Within months of the appearance of the new swine flu virus in North Carolina, it surfaced in Texas, Minnesota, and Iowa (Zhou et al. 1999). Within one year, it had spread across the United States (Webby et al.2000). The rapid dissemination across the nation was blamed on the cross-country transport of live pigs (Wuethrich2003b). In the United States, pigs travel coast to coast, frequently born in North Carolina, fattened in the corn belt of Iowa, and then slaughtered in California. It is often cheaper to transport the animals to the feed rather than transport the feed to the animals (USDA ERS2003). While this regional segmentation of production stages may cut down on short-term costs for the pork industry (Bur-rell 2002), the highly contagious nature of zoonotic diseases like influenza, perhaps made further infectious by the stresses of transport (Wuethrich 2003b), must be considered when calculating the true cost of long-distance live animal transport.
    More here: The Human/Animal Interface: Emergence and Resurgenceof Zoonotic Infectious Diseases

  32. #32 Lisa the GP
    April 27, 2009

    Blogger Matthew Nemo Saroff I think summed up the current situation very concisely:

    “It may end up as bad as Hong Kong flu, but the problem in Mexico is a dysfunctional public health system.”

  33. #33 revere
    April 27, 2009

    Dizzy: Just FYI, Fluwiki has been around since June 2005 and was started by yours truly, DemFromCT and the late Melanie Mattson. I wrote a lot of the basic science stuff. The most active part now is the Forum: http://www.newfluwiki2.com/

    Jimmy Wales had no part in it.

  34. #34 Dizzy
    April 27, 2009

    Revere, I think flu.wikia.com is a different fluwiki? It seems to be an offshoot of wikipedia, same format.

  35. #35 Reiko Shimizu
    April 27, 2009

    What is the mortality rate of this virus?

    Death number in Mexico rises to 149 now from 103 previously reported.

  36. #36 Red Crayon
    April 27, 2009

    I realize the approx. 150 deaths (as of
    this writing) in Mexico are NOT all
    confirmed flu deaths, much less swine

    However, does anyone have a pointer
    to the sex- and age-profile of these
    deaths? The signal to noise out there
    is pretty low.

    Right now, listening live to the Mexico
    Health Minister press conference, he
    says 20 of the deaths are confirmed
    swine and that “most” are age 20-50.
    This is at 16:39UTC on 27 April.

    He also says some of these flus that
    are coming out of the woodwork in
    Mexico are confirmed H3N2, i.e. not

    Thanks in advance if anyone has a
    pointer to firm information on the
    age profile.

  37. #37 Stoker
    April 27, 2009

    Dizzy, the comments on the Guardian blog are terrifying in their complacency. In fact they mirror those of various UK Govt ministers. IMO it is a huge mistake to issue reassurance based on the lack of deaths outside Mexico:
    a) We can’t yet extrapolate from the Mexico City data as we just don’t have the data
    b) The parallels between H1N1 and the 1918 pandemic – its emergence in Spring and the age of its victims – are too extraordinary to ignore
    c) The 1918 pandemic took the form of three waves, the first of which caused only mild disease and relatively few deaths.
    Either the British government spokesman is ignorant of these striking patterns, or he is lying through his back teeth. There’s nothing wrong with a bit of panic buying if it means everyone has a decent stock of bottled water and paracetamol.

    I’d like to thank Revere for this site and look forward to exploring the rest of it, if I’m around that long!

  38. #38 phytosleuth
    April 27, 2009

    Red Crayon, this site might help but take only as guestimate.

  39. #39 Red Crayon
    April 27, 2009

    This is not a good time (or place) for
    a 6.0 (preliminary) magnitude earthquake


  40. #40 Phillip Huggan
    April 27, 2009

    “c) The 1918 pandemic took the form of three waves, the first of which caused only mild disease and relatively few deaths.”

    Stoker, this is the scariest corrollary. The Spanish Flu appears to have either mutated while infecting a human host or mutated a 2nd time in an animal reservoir. This is why I’m not forgiving of some panicked Mexican hog import bans. In my panicked mind, maybe this Swine Flu came from hogs in a Mexican reservoir and maybe it will mutate again in the same reservoir. I doubt there is any data about when the Spanish Flu mutated a second time. The only other expanation I can think of is the 1st Spanish Flu wave somehow triggered an immune system over-reaction during subsequent highly lethal waves; that the 1st wave caused high death rates of second wave. All speculation on my part.

