Saturday, May 23, 2009

From simple to stupid

Epidemic: from the Greek, epi- (upon) + -demos (the people)

Pandemic: from the Greek, pan- (all) + -demos (the people)

Pandemic (according to the WHO): from external pressure and internal weakness, highly-virulent + "justified" panic + all + the people

The definition of a pandemic used to be simple: a worldwide outbreak of disease in excess of what would normally be expected (a global epidemic).  

The WHO even came out with a definition of worldwide spread (community transmission in 2 or more WHO regions).

But now, apparently, the WHO intends to change the definition of a pandemic from simple to stupid.

Bowing to pressure from member nations, the WHO is (according to the New York Times) going to change the definition to include the severity of disease, and will probably do so in such a way that the current H1N1 outbreak will never count as a pandemic (unless it becomes more virulent, which it very well might).

Now, you may remember that we've had three pandemics in the last century, one in 1918, one in 1957 and one in 1968... or, at least, that used to be true.  If this new definition goes into effect as described, we'll have to erase those last two from the list, because they were no more severe than this new H1N1 strain appears to be right now.

Whether a given outbreak is a pandemic or not is a separate question from how severe that pandemic is.  

If the WHO thinks a severity scale would be useful, then by all means they should create one. There are some good arguments against using a severity scale (flu viruses evolve so quickly, severity varies between and within countries, etc.), but it's possible a severity scale would help countries and communities to better plan for and respond to a pandemic... but the role of a severity scale should be to better describe an existing pandemic, not to determine whether an outbreak is a pandemic.

If the WHO goes through with this, there will be two definitions of a pandemic: One used by epidemiologists and other public health professionals, and one used by the WHO --because the WHO's new idea for a definition doesn't make any rational sense.  By setting up such a situation, the WHO will be undercutting its own credibility in a time when its ability to lead is more important than ever.

Instead of caving to the pressure of politicians from the member nations who feel that declaring a pandemic would cause "unjustified panic," the WHO should be using this as a teachable moment, to educate the public about what a pandemic is, what can be done about it, and why panic is never a justified reaction regardless of severity.


Wednesday, May 20, 2009

Obesity and H1N1

The Washington Post just ran a story with the headline "Survey finds link between obesity and flu severity."  Now, I'm usually a big fan of The Post, but that turns out to be completely inaccurate.  

The study in question, entitled "Hospitalized Patients with Novel Influenza A (H1N1) Virus Infection --- California, April--May, 2009," was published online as an early release by the CDC's Morbidity and Mortality Weekly Report (MMWR), and there is nothing in that study to indicate that obesity is a risk factor for severe disease with H1N1.  Nothing at all.  

The authors don't interpret their findings that way in the paper, and the simplest of math shows that such a conclusion makes no sense on the basis of this data.

As the wonderful XKCD t-shirt my wife got for me says, "Stand back, I'm going to try SCIENCE!"

The prevalence of obesity among the 30 hospitalized cases in California was 4/30 = 13.33%
The prevalence of obesity in California (in 2001) was about 20.9%

13.33% is less than 20.9%

Now, you shouldn't take that to mean that obesity is protective against the H1N1 virus.  (The numbers are just too small for statistical stability.)  But there's absolutely no reason on the basis of this data to conclude that obesity "obesity may raise risk for flu complications," as the Post's running title for this piece reads.  Which is why the authors make no such assertion.

Does that mean the same thing as "there's absolutely no reason at all to conclude that obesity is a risk factor for severe disease with H1N1?"  No, it does not.  Thirty cases are too few to draw definitive conclusions.  And, in fact, the article goes on to say:

"We were surprised by the frequency of obesity among the severe cases that we've been tracking," said Anne Schuchat, one of the CDC epidemiologists managing the outbreak. She said scientists are "looking into" the possibility that obese people should be at the head of the line along with other high-risk groups if a swine flu vaccine becomes available.

And it is entirely possible that there's something to that, though the article gives us no direct evidence to support it.

But if any such evidence exists, it certainly isn't to be found anywhere in the MMWR paper.  And the paper's authors make no claim that it is, so don't blame them for the inaccuracy.  

Tuesday, May 19, 2009

Swine flu + Japan = Karaoke boom?

Apparently, a lot of students at Japanese high schools that have been shut down due to the H1N1 outbreak haven't been staying home; instead, they've been going out for karaoke

As someone who discovered firsthand that karaoke microphones make good fomites (someone shared a nasty cold with me once, by way of a karaoke mic), I'd like to point out that this is a Very Bad Idea.  --All the more so, since a lot of the karaoke venues in Japan include smallish private rooms, where the ratio of students to square feet (and, therefore, the opportunities for large droplet spread) can be quite high.

