Thursday, April 30, 2009

Reality wins

Yesterday, the WHO moved to increase the Pandemic Alert Level to Phase 5 (defined below).

Phase 5 is characterized by human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short.

I'm glad they have finally chosen to acknowledge reality and follow their own guidance.  We will need the WHO to be a credible player if we are to have any hope of coordinating a global response to the pandemic.

Wednesday, April 29, 2009

Edging closer to Phase 6, an Official Pandemic

The BBC just reported that there has been a confirmed case of human-to-human transmission in Spain. 

Here is the definition of Phase 6:

Phase 6, the pandemic phase, is characterized by community level outbreaks in at least one other country in a different WHO region in addition to the criteria defined in Phase 5. Designation of this phase will indicate that a global pandemic is under way.

"Community level outbreaks" are "sustained disease outbreaks in a community," and that criteria hasn't been met by this case; we'd need to see more than one generation of human-to-human transmission before we could call it a sustained disease outbreak in this community, but hope is swiftly waning that this outbreak will fail to become a pandemic --especially since we haven't been able to contain it in the Northern Hemisphere, where the flu season is coming to an end.

Today also saw the first confirmed death from the H1N1 strain in the US, a toddler from Texas.  My heart goes out to the parents and to the families of all of those who have died in Mexico, already.  I hope that not too many more of us will have to face what they've been through.

From the comments: Is the bioengineering theory really rubbish?

Doxocopa writes:

"Complete rubbish???

For a start... still, not yet a SINGLE PIG INFECTION was reported, as far as I'm aware. Could you please answer two things?
1 - If no pigs seem to be affected at all, how on earth a pig flu virus turned suddenly to a human airborne disease? - First human cases from other species Flu virus begun by direct contact with the infected animals
2 - This virus is indeed a genetic chimera; independently of what people think about its origins, so probably can infect humans, pigs and birds, so how can it survive in Nature without an epidemiological reservoir?"

Hi Doxocopa,

Thanks for commenting.  Yes, actually: it's complete rubbish.  But I can certainly understand why the situation would be confusing to someone who hasn't studied the flu... especially because this strain was unfortunately saddled with the misnomer "swine flu."  What we're really all paying attention to right now is a HUMAN flu with swine-, avian- and human-flu progenitors.

This flu has four grandparents, if you will: two from different regions of swinelandia, one from birdlandia, and one from humanistan –and it LIVES in humanistan: really, it’s a human flu, even if it is an immigrant.

So, to answer question 1:

What does it mean that we haven’t seen any cases in pigs yet?  It could mean any one of a number of different things:

1. The virus may cause asymptomatic infection in pigs or cause only very mild symptoms.  That is, they might get infected and be able to spread the disease (both to humans and other pigs) without showing any sign of having the disease.

2. It may be that the cases in pigs have simply been missed, even if the disease was severe.  There are a number of diseases that cause illness in pigs, including “normal” swine flu, and the affected farmers may not have recognized that anything new was happening.  We can’t be sure yet where the virus first emerged, but there may simply not be a very robust veterinary public health surveillance infrastructure in the country of origin.

3. The recombination may have occurred a human, instead of a pig.  We are also capable of being infected by human, swine and avian flu strains.

4. Even if the recombination DID occur in pigs, that doesn’t mean that the new virus was best-suited to reproducing in pigs vs. humans.  Remember, the pig in question would have been infected by 2 or more strains of flu at the same time; its immune system was likely compromised.  A compromised immune system may be the reason it was infected by more than one flu strain in the first place.  Even if not, the infections, themselves, would have worn down its immune response. (Secondary bacterial pneumonia is what usually kills most people who are killed by seasonal influenza.) 

If this is true, even if the virus was better-suited to humans than pigs, the virus may have reproduced sufficiently in this one pig to infect a human handler and enter into circulation in the human population.  It might never have been, and might never be, primarily a disease of pigs.


As for question 2:

What is the “epidemiological reservoir?”  Humans appear to be the primary host species for this virus.  That’s why I saw “swine flu” is really a misnomer.  As far as anyone knows right now, this is solely a disease of humans, and WE are how the virus is “surviv[ing] in nature.”