  41. #41 Ed Whitney
    April 27, 2009

    There have been many comments in the media about differences in severity between the flu seen in Mexico and in the US. This morning’s Denver Post reports that there have been 103 deaths in Mexico out of 1613 suspected cases. There have been 20 confirmed cases and no deaths in the US. If the Mexican data give us an unbiased estimate of the case fatality rate, it would be about 6.4%. Under a Poisson distribution, the probability of no fatal cases out of 20 would be about 27%. I am puzzled by the media attention to a difference in disease severity when the data so far appear consistent with equal severity in the two countries. Am I missing something?

  42. #42 K
    April 27, 2009

    Speechless, Smithfield has unsanitary hog facilities in the US too. I have it from someone who knows that this article is mostly true. Do take at least a quick look.

    North Carolina has places where it is hard to breathe for local residents due to the fumes from the pig lagoons (where the shit goes) “In 1998, corporate hog farms in North Carolina spent $1 million to help defeat state legislators who wanted to clean up open-pit lagoons. The state has consistently failed to employ enough inspectors to ensure that hog farms are complying with environmental standards.”

    The pork industry has been dealing with other pig only diseases because of the way they breed hogs. One is Postweaning multisystemic wasting syndrome (PMWS)

    In the name of efficiency, money making, capitalism etc we are setting ourselves up for some very BIG problems…..too bad for us

  43. #43 M
    April 27, 2009
  44. #44 Jimmy
    April 27, 2009

    I wonder about the seasonality, Revere. Seasonal flu appears to thrive in colder temperatures/seasons but both H1N1/1918 and this Swine Flu the virulent form seems to thrive in hotter seasons/areas. Why would seasonal flus peter out in Summer typically but virulent versions persist throughout hotter seasons? Is it the virulence which enables the flu to survive through hotter seasons by being spread among more hosts or is the virulent virus more tolerant of higher temperatures?

  45. #45 Rock
    April 27, 2009

    “Am I missing something?”

    Well, there’s 2 things:
    1) People are generally not good at probability (myself included).
    2) People in position to point this out to the media do so mutedly or say “we simply don’t know at this time” in an effort to avoid panic.

    We have to hope that in fact understating how dangerous the situation is doesn’t lead to a tepid response that costs lives. I’m worried that is the case however. Not to ramp up fear, but a pandemic like 1918 is definitely still a possibility at this point. That may not happen — as revere points out we simply don’t know.

  46. #46 Maura
    April 27, 2009

    I’ll ask it more briefly this time, but I received no answer because of the rapid flow of info burying earlier posts.

    Can someone reassure me that this is improbable, because if it’s not I see this as being a much more worrisome possibility. Simply put: This new H1N1 has new elements, including AVIAN FLU!!! I DO think it will prove to have facilitated H2H transmissibility. My worry is that when it reaches Egypt or Indonesia, where humans are not infrequently infected with H5N1, there will occur reassortment within one of these individuals who becomes host to both H5N1, and this new breed of H1N1.

    What are the chances for reassortment occuring in such a situation, rendering H5N1 much more capable of H2H transmission…thus, THE PANDEMIC that everyone already knows to fear?

    Posted by: Paul

    Does anyone have an answer to Paul’s question? What is the probability of coinfection and reassortment/recombination with H5N1?

  47. #47 rb
    April 27, 2009


    No, you’re not, and the level of misinformation is likely even worse than you state.

    If we assume, for instance, there is greater attention to mild cases in the U.S. than in Mexico (as seems likely), then the evidence of differential CFR is even flimsier.

    On the other hand, the same assumption suggests that the estimate of CFR based on the Mexican data is upward-biased. Hopefully that is in fact the case.

  48. #48 Phila
    April 27, 2009

    Lord knows you folks have enough on your plate as it is, but I hope you’ll consider writing a post on H1N1 conspiracy theories, which are already getting out of hand, judging from the comments I’ve seen on blogs and news stories.

    One of the most frustrating claims I keep seeing is that this virus has come “out of nowhere,” and therefore must’ve been manufactured (or at least, should be suspected of having been manufactured). The number of people I’ve encountered who believe that there’s no way this strain could’ve occurred naturally is really depressing; people are always looking for a hidden narrative.