Is this an argument for not shutting down schools, then?
Probably not.  

Unless a very high percentage of students from these closed schools are crowding into the karaoke joints or other venues where there is a relatively high risk of transmitting the flu, school closings are still likely to be more effective than not in slowing the spread of the virus.

Friday, May 15, 2009

Another edition of "Complete Rubbish"

Adrian J. Gibbs, a retired plant virologist recently claimed that the H1N1 "swine flu" virus must have originated as the result of a laboratory accident.  

According to the New York Times, his theory (or, rather, his poorly thought out hypothesis) has now been debunked by the WHO. 

A brief excerpt from the article:

Dr. Gibbs, who had studied the gene sequences of the swine flu virus posted on public data banks, argued that it must have been grown in eggs, the medium used in vaccine laboratories. He reached that conclusion, he said, because the new virus was not closely related to known ones and because it had more of the amino acid lysine and more mutations than typical strains of swine flu.

His theory was reported by Bloomberg News on Tuesday. Even though scientists at theCenters for Disease Control and Prevention were skeptical and some prominent virologists openly derisive, news outlets have repeated and magnified the theory, adding speculation about bioterrorism that even Dr. Gibbs repudiated. He was also interviewed Thursday on the ABC News program “Good Morning America.”

Dr. Fukuda said a W.H.O. panel of experts had concluded that “the hypothesis does not really stand up to scrutiny.” The lysine residues and mutation rates were typical, he said, and many swine flus seem unrelated because not enough pigs are tested each year.

The article went on to make some astute points about the damage that misinformation like this has caused in the fight against diseases like AIDS and polio.

This is why the cultural expectation in science is that you publish, then pronounce.  Or, in cases where the early dissemination of your research could save lives, that you at least get your work through the peer review process before typing up your press release.  

Because science matters.  Getting it wrong matters. Reducing the public's trust in the people working to protect them matters

Dr. Gibbs should have known better.

Related posts:

Bogus bioweapon claims for H1N1 Swine Flu

From the comments: Is the bioengineering theory really rubbish?

Thursday, May 14, 2009

Disturbing results of a recent survey

According to a new poll by Zogby / University of Texas: 
  • Only 30% of Americans would get a vaccine against the H1N1 "swine flu" virus, if one were available.
This shows that we aren't getting the message across to the majority of Americans: This virus may appear relatively mild right now, but we can't trust it to remain so.  The first wave of infections caused by the 1918 pandemic flu virus was also mild... and then it went on to kill tens of millions of people in a world of only 1.8 billion.  We don't know that the same thing will happen with this virus, but we also don't know that it won't.  If a protective vaccine becomes available, take it.  Immediately.
  • A whopping 38% of those surveyed managed to combine ALL of the following: Not vaccinated against the flu, not practicing good hygiene, and not restricting travel or mall shopping.
Now, I'm not too concerned about that last part at the moment.  Healthy people aren't being encouraged to curtail their social interactions right now.  But unvaccinated people who practice poor personal hygiene (e.g. they don't wash their hands regularly) aren't only putting themselves at risk: they're gambling with everybody's health.  By making choices that make them more likely to become infected, they are also increasing the risk that they'll pass that infection on to someone else.

Which is why the next bullet is so striking:
  • "The same was true of 25% of health care workers polled, 28% of caregivers in nursing homes and 33% of those whose children are vulnerable due to asthma, diabetes, or HIV. Particularly concerning is that only 48% of these children were vaccinated." (emphasis added)
Now, you might be thinking: "Yes, but maybe these people would vaccinate if there were an H1N1 vaccine; this is just how they react to the 'regular' flu, after all."

To which I respond:
  1. These people all provide care to those who are at high risk of severe complications (including death) from "regular" seasonal flu.  
  2. Are you forgetting the poor hygiene issue?  Handwashing, good cough/sneeze etiquette, and the like are not just for special occasions.  They save lives every day.
These groups have a special responsibility as care providers to ensure that they are not putting their patients (or high-risk children!) in danger through their own negligence.  Some of those parents may not know any better, but none of the healthcare workers / nursing home caregivers have that excuse.