What's more, this virus would be a profoundly stupid bioweapon.  No one would benefit from it.

Tuesday, April 28, 2009

Phase 4 Pandemic Alert - Is this the right level?

Yesterday, the World Health Organization (WHO) in an emergency meeting raised the pandemic alert level to Phase 4 (statement here).  

The practical difference in the US was pretty much nil, since we have active cases to contend with already, but in some countries this is likely to lead to a stepped-up response.  

Because the WHO's pandemic alert level is written into some national pandemic flu plans as a trigger point for specific actions, it is a relevant issue and it's worth considering whether Phase 4 is the right level at this time.

Here is the definition for Phase 4:

Phase 4 is characterized by verified human-to-human transmission of an animal or human-animal influenza reassortant virus able to cause “community-level outbreaks.” The ability to cause sustained disease outbreaks in a community marks a significant upwards shift in the risk for a pandemic. Any country that suspects or has verified such an event should urgently consult with WHO so that the situation can be jointly assessed and a decision made by the affected country if implementation of a rapid pandemic containment operation is warranted. Phase 4 indicates a significant increase in risk of a pandemic but does not necessarily mean that a pandemic is a forgone conclusion.

We certainly seem to meet this criteria with the outbreaks in Mexico, but let's take a look at Phase 5:

Phase 5 is characterized by human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short.

We meet this criteria, as well, with the outbreak in Mexico and laboratory-confirmed human-to-human transmission from husband to wife in Kansas.  Both countries are in the Americas Region.

We don't yet meet the criteria for Phase 6 --or at least we can't confirm that we do:

Phase 6, the pandemic phase, is characterized by community level outbreaks in at least one other country in a different WHO region in addition to the criteria defined in Phase 5. Designation of this phase will indicate that a global pandemic is under way.

As they said over at Effect Measure, "... [the] WHO has been timid and slow" in responding to this crisis, and with this decision it seems they're continuing in that pattern.  

I realize that there are political and economic costs attached to moving to Phase 5 and that, with the world economy in shambles, this is an especially difficult time for the global community to have to face those costs.  But what does it do for the credibility of the WHO when anyone who can read can plainly see that we should be in Phase 5 by the agency's own definition?  

The World Health Organization does a tremendous amount of good in the world and they have an important role to play in managing this outbreak.  It's time for them to refocus and re-emerge with the courage to do this job as only they can; they should start by following their own guidelines.

Monday, April 27, 2009

Bogus: Bioweapon claims for H1N1 Swine Flu

Some segments of the blogosphere are all atwitter (pun intended) with the theory that the H1N1 Swine Flu must be the work of some nefarious group of bioengineers because the virus contains segments from 4 different progenitor viruses --2 different swine flu viruses, an avian flu virus and a human flu virus.  Some even seem to imply that US government researchers working on the 1918 pandemic flu virus (which was also an H1N1 virus, though very different) might have been involved in weaponizing it.

Much of this seems to be driven by a story written by Wayne Madsen of Online Journal:
It turns up all over the place, at PrisonPlanet.comKnow4LifeInTheseNewTimes, and elsewhere.

Jeff Denmark at Drudge Retort quotes the article:

"According to two mainstream media journalists, one in Mexico City and the other in Jakarta, who spoke to WMR on background, they are convinced that the current outbreak of a new strain of swine flu in Mexico and some parts of the United States is the result of the introduction of a human-engineered pathogen that could result in a widespread global pandemic, with potentially catastrophic consequences for domestic and international travel and commerce." 

And goes on to say: "WMR has been informed that the CDC and U.S. Army dug up the body of an Inuit woman who died in 1918... from an outbreak of Spanish flu. . . . . WMR has been told the genetic material recovered by the U.S. government from the corpse of the Inuit woman provided the basis for the development of the H5N1, or bird (avian), flu strain at the U.S. Army Medical Institute of Infectious Diseases (USAMRIID) laboratory at Fort Detrick, Maryland, the point of origin for the Ames strain of anthrax used in the 2001 bio-war attacks against the U.S. Congress and the media."