    The “wag the dog” theory that this has something to do with torture memos is popular in some circles too. Obviously, some of the people who believe these things will never change their minds. But others are just confused, and would probably be helped by a post that presents the arguments against these assumptions.

  49. #49 Rock
    April 27, 2009

    “On the other hand, the same assumption suggests that the estimate of CFR based on the Mexican data is upward-biased. Hopefully that is in fact the case. ”

    I’m unqualified to really comment, but I’ll do so anyway. I think if one wants to be optimistic, the reason in the above quote is the best available right now. It seems more likely that the actual CFR in Mexico could be lower than reported than that the CFR for the disease in America would be substantially different.

  50. #50 revere
    April 27, 2009

    To all: I apologize in advance but I cannot keep up with all the good questions here. My real persona is besieged with media and my (non flu) day job as a Professor. I am doing the best I can and will try to catch up a bit later but meanwhile, scare each other. Or not.

  51. #51 Lisa the GP
    April 27, 2009


    some of this may be review for you, my apologies if so.

    Flu has a ‘segmented genome’. Its genes come on 8 strands of RNA. Lets call them strands a through h.

    When flu is packaged into a viral coat, one strand each of a through h is included.

    When two flus infect a single organism, each new flu virus still contains one strand each of a through h. But the parent virus of each strand is random. So you might have an ‘a’ strand from a swine virus and a ‘b’ strand from a human virus, etc., if a swine and a human virus simultaneously infected a pig.

    So now you have this hybrid virus floating around in pigs somewhere. Say a sick pig eats a bird that dropped dead of a bird flu in the pig pen. Well, you can have the same thing happen. You wind up with a virus that has strands originating from birds, humans, and pigs. But it doesn’t ‘contain’ a complete copy of any of the parent viruses.

    Now, among swine, among birds, among humans, there are many different strains of flu virus floating around. Some cause severe illness, some cause mild illness. Of the hundreds of bird flu strains in the world, only one of them so far has been identified as highly deadly to mammals. That strain is the one that has made news as ‘bird flu’. It is a form of H5N1, which is a kind of Influenza A (seasonal flu in humans is H1N1 like this mexican virus, or H3N2–these are also kinds of Influenza A). The killer strain of H5N1 is found in Asia and parts of North Africa. But there are other strains of H5N1 that cause only mild illness, all over the world, including in the US and Mexico, and they are not worrysome unless you’re a chicken farmer who wants your chickens to fatten up quickly. There are also many strains of ‘bird flu’ that have other H’s and other N’s.

    So, the fact the Mexican virus contains elements of a bird virus really doesn’t tell us anything about how ‘bad’ the virus is. It only tells us that the virus is new to humans, which means our immune systems haven’t yet learned how to defeat it. There’s no particular reason to assume it is any harsher or milder than seasonal flu, since the Mexican data so far is garbled.

    But since people aren’t immune to it, when it reaches a new region a lot of people will be sick at the same time. Even if only 1 in 400 needs a hospital, if you have 4000 people sick, that’s going to give you 100 serious cases to swamp the hospitals and give you ‘a lot of flu deaths’. Meanwhile the other 3900 people might mostly have little more than a sniffle, so they don’t seek care. Maybe 900 see their doctor and suddenly everyone panics because there are 100 deaths and 900 cases (because most of the cases were too mild to detect).

    Now, you get 100 cases and 900 more suspected cases. In an abundance of caution you take those numbers at face value and start social distancing etc. But you know, as more information develops and you get a more accurate picture, the likelihood is that you will turn out to have over-reacted.

    But that’s okay, even though it costs money, because money is cheaper than lives. So you react and if it turns out to be an over-reaction, well, so be it. Better safe than sorry.

  52. #52 Lisa the GP
    April 27, 2009

    There have been some problems with live virus contamination of experimental, lab-destined vaccines from Baxter, and some incidents of live virus contamination of anti-bird flu veterinary vaccines for chickens in China. (NO incidents of human flu vaccine contamination. I think there’s stricter controls on human vaccine production than on veterinary vaccines in some parts of the world.)

    What do you guys think of the possibility that the european swine flu genetic elements might have piggy-backed on a contaminated veterinary vaccine?

  53. #53 Grace RN
    April 27, 2009

    Maura, as best I know, all pandemic flu viruses-all type A flu viruses, originate from an avian source.