No amount of good advice from the government can take the place of personal responsibility.  Do your part: cover your mouth when you cough or sneeze (preferably with a tissue or the crook of your elbow); wash your hands regularly (try for at least five times a day, for at least 20 seconds); get a flu shot* if you're medically fit to do so (especially if you provide care to people who are at high risk of complications), and vaccinate your kids*, unless your healthcare provider tells you not to.  

*The current flu vaccine won't help against the H1N1 "swine flu" virus, so when a vaccine for that strain becomes available (hopefully by this fall), roll up your sleeve and take it.  And make sure your kids get it, too.

Sunday, May 10, 2009

Pandemic Partners - A way to help each other during a pandemic

During a pandemic, we all know a lot of people are going to get sick.  

Whether they get treated in a hospital or recover at home, a lot of those who get sick are going to need some help... and not just with their illness.  Even the seasonal flu can knock you onto your back for a week or more, and a pandemic flu virus is likely to to be worse.  So a lot of people who get sick will also need some help managing their day-to-day lives until they're back on their feet, simple things like:
  • Making sure there is food in the house
  • Contacting healthcare providers  
  • Helping provide care for children or other dependents
  • Helping provide care for pets
  • Contacting family members
  • Picking up medicine from the pharmacy

But in today's society there are many of us who could fall off the map without anyone noticing right away.  In many cases, it's all too possible for a person to be home sick for weeks before anyone thinks to check on them, and this will be even more true during a pandemic.  

Because the same social distancing measures that will help to protect us from the flu (staying away from other people as much as possible, working from home if you can, etc.) will also reduce social interaction to the point that even those who would ordinarily be missed after a very brief illness will be at risk of falling through the cracks.

To help fix this problem, people can pair up with people they trust (friends, neighbors, family members, co-workers, members of their place of worship) to keep track of one another during a pandemic and help each other as needed.

The Reveres over at Effect Measure mentioned one program to do just that, a faith-based initiative called Flu Friends.

A similarly-alliterative initiative called Pandemic Partners is also under development to help people help each other through a pandemic.  Right now, it mostly consists of a set of forms people can use to share the information their "pandemic partners" will need to be able to assist them.

Copies of the form are available as a Word Document: Pandemic Partners.doc 

The forms are a work in progress, so if you have any suggestions for improving them, let me know and I'll pass them along.

Friday, May 8, 2009

FDA Q&A on PPE (especially N95 respirators)

With a title like that, I can't help but feel as though I'm back in the Army.  It's the only organization in the world that would take a nice 3-letter word like "job" and expand it into "military occupational specialty," just to abbreviate it with the 3-letter acronym MOS...

Anyway, here is the latest and greatest from the Food and Drug Administration (FDA) on the use of FDA-regulated personal protective equipment (PPE) for preventing infection with the H1N1 flu virus.  

Some of the questions it addresses are regulatory clarification issues that are unlikely to be of much interest to the general public, but they also include some excellent basic advice on PPE, including things like "What is the difference between a face mask and an N95 respirator?" and "Is it OK to re-use or share a disposable N95 respirator?"

You can also find the original version here.

The FDA and Personal Protection Equipment for the 2009 H1N1 Flu Virus
Questions and Answers

Q:  What are facemasks and N95 respirators?

A: Facemasks and N95 respirators are devices that when properly worn may help prevent the spread of germs (viruses and bacteria) from one person to another.

Facemasks and N95 respirators do not provide complete protection from airborne germs and other contaminants.  They are one part of an infection-control strategy that should also include frequent hand washing, social distancing, and staying home when sick.

Facemasks and N95 respirators should not be shared. Facemasks and respirators may become contaminated with germs (viruses and bacteria) that can be spread between people.  

It is important to understand that if you are exposed to infectious material while wearing a facemask or N95 respirator, it should be considered contaminated. After you remove it and dispose of it properly, wash your hands thoroughly.

Q: What’s the difference between a facemask and an N95 respirator?

A: A facemask is a loose-fitting, disposable device that creates a physical barrier between the mouth and nose of the wearer and potential contaminants in the immediate environment.

If worn properly, a facemask is meant to help block large-particle droplets, splashes, sprays or splatter that may contain germs (viruses and bacteria) from reaching your mouth and nose. Facemasks may also help reduce exposure of your saliva and respiratory secretions to others.

While a facemask may be effective in blocking splashes and large-particle droplets, a facemask, by design, does not filter or block very small particles in the air that may be transmitted by coughs, sneezes or certain medical procedures. Facemasks also do not provide complete protection from germs and other contaminants because of the loose fit between the surface of the facemask and your face.