This is, as they say in Jolly Olde England, complete rubbish.

"How, then" you may ask "did a brand new virus that's made up of four different viruses suddenly spring into being and spread all over the world? Doesn't it have to be the result of bioengineering?"  

...Actually, no.
This is exactly the sort of thing we've been expecting for years.  

If more than one strain of flu virus infects the same cell, the two strains can mix up their genes, leading to what is called a recombinant virus.  That simply means that the genes from the two (or more) viruses have recombined to create a new strain.  In effect, it's a lot like sexual reproduction in humans; parents mix up their genes with the result that a child might have her mother's hair and her father's eyes.

This recombination happens especially easily in pigs, because they can be infected by swine flu viruses, avian flu viruses and --you guessed it-- human flu viruses.  The pig as a "mixing vessel" scenario is something we've long known to be a threat when it comes to pandemic flu.  In fact, this is believed to be what caused the last two pandemics, in 1957 and 1968, as this figure illustrates.

This is perfectly natural and expected.  That doesn't make it good, of course, but there's no hidden conspiracy behind it.  The virus arose naturally and the epidemiological evidence seems to show pretty clearly that it's spread so quickly because of air travel --something else we knew to expect-- not because it's being used as some kind of very inefficient bioweapon.

We humans are all on the same side on this one.

Sunday, April 26, 2009

Protecting yourself

Although things aren't looking good so far, it's still too early to say for certain whether the swine flu outbreak will mushroom into a pandemic.  But it's a good idea to start giving some thought to how you can protect yourself and your family from infection, if the virus should continue to spread.

Here are some evidence-based protective measures you can take to help prevent infection:

1. Wash your hands

...then wash your hands some more.  In fact, one of the studies examined in the relevant Cochrane Review showed that simply washing your hands at least 5 times a day cuts the risk of coming down with a respiratory infection by almost 50%.  

Handwashing is one of the most important things you can do both to keep from getting the virus and to keep from spreading it, if you happen to be infected.  --And it's important to understand that you may well be contagious for 24 hours before you show any symptoms.  That's one of the reasons why influenza is so much harder to control than the SARS epidemic was.

Most people, even those who have the training to know better, don't wash their hands correctly.  For instance, did you know that every time you wash your hands, it should take you 20-30 seconds to scrub them thoroughly (long enough to sing the alphabet song once or the "happy birthday" song twice)?  For more on how to wash your hands correctly, see the CDC's video "Put Your Hands Together."

2. Stay away from infected people (and stay home if you're infected)

This is called "social distancing" and it sounds pretty obvious, but it's one of the hardest recommendations to stick to.  That's because during a pandemic simply going to work, going out to buy groceries, going to a doctor's appointment or going to school could put you in contact with infected individuals or put others at risk if you're infected.  

And, as I mentioned above, people (yourself included) can be contagious for 24 hours before showing any symptoms.  When it comes to a flu pandemic, the fact that people feel well or look well is not a reliable measure of the risk they pose to others.  

If this does become a pandemic, the safest thing you can do is stay home and avoid contact with others as much as possible.

3. Use personal protective equipment (PPE) when you might come into contact with infected individuals

There has been a lot of talk over the last few years about the use of N-95 particle respirators as a way of avoiding infection, and they have been shown to work pretty well when used correctly... but the Cochrane Review I mentioned earlier found that there was no statistically significant difference between their performance and that of simple surgical masks.  Another study found that using nylons (AKA pantyhose) to hold the surgical mask tighter against your face improved their performance even further.  This is a more foolproof form of protection than the N-95 mask, which must be correctly fitted and it may be more comfortable, as well, which has implications for compliance.  --Paper masks were not shown to be effective.

Eye protection (in combination with masks) was also shown to be effective by the Cochrane Review.  It's not clear whether this is primarily because goggles protected users from airborne droplets or because it prevented them from rubbing their eyes and thus introducing infectious material from their fingers into their eyes, but either way they made a difference.