  54. #54 Walrus
    April 27, 2009

    Does anyone have any estimates of attack rates and CFR?

    I am trying my own untutored estimates via spreadsheet to try and make an (un) educated guess.

    The figures for Mexico seem to say that about 60% of hospitalised cases recover “easily” (with or without Tamiflu?), about 40% are “serious”, and around 7% are dying.

    However there is the question about how many cases even make it to Hospital in Mexico? How many simply die undiagnosed?

    The R0 is maybe between 1.5 and 2.0. But the CFR?

  55. #55 Paul
    April 27, 2009

    Thanks for the come-back, revere; it’s so far up there, I almost missed it. Maura, thanks for your support – you probably missed revere’s response, as it got buried in an avalanche of new comments. Lisa GP, thank you also for your extensive explanation. I can’t say I fully grasp the concepts, but between your and revere’s answers, I think I’m safe in inferring that there is not a great probability of that reassortment happening.

    One thing though, revere: you say it’s not a question of transmissibility, but rather of virulence. But doesn’t a strain that’s highly transmissible (if this even turns out to be the case for the new H1N1), and less virulent get around much more and infect many more hosts, who survive to spread it? My concern, was the possibility of this H1N1 contributing its transmissbility characteristic to the highly virulent H5N1.

    But I’m probably just kicking a dead horse, or pig or chicken, or what have you. What happens is going to happen, and despite all these interesting speculations and explanations, I don’t see where we have a hell of a lot to do to stop whatever reassortment turns up.

  56. #56 suzanne bunton
    April 27, 2009

    just in case you all haven’t seen this,

    Niman has made a nice world map of the Mexican H1N1 outbreak.


    So, now that one of my silent wishes (i.e., for a color-coded global map of cases) has been granted, i’ll voice my other:

    I wish that reports of suspected and confirmed cases would state WHERE in Mexico (if anywhere) the patients have recently been.

  57. #57 dmv
    April 27, 2009

    What’s the over/under on Besser getting a more permanent leading role at CDC after this? One thing that struck me has been his effectiveness in dealing with the press and with questions. Or is it silly and stupid of me to dream of competent professionals being appointed to run agencies, as against politicos and contributors?

  58. #58 Phillip Huggan
    April 27, 2009

    Paul, there are only a few dozen human cases of Avian Flu annually (in contrast to your assertion such cases are “not infrequent”). Once/if diagnosed they go under quarantine. IDK the genetics of DNA swaps, but a far more likely reservoir of this Swine Flu and H5N1 hypothesis is in Avian flu infected bird flocks and whatever the animal reservoir is here. Some samples sent from Mexico and USA human swine flu cases are genetically very similiar so whatever the probability is of your hypothesis, it is lower than other potential dangers (this Swine Flu probably has no need of human H5N1 cases to mutate).

  59. #59 grothendieck
    April 27, 2009

    Does anyone know if the Winnipeg lab or the CDC have published the genomes of the different samples of these new swine influenza strain? I want to know the intragroup variability and also the antigen similarity with the other (curable) strains

  60. #60 phytosleuth
    April 27, 2009

    “What do you guys think of the possibility that the european swine flu genetic elements might have piggy-backed on a contaminated veterinary vaccine?”

    Eliminating possibilities takes time. Add it to the list and then prioritize it. But even before we know the answers we could take a hard look at the practices allowed and whether there are safer ones that can still accomplish the goal.

  61. #61 phytosleuth
    April 27, 2009

    WHO published this:

  62. #62 revere
    April 27, 2009

    grothendieck: courtesy commenter jpowell:

  63. #63 Stoker
    April 27, 2009

    Phillip Huggan: “The only other expanation I can think of is the 1st Spanish Flu wave somehow triggered an immune system over-reaction during subsequent highly lethal waves; that the 1st wave caused high death rates of second wave. All speculation on my part.”
    That is my fear, too, Phillip. I’m also concerned about the indiscriminate prescribing of anti-virals to people with symptoms of “mild” illness. Didn’t the clinical trials which showed the (limited) efficacy of Tamiflu and Relenza also show that the pathogens adapted to them quite quickly?

    The events surrounding the two Scottish cases is interesting: out of 22 tested contacts that the couple have had since returning from holiday last week, 7 have contracted H1N1. Is this a very high transmissibility?