An N95 respirator is a respiratory protective device designed to achieve a very close facial fit and efficient filtration of airborne particles. In addition to blocking splashes, sprays and large droplets, the respirator is also designed to help prevent the wearer from breathing in small particles that may be in the air.

To work as expected, an N95 respirator requires a proper fit to your face.  It is designed to fit tightly over your mouth and nose, with no gaps.  And gaps will allow air to pass around and reach your nose, mouth, and lungs without being filtered. 

The ‘N95’ designation means that when subjected to careful testing, the respirator blocks at least 95 percent of small test particles. If properly fitted, the filtration capabilities of N95 respirators exceed those of face masks. However, even a properly fitted N95 respirator does not completely eliminate the risk of contracting illness through airborne viral particles.

N95 respirators are not designed for children or people with facial hair.  Because a proper fit cannot be achieved on children and people with facial hair, the N95 respirator may not provide the expected protection. Also, people with chronic respiratory, cardiac, or other medical conditions that make it harder to breathe should check with their healthcare provider before using an N95 respirator because the N95 respirator can require more effort to breathe.

FDA has cleared the following N95 respirators for use by the general public in public health medical emergencies:

    * 3M™ Particulate Respirator 8670F
    * 3M™ Particulate Respirator 8612F
    * Pasture Tm F550G Respirator
    * Pasture Tm A520G Respirator

These devices are labeled "NOT for occupational use.”

Q: Do  N95 respirators reduce the chances of contracting the 2009 H1N1 flu virus?

A: When worn properly, N95 respirators help reduce your exposure to airborne germs.  They do not provide complete protection from airborne germs and other contaminants, however. They are one part of an infection-control strategy that should also include frequent hand washing and staying home when sick.

Q: Is it OK to use one disposable N95 respirator for a long time?

A: Disposable N95 respirators are not intended to be used over long periods of time. If the respirator is damaged, torn or soiled, or if it becomes difficult to breathe while wearing it, remove it and replace it with a new one. 

It is important to understand that if you are exposed to infectious material while wearing an N95 respirator, your respirator should be considered contaminated. After you remove it and dispose of it properly, wash your hands thoroughly.

Additional references on this can be found at the following:

U.S. Centers for Disease Control and Prevention
“Recommendations for Facemask and Respirator Use in Certain Community Settings Where H1N1 Flu Virus Transmission Has Been Detected”

“The Department of Health and Human Services Guidelines for the Use of Facemasks and Respirators in Non-Occupational Settings during an Influenza Pandemic”

Q: Is it OK to re-use or share a disposable N95 respirator?

A: Disposable N95 respirators are not intended to be used more than once. They should also never be shared. Their protective capabilities cannot be assured when they are reused either by yourself or another person. Perhaps more importantly, by sharing, one may inadvertently be exposing another person to infectious material.

It is important to understand that if you are exposed to infectious material while wearing an N95 respirator, your respirator should be considered contaminated. After you remove it and dispose of it properly, wash your hands thoroughly.

Q: What other personal protective equipment does FDA regulate?

A: Personal protective equipment (PPE) is any type of face mask, glove, eye shield, or specialized clothing that acts as a barrier between infectious materials and the skin, mouth, nose, or eyes (mucous membranes). When used properly, PPE can help prevent the spread of infection from blood, body fluids, or respiratory secretions. 

The U.S. Department of Labor's Occupational Safety and Health Administration (OSHA) requires employers to provide appropriate PPE for workers who could be exposed to blood or other infectious materials (bloodborne pathogens). OSHA may also require employers to provide PPE to protect against other hazards at work. Although OSHA requires the use of specific equipment, it does not regulate the marketing of these devices nor grant claims of disease prevention. For more information, go to

The U.S. Centers for Disease Control and Prevention (CDC) gives recommendations for protecting yourself from infection, including swine flu. For more information, go to

The National Institute for Occupational Safety and Health (NIOSH) has established certification requirements for various respiratory PPE, which are found at 42 CFR part 84. NIOSH tests products for compliance with these regulations and issues a certification for products that comply. NIOSH certification evaluates the performance of respiratory protection equipment in functional terms and not in terms of claims for use in preventing disease.  Employers subject to OSHA and the Mine Safety and Health Administration (MSHA) regulation may be required to provide NIOSH-certified respiratory protection equipment to satisfy their OSHA and MSHA requirements.

Q: Where can I find additional information on personal protective equipment (PPE)?

A: For more information on Personal Protective Equipment (PPE), go to:

Q: What is the purpose of the FDA's Emergency Use Authorization for certain N95 disposable respirators?