  64. #64 William CB
    April 27, 2009

    I’m also not an expert, but there seems to be a sharp difference in tone between the discussion here and what is appearing elsewhere. Obama says “concern” not “alarm”, and that is also the kind of message I get from Professor Hugh Pennington (nobody’s patsy) at http://www.channel4.com/news/articles/science_technology/world+wakes+up+to+swine+flu/3112457. Here I’d say the underlying message is “alarm” not “concern”. If that’s not what the community of people here intends, then I think you should say so – now.

  65. #65 Stoker
    April 27, 2009

    William C B.

    Prof Pennington has a paid appointment as a government adviser, does he not? He may be no “patsy” but he will certainly be toeing the party line.

    I think that the posters here are alarmed that the public (who seem to have generally already dismissed pandemic flu as another “scare story whipped up by the media/govt/boffins, etc etc” are being falsely reassured.

    Reassurances which are being touted but which people with a little knowledge can legitimately question:

    – Tamiflu/Relenza will reduce the severity and duration of symptoms in much of the world’s population for an indeterminate period of at least several months,

    – This H1N1 will only kill people in second- and third-world countries,

    – Survival/Avoidance of this H1N1 is the major/only priority

    I could go on but have to go out now. I would just say that public complacency is probably more risky than the current outbreak.

  66. #67 funky chicken
    April 27, 2009

    Looking at the map, the CA cases are all dated in the last week of March and first week of April. I’m having a very, very hard time believing that this virus spreads like wildfire everywhere it goes….except for southern CA.

    Is there a much larger caseload in SoCal that isn’t being reported among the hispanic population?

  67. #68 hornblower
    April 27, 2009

    Vancouver radio broadcaster CKNW is reporting:
    “Mexico’s health department says trhe (sic) World Health Organization is raising pandemic alert level to 4, verifying human-to-human swine flu.

    Sent at: 1:15pm”

  68. #69 Gail
    April 27, 2009

    The following information is coming out of Mexico:
    Mexico has confirmed 20 cases of swine flu, yet reports there are at least 100 deaths from swine flu, and 1000 or more unconfirmed cases.
    Those statements indicate big problems in disease surveillance in Mexico. We do not know if the deaths were caused by swine flu, and there are no reports of follow-up diagnosis for the cause of these deaths. It seems to me that there is already widespread panic in Mexico about the lethality of this disease and not many facts to base the fear upon. Anybody want to comment?

  69. #70 Gail
    April 27, 2009

    The following information is coming out of Mexico:
    Mexico has confirmed 20 cases of swine flu, yet reports there are at least 100 deaths from swine flu, and 1000 or more unconfirmed cases.
    Those statements indicate big problems in disease surveillance in Mexico. We do not know if the deaths were caused by swine flu, and there are no reports of follow-up diagnosis for the cause of these deaths. It seems to me that there is already widespread panic in Mexico about the lethality of this disease and not many facts to base the fear upon. Anybody want to comment?

  70. #71 grothendeck
    April 27, 2009

    Stoker:Its frustrating to see how Mexican media haven’t reported already the info in the Guardian story on the 4-year old from Veracruz who got positive for this swine flu, which makes most likely that the origin of the virus was that Smithfield production facility in Mexico. Its very strange since apparently the info was disclosed by the Health Minister himself during today’s his press conference

  71. #72 Stoker
    April 27, 2009

    Gail, my feeling is that there have been concerns about respiratory disease *of some sort* for some weeks amongst the people of Mexico. The recent announcement of a flu epidemic which (as far as we know) has killed a disproportionate number of young males has fuelled a kind of retrospective panic. A similar effect is happening here, where people are re-assessing the viruses they had over the winter.

    As I see it: IF people in Mexico have been seriously ill since February (see link I posted earlier) and IF they have all had this strain of flu, we are surely talking about a pathogen which is very easily passed from human to human. The morbidity rates (ie, are we talking about 20 deaths, or 149, or more if deaths have been previously wrongly attributed) and the proportion of young children/elderly within this figure are key to whether or not a full-scale alert needs to be put into place. And this is the information we just don’t have at the moment. Hopefully closer monitoring in the US, Canada and UK will be more informative.

  72. #73 William CB
    April 27, 2009

    Stoker (and revere, editors): I’m not here to defend Pennington, but to dismiss the views of anyone with a government stipend actually is paranoia. Isn’t the point to judge the argument not the person? So, to put the case for “concern” as opposed to “alarm”, isn’t the bottom line this: We don’t actually know whether the thing that’s killed 149 people in Mexico actually is the swine fever strain that’s being tested for elsewhere; until there’s clarity as to what’s going on in Mexico, all this speculation is, er, just that.

  73. #74 g336
    April 27, 2009


    CBS radio news reported at 3:00PM Pacific time, that the WHO (World Health Org) has just upgraded to Phase 4 or Stage 4, in their 6-stage alert system.

    On Friday or Saturday, Revere said that we are effectively at Stage 4, and if WHO does not declare shortly, WHO will lose all credibility.

    I won’t begrudge WHO a day, IMHO it’s OK that they raised the alert today rather than Friday or over the weekend. In any case doing it on a Monday assures greater news coverage which is useful.

  74. #75 Matthew_The_Timid
    April 27, 2009

    I’d be intersted in learned opinions regarding an interesting thought that I read elswhere today:

    Mexico City has one of the most severe air pollution problems in the world. (I seem to recall hearing that living there was akin to smoking a pack a day, but I may be wrong.)

    Could that be a contributng factor to the fatality differential between MX and the US? What of the prevelence of smoking among that demographic?

  75. #76 revere
    April 27, 2009

    Matthew: Others have raised this and it is true that Mexico City has very severe photochemical air pollution. But this wouldn’t be consistent with the 20 – 50 year old previously healthy picture of deaths being painted (which may or may be correct). We would except air pollution co-morbidity to affect the elderly the most.

  76. #77 Vervestar
    April 27, 2009

    When…and how….will we be able to get the socio-cultural data about the people who are ill….and those that have died?

    And, why is it so difficult for this data to be mapped? We need to use up to date visual analytic tools to monitor the location and time variables…..as well as all the other social data…..this kind of outbreak is about more than simple gender and age……

  77. #78 grothendieck
    April 27, 2009

    revere, matthew:

    Air quality in Mexico City can be a factor but lets not forget that the fatalities happened in distinct states, not just in Mexico City.

  78. #79 revere
    April 27, 2009

    Verve: What exactly do you propose to map? And how finely? You couldn’t get that info in the US because of privacy concerns. And I’m not sure what you want to know beyond the city.

  79. #80 Stoker
    April 27, 2009

    Grothendeck, sorry just saw your message. That report is reassuring in that official figures show only 2 deaths out of 1800 ill, and they were babies. However the incidence of 60% does not bode well if this does sweep the globe and encounters H5N1. Even more worrying are the reported health authorities’ attitude: “flu has been eradicated in Mexico” and the cases consequently being recorded as pneumonia.

  80. #81 Douglas McClean
    April 27, 2009

    An earlier commenter said:

    “I don’t think it’s impossible that people of European, African and Asian descent would have greater resistence to a pathogen than people of indigenous American descent. There is historical precedent in the great die-off that occurred among native Americans when Europeans landed.”

    I hope the experts here will correct me if I am wrong, but it is my understanding that this historical precedent is off-topic because the then-existing disparities were due to different exposure to different pathogens on different continents, and not to genetic factors. I would expect that in the following centuries that most human diseases have been spread by travel to range over most of the world.

  81. #82 River S.
    April 27, 2009

    The number of confirmed cases in the US is rising quickly. In an article published on Yahoo.com two hours ago entitled “U.S. swine flu case number rise, more expected,” Reuters is reporting:

    “In New York City, Mayor Michael Bloomberg said more than 100 sick students at a high school in Queens were being tested and that 45 were confirmed or likely cases of swine flu.

    “‘We believe that there are probably more than 100 cases of swine flu at the school and lab tests are confirming what we have suspected,” he told a news conference.'”

    If 45 students in NYC have been confirmed to have been infected with swine flu, what is the current number of total confirmed US cases thus far? Also, did all of those students in NYC travel to Mexico, or are some now ill through transmission? If so, would this be the second incidence of transmission, the first being the wife of the Kansas man who returned ill from Mexico?

    Thanks for all the great info thus far! Very helpful, indeed!

  82. #83 grothendieck
    April 27, 2009

    With respect to genetic differences being the cause of the (so far) disparity in CFR between Mexico and the US/Canada/European cases: Correct me if I’m wrong but I have never read that (since the last H. sapiens ancestor came out of Africa) the certain populations of the human species have been genetically adapted to resist certain pathogens. There are cases like the anemia resistant individuals, but in terms of a whole population being descendant of a resistant community to certain pathogens, that for me is unheard of.