A: The FDA issued an Emergency Use Authorization (EUA) for certain disposable respirators known as N95 respirators.  This EUA permits the deployment of these products, accompanied by fact sheets with information for use during the 2009 H1N1 flu virus emergency, from the Strategic National Stockpile for use by the general public to help reduce wearer exposure to airborne germs during this emergency. The term "general public" in this EUA is broad and includes people performing work-related duties.

Q: Does the FDA’s Emergency Use Authorization for certain disposable N95 respirators cover only products in the Strategic National Stockpile?

A: The FDA’s EUA for certain disposable N95 respirators for use by the general public during the 2009 H1N1 flu emergency is limited to only those products deployed from the Strategic National Stockpile (SNS) before or after the signing of the EUA on April 27, 2009.  The specific products covered by the EUA are identified by manufacturer and model number (see

Q: Does the FDA’s Emergency Use Authorization for certain disposable N95 respirators permit them to be re-used in health care settings?

A: The FDA’s EUA for certain disposable N95 respirators for use by the general public does not permit the re-use of N95 respirators.
Q: Does the FDA’s Emergency Use Authorization for certain disposable N95 respirators cover health care employees?

A: Yes, the term "general public" in this EUA is broad and includes people performing work-related duties, for example in occupational health care settings.  However, this EUA does not affect Occupational Safety and Health Administration (OSHA) requirements.  If respirators are used for people in occupational settings, employers must comply with the OSHA Respiratory Protection Standard, (29 CFR 1910.134), which can be found at

Q: Does the FDA’s Emergency Use Authorization for certain disposable N95 respirators lift the fit-testing requirements?

A: No, the EUA does not waive fit testing and other OSHA requirements that apply when respirators are used for people performing work-related duties.

The FDA’s EUA and accompanying fact sheet can be found on the FDA’s Web site at:  For further information on OSHA requirements, go to

Thursday, May 7, 2009

The experts (and I do mean experts) at Effect Measure have posted an excellent discussion of why "swine flu parties" are a really bad idea.

I'd like to thank them for doing so.  Not only does this post get out an important public health message that will help people make better decisions about how to keep themselves (and their families) safe... but it also saves me some work!

Hong Kong Quarantines: No proof they were effective

Once again, our friends at the Wall Street Journal are a bit confused by the H1N1 outbreak, and public health principles in general.  

In a story on the Hong Kong quarantines today entitled Flu Lockdown Spurs Quarantine Debate, Peter Stein gets it wrong when it comes to the evidence for/against the effectiveness of the quarantine measures, saying:

"No new cases of the A/H1N1 virus, also known as human swine flu, have emerged in Hong Kong since officials ordered nearly 300 people quarantined at the Metropark Hotel Friday, apparently vindicating the policy."

He is right in noting that no new cases of the virus occurred... but he neglects to mention the fact that this means none occurred in the people who were quarantined, either.  

That means is that none of these people who were locked away from their lives for days on end could have transmitted the virus to anyone.

The lack of new cases that Mr. Stein puts forth as evidence of the quarantine's apparent effectiveness is exactly the same thing that would have happened had there been no quarantine at all.

Wednesday, May 6, 2009

Update: Suspected H1N1 case in Indonesia tests negative

Did I say it's the place to turn for the latest news, or what?

The Bird Flu Information Center is now reporting that the patient with the suspected case of H1N1 in Indonesia has tested negative for the virus.

Suspected H1N1 in Indonesia

Apropos of my last post:
The Jakarta Post is reporting the first suspected case of H1N1 in Indonesia.  

The patient was identified by thermal scanning in the airport at Surabaya after arriving from Hong Kong, and is being treated in an isolation unit at a nearby hospital.  H1N1 infection has not yet been confirmed.

Indonesia is epicenter of the H5N1 epidemic in humans.  Not only is it the country with the most H5N1 infections to date, it is also home to the deadliest version of the virus.  The most recent official numbers* from Indonesia are 115 dead out of 141 cases, for a case fatality rate of 81.6%.  

*As you can see here, the WHO hasn't received official reports of any cases at all this year, despite the fact that we know the disease continues to occur in Indonesia, so any recent changes that might be occurring in the spread or virulence of the virus would not be reflected in these numbers.

If you're interested in (necessarily) unofficial reports of suspected cases and the latest news on H5N1 avian influenza in Indonesia, check out Bird Flu Information Center. 

Tuesday, May 5, 2009

H1N1 + H5N1 = ?

Until the surprise outbreak of what the CDC is now calling "novel influenza A (H1N1)" a couple of weeks ago, if you had asked which strain of flu virus was most likely to cause the next pandemic, most experts (and even news-consuming lay people) would have told you the same thing: H5N1

The H5N1 flu virus is either a panzootic in birds (a panzootic is just like a pandemic, but for animals), and has shown the ability to infect a number of other species in a more limited way, including the friendly neighborhood tom cat... and yes, the occasional human.

And we've been quite lucky that it's only been the occasional human, because of the 421 confirmed cases we've seen over the years, 257 have been fatal.  That's a case fatality rate (CFR) of just over 61%.  It's a mean and nasty bug.

So, at this moment when much of the world is learning about recombinant flu viruses for the first time, it's not surprising that a lot of people (or at least a lot of the people who post comments in blogs and bulletin boards) are wondering whether the H1N1 virus and the H5N1 virus could combine to create a virus far more lethal than H1N1 and far more capable of human-to-human transmission than the H5N1 virus.

The bad news is that, yes, it's possible.

The good news is that it's not terribly probable, because -while the H5N1 virus is capable of infecting humans and a broad range of animals- for the most part it continues to be a disease of birds.  It typically doesn't reproduce very well in pigs at all, and humans seem to be a dead-end host for the virus so far.

The Novel Influenza A/H1N1 virus, of course, is mostly a disease of humans (though it is apparently willing to move back in with the pigs too).

In an interview with Science Insider, virologist Yi Guan of SARS fame shared his thoughts on the possibility:

Discussing the our inability to predict whether the H1N1 virus will become more virulent....

Q: It depends on further mutations?

Y.G.: It depends on mutations and whether the virus further reassorts with other viruses—like H5N1. That could be a super nightmare for the whole world.

Q: You’re talking about the Armageddon virus?

Y.G.: The chance is very, very low that these two viruses will mix together, but we cannot rule out the possibility. Now, H5N1 is in more than 60 countries. It’s a panzootic, present everywhere except North America.

Q: If the nightmare comes true?

Y.G.: If that happens, I will retire immediately and lock myself in the P3 lab. H5N1 kills half the people it infects. Even if you inject yourself with a vaccine, it may be too late. Maybe in just a couple hours it takes your life.

Sounds pretty scary, and it could be... but you'll recall that he said the chance of it happening is very, very low.  

This is a good illustration of the difference between a hazard (something that can cause harm) and a risk (the likelihood of that harm actually occurring).  

An H5N1/H1N1 recombinant virus represents a serious hazard, but the risk of it actually happening is thankfully rather low.

That doesn't mean we can afford to take our eyes off the ball, however.  The H5N1 virus is no less of a threat today than it was before the H1N1 outbreak began, and we ignore it at our peril.  President Obama says that the President of the United States needs to be able to walk and chew gum at the same time, and he's right.  Here's to hoping the global public health preparedness community can do the same.

Monday, May 4, 2009

Some statistics from today's CDC H1N1 Swine Flu Briefing

The following information comes from today's press conference with Dr. Besser, Acting Director of the CDC.

Stats for the United States:
  • 279 confirmed cases in 36 states
  • > 99% of probable cases so far have tested positive
  • > 700 probable cases in 44 states
  • Median age of confirmed cases: 16 years old 
  • Age range for confirmed cases: 3 months to 81yrs
  • 62% of confirmed cases are in patients < 18 years old
  • The most recent confirmed case occurred on May 1st
  • 35 known hospitalizations 
  • 1 known death
Because probable cases are so likely to be confirmed when they are tested, they provide us with a more clear and timely picture of where we stand in the way of actual infections right now than the number of confirmed cases.  

No matter what the situation, the "confirmed" number will always lag behind reality, but right now it's lagging even further behind because of the significant backlog of samples to be tested.  This is inevitable when a novel pathogen emerges and a new test has to be invented to deal with it; the CDC's public health laboratory scientists have exceeded any rational expectations in the speed and the quality of their response.  

Dr. Besser said that the CDC intends to start reporting probable cases on its website the near future.

He also said that the number of probable cases is likely an underestimation of the real number, as well, because the CDC's definition of a probable case requires that a person have flu-like symptoms and test positive for Influenza A, but negative for the H1 & H3 subtypes --and we know this testing is not happening for every person with influenza-like illness (ILI).