  83. #84 Lisa the GP
    April 28, 2009

    all the NY cases have been at a single school. There have been no new outbreaks in 5 days.

    At this point in time it appears that perhaps they caught the school outbreak early enough to contain it.

  84. #85 MNPundit
    April 28, 2009

    Indeed, schools are germ factories, make no mistake.

  85. #87 Pedro Garcia
    April 29, 2009

    what is incredible is that here in Veracruz… the drug dealing leading narcatic traficante… Governor Fidel Herrera.. still denies that there are any comfirmed cases in the state of Veracruz… where the Virus actually started in the City of La Gloria, Perote Veracruz… The virus was misdiagnosed in the early stages… if it had been diagnosed properly, then all of this could have been possibly avoided. You can not imagine the amount of corruption in the country… Also… mentioned above about SmithField…. and there desire to make money.. has blinded them to higher Sanitary standards, … but to be fair.. Mexico is one of the largest consumers of Pork in the world.. and the standards of sanitation in this Country is many years behind that of the USA and is not necessarily due to SmithField of Virginia´s lack of interest….I believe it is cultural.. and very difficult to change the mind set and habbits of the people here, However, I hope that this outbreak or elevated Flu season… .. is a wake up call!!! Keep up the great posts!!!

  86. #88 Dave
    April 30, 2009

    FDA permits Tamiflu use for swine flu.

    The Food and Drug Administration authorizes the emergency use of certain antiviral drugs to control the global

    outbreak of swine flu.

    In the report released late Monday, the FDA has permitted the use of unapproved or uncleared antiviral

    products following a declaration of an emergency state.

    The FDA therefore allowed public health and medical personnel to prescribe Relenza (zanamivir) and Tamiflu

    (oseltamivir), which have not been approved for swine flu, to control the widespread outbreak.

    Tamiflu, originally approved for adults and children aged 1 and older, can now be used in children under 1.

    Physicians can also change the recommended dosage for children older than 1 under the emergency use


    The rRT-PCR Swine Flu Panel diagnostic test is also authorized for testing samples from individuals with

    certain flu infections particularly those whose virus subtypes cannot be identified with available tests.

    According to the latest report released by the US Centers for Disease Control and Prevention (CDC), about 64

    confirmed cases of swine flu have been found in five US states.

    Online orders may be placed at:

  87. #89 John
    April 30, 2009

    Do you know how many people die regularly from flu?

    About 40,00 a year in the U.S.

    Worldwide? From 250,000 to 500,000 a year.

    Go ahead, panic.

  88. #90 Phillip Huggan
    April 30, 2009

    The rationale for panic would be the odds of a flu mutation which unleashes a pandemic that is fatal to 0.1%-60% of those infected (I forget if regular flus kill 1/10000 or 1/100000) was maybe only 3% annually or less, before this mutant Swine Flu appeared. Now the odds for 2009 are probably 4-5x higher.

  89. #91 revere
    April 30, 2009

    Phillip: There is never a rationale for panic. We are certainly at the “very concerned” level and that seems like a good place to keep it while this thing lasts. People don’t panic if they have a handle on the situation. The key is to keep people informed. BTW, case fatality for seasonal flu is about 0.1% of cases.

  90. #92 Phillip Huggan
    April 30, 2009


  91. #93 ask first shoot later
    April 30, 2009

    What is a possible explanation for a very high rate of infected visitors to Mexico, who now returned to their countries of origin (e.g. Israel, New Zealand, Spain, South America, etc.) ???

    If one makes a statistical projection based on: 1) each country’s Mexico visiting rate and 2) on the population of Mexico – the number of infected in Mexico should be anywhere from 20,000 to 200,000.

  92. #94 Clifford Whitehead
    May 1, 2009

    I have a question, which I have been unable to get an answer to.
    Acording to the latest information available there are several cases of avian flu H5 N1 in the far east and Egypt. My understanding is that the Mexican H1 N1 virus is a genetic combination of swine flu, avian flu and human flu. What is the effect of an individual with avian flu H5 N1 coming in to contact with swine flu H1 N1?

  93. #95 Jimmy
    June 8, 2010

    yes indeed the swine flu is tragic to us all

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