The CDC is now rolling out H1N1 Swine Flu test kits to the states, so state public health laboratories will be able to test for the virus.  Over time, this will help to reduce the backlog for confirming cases, but states will still not be able to test all possible or even probable cases.  

That's okay, though, because the point isn't to ensure that we confirm all cases of the disease, it's to ensure that we know where, when, and in whom the virus is spreading.  --That's the data we need to make sure we're taking the right steps in the right places to protect the public. 

Sunday, May 3, 2009

Egypt's ham-fisted, pigheaded ploy leads to riots

In Egypt today, Coptic Christian shantytown residents rioted over government attempts to slaughter all pigs in the country.  The government's action was ostensibly undertaken as an attempt to prevent the introduction of the H1N1 swine flu virus into the country.  However, as the story linked above (from the Telegraph) says: 

"The Egyptian authorities have admitted since ordering the slaughter last week that it was mainly a pretext for carrying out a reorganisation of the country's pig farms, which are used to supply the country's Coptic Christians, ten per cent of the population.

The goal, apparently, is to ensure that pigs in the country are no longer raised in small, "unhygienic" holdings, for instance by trash collectors who feed their hogs with the trash they collect.

A story by Reuters opines that:
"...culling swine, largely viewed as unclean in Muslim Egypt, could help quell any public panic in the most populous Arab country."

So far, the only known case of this H1N1 Swine Flu strain actually being found in pigs occurred in Alberta Canada when a farmworker who had recently visited Mexico passed the virus on to his porcine charges.  That's right, human-to-swine spread, not swine-to-human.  (The pigs are all expected to recover, by the way.)  

There have been no cases of the disease identified in Egyptian swine (or any other beyond that one farm in Alberta).  There is certainly no epidemiological justification for slaughtering an entire nation of uninfected pigs.  

Both the World Health Organization (WHO) and the Food and Agriculture Organization (FAO) have issued statements condemning the action, but Egypt is clearly not as interested in the science of the situation as they are in the propaganda value of being seen to do something (especially if that something only hurts a powerless minority group).

So far, the only Swine Flu-associated casualties in Egypt aren't cases of the disease, but 13 to 15+ civilians and police who have been injured in the rioting.  Let's hope it gets no worse. 

Saturday, May 2, 2009

Morbidity vs. Mortality

A Wall Street Journal article by Ron Winslow and Avery Johnson opines that a deadlier strain of flu virus would overwhelm the US healthcare system.

Sadly, it won't even take a deadlier strain to accomplish this.  Even if every single person who gets the virus recovers, a pandemic will cause a surge in the number of people sick enough to require hospitalization.  And that alone will wreak havoc on our healthcare infrastructure.  

We have, essentially, zero excess capacity in our healthcare system tpday.  I was involved in a full-scale emergency response exercise a few years ago and the local ambulance company did not expect to have any ambulances to spare for use in the exercise.  (They did eventually manage to find exactly one, but the real response to such a disaster would have called for many more.)

When I was helping the same health department with their pandemic response plan, we polled the local nursing homes to see what they had in terms of excess beds and respirators.  The answer was, "none to speak of."  --And hospitals are the same way.  

Severe economic pressures force these organizations to grow leaner and leaner all the time, to trim excess capacity wherever they find it.  And we haven't developed any worthwhile incentives to reverse that trend.

So people don't have to die in large numbers in order to overwhelm our healthcare system; they just have to get sick enough to require care.  Indeed, the sad truth is that those who die during a pandemic may use up fewer "bed days" than those who get sick, but pull through. 

Most hospitals right now couldn't deal with the results of a bus crash by themselves.  In order to meet the needs of an influx of patients like that, hospitals rely on their ability to transfer (or divert) patients to other nearby hospitals.  During a pandemic, however, this won't be an option, because those nearby hospitals will be equally overwhelmed.

Like many others who are looking at this problem for the first time, the authors of this article are putting an undue emphasis on mortality (death) versus morbidity (sickness) when it comes to the effects on the healthcare system.  In many ways, mortality is the most important thing about a pandemic.  It's certainly what worries me the most on a personal level.  But when it comes to the healthcare arena, it takes a back seat to morbidity.  

Because the thing that's going to transform the healthcare infrastructure from a moderately well-oiled machine into just a greasy pile of slag isn't the number of people who die, but the wholly unmanageable number of people who get sick.

First Cases Identified of Swine Flu in Pigs

The Canadian Press is reporting that an official announcement will soon be made that the epidemic strain of H1N1 Swine Flu has been found in pigs in Alberta, Canada.  The pigs are thought to have been infected by a farm worker who became ill after traveling to Mexico.

Too soon to say

Suddenly, stories like this one abound, implying that the outbreak of H1N1 Swine Flu may not be such a big deal after all.

Of course, we all hope it turns out not to be a big deal, but as they finally got around to mentioning in paragraph 5 of the new article, it's "...too soon to be certain what the swine flu virus will do."

We are so early in this outbreak that we really don't know much about the epidemiology of this virus at all.  
  • How many people have the disease?
  • How many people have died?
  • How readily is it transmitted from person to person?  
  • What risk factors are there for infection (does it spread well among people crammed into the same airplane for several hours, but poorly in more open settings; are smokers or the elderly or some other group more likely to catch it)?  
  • How lethal is the virus to those who catch it?  
  • Who is most at risk of severe disease?
  • When it does kill people, is it the flu infection itself (primary viral pneumonia) that causes death or is it secondary bacterial pneumonia that moves in after the flu virus is gone?
And it will be awhile before we have many of the answers.  In the UK, they are waiting for the results of more than 600 tests for the virus.  Mexico has a backlog of over 35,000 samples waiting to be tested, and their total number of confirmed cases shot up by nearly 250 overnight to 397 as a result of additional testing (not necessarily correlated to any new cases).  In the US, it's taking 4 days to get test results, which -with a virus that has only a 24 to 96-hour incubation period- means that our picture of confirmed cases here at home is far behind the times, as well.

And all that only goes to the epidemiological situation now.  The situation is likely to change over time, as the virus mutates.  In the case of the 1918 Pandemic, for instance, the first wave of infections spread around the world in the spring, and it was pretty mild.  It wasn't until the fall, when the next wave of infections struck, that the virus became so frighteningly lethal.

So I'm very pleased that the CDC, the Department of Health and Human Services, and the Department of Homeland Security are all continuing to take the situation very seriously and are doing an excellent job of letting the public know what we do and don't know.  

Dr. Besser, Acting Director of the CDC, has done a particularly good job of communicating the expectation that the government's response, the guidance to the public and the guidance to healthcare professionals will all continue to change as the situation evolves --and that that's a good thing. 

Friday, May 1, 2009

Yesterday's webcast on the swine flu outbreak

Here is yesterday's webcast from the Department of Health and Human Services and the Department of Homeland Security.

Dr. Besser, Acting Director of the CDC, Secretary Sebelius of the Department of Health and Human Services, and Secretary Napolitano of the Department of Homeland Security did an excellent job of answering questions from the public.

More on face masks

I just ran across a very helpful article on the use of face masks to prevent the transmission of influenza-like illness in the home.  The researchers asked parents who had children with respiratory illness to wear either surgical masks, non-fit tested P2 masks (= N-95 masks), or no mask to see if the masks protected them against infection. 

The key findings were: 
"We estimated that... the relative reduction in the daily risk of acquiring a respiratory infection associated with adherent mask use (P2 or surgical) was in the range of 60%–80%." (emphasis added) 

"Adherent" in this context means that the people actually wore the mask most or all of the time.  And...

"... [less than] 50% of those in the mask use groups reported wearing masks most of the time."

You can't win if you don't play, folks.  The take home message here is: Masks help... but only if you use them consistently.

Interestingly, the authors also found no significant difference in adherence between P2 (N-95) mask users and surgical mask users, despite the widespread opinion that N-95 masks are more uncomfortable than surgical masks.

From the Comments: Disinfection

Disinfecting surfaces in your home and workplace is an important way to protect yourself against the flu (including this H1N1 strain).  Pay particular attention to places you're likely to put your hands, like doorknobs, keyboards, mice (the computer kind), faucet taps, countertops, etc.  

Don't forget: Be careful not to mix different kinds of cleaners (i.e. bleach-based and ammonia-based) or you'll have definite toxic fumes to deal with, instead of possible swine flu.
john said...

can you tell me about disinfections techniques. In particular are anti-bacterials good against flu virus thanks

PanFluWatch said...

Yes, thankfully the flu virus is easier to kill than bacteria, so any disinfectant designed to kill bacteria (antibacterial disinfectants) should also protect you against the flu.

For more useful information on this topic, see these pages from

Catch it, bin it, kill it

A very good public service ad from the UK's Department of Health: Catch it, bin it, kill it.

In addition to giving advice to the "sneezer" depicted in 
the video, this also illustrates why it's so important to 
wash your hands frequently during this outbreak --even 
when you're not aware of having gotten anything on them.