The same Cochrane Review showed that gloves were highly effective in preventing infection. The studies on this topic took place in a hospital setting, where healthcare providers changed their gloves after seeing each patient, so wearing the same pair of gloves all day isn't likely to help.  It's also very important to understand that wearing gloves does not eliminate the need for handwashing.

Protective gowns (e.g. surgical gowns) were also shown to significantly reduce infection.  Again, this was in a hospital environment, but it highlights the importance of clothing as a possible fomite (an inanimate object that can transmit infection).  Surgical gowns may not end up seeing much use in day-to-day interactions outside the hospital, but this finding implies that it might be worth changing your clothes after coming into contact with someone who may be infected. 

All of the above, plus handwashing
Not surprisingly, the most effective intervention was a combination of all the forms of personal protective equipment above plus frequent and thorough handwashing.

4. Thoroughly disinfect surfaces where you live and work

Doorknobs, computer keyboards and mice, telephones, tables, kitchen counters and other surfaces can all transmit infection.  Thoroughly cleaning these surfaces with disinfecting agents can help reduce the spread of a flu virus.

5. Use a humidifier

This study (and a few others) suggest that humidifying indoor air may reduce the risk of flu transmission.  The evidence is fairly limited here, but the argument seems sound to me.

6. Practice good cough and sneeze etiquette 

Don't cough or sneeze into your hands.  If you don't have a tissue available, cover your cough or sneeze with the crook of your elbow instead of your hands.  That way, you won't be spreading germs to everything you touch.  If you do have a tissue available, you can cough or sneeze into that, then throw it away and wash your hands as soon as possible.  

7. If you have children, make sure they do all of the above

Children are especially good at transmitting the flu virus, which is why schools are likely to be closed down during a pandemic.  Making sure that your children learn to take the above precautions (especially frequent and thorough handwashing) can help to keep them safe... along with everyone around them.  

Swine Flu Map

Update: The map has been re-designed to be easier to read and continues to be updated frequently.  The link for the map has changed, and the link listed below is the latest version.


This site maps confirmed and suspected cases related to the swine flu outbreak and gives information on mortality, along with reports of suspected cases that turned out not to be swine flu:

It's a useful tool for visualizing the outbreak and because it links to the news reports that back up the data it's mapping, you can assess the reliability of the information yourself.  So far it's being updated very frequently, despite (or perhaps because of) the fact that we're in the middle of the weekend, so keep an eye on this site for the latest.

Time to update your pandemic flu plan

With the H1N1 “swine flu” outbreak unfolding across the globe, the threat of a flu pandemic is higher than it has been in decades.  We don’t yet know whether this new virus will become the next pandemic or (as we all hope) simply fizzle out, but now is a good time for families everywhere review their plans for coping with a pandemic and make sure they’re up to date.

What is a flu pandemic?

A flu pandemic is caused by an Influenza A virus, the same type of virus that causes the seasonal flu we deal with every year.  The difference is that a pandemic flu strain makes a lot more people sick than the seasonal flu and that it doesn’t just occur during the regular flu season. –A pandemic may last 18 months or more.  One other important difference is that, unlike the seasonal flu, which is normally only dangerous to infants and the elderly, pandemic flu strains often cause severe illness among teenagers and young adults, as well.  This is a pattern we’re seeing in the preliminary data from the swine flu outbreak, which is cause for concern.

Three conditions must be met in order for a flu virus to cause a pandemic:

  1. It’s new to humans so that we have little or no pre-existing immunity to it
  2. It readily causes significant disease in humans
  3. It spreads easily from person to person

  “Swine flu” is a flu virus that normally infects pigs, and most swine flu viruses only meet the first of those three criteria: we’re not immune to them, but they don’t easily causes disease in humans (and such diseases are usually mild when they do occur) and they are rarely ever transmitted from person to person.  While the virus implicated in this outbreak is causing significant disease in humans and, based on early reports, is probably spreading from human to human, it is too early to say whether it is doing so at a level that could cause a pandemic to occur.  But whether this is the start of the next pandemic or not, it’s an important reminder about the importance of having a plan in place for keeping your family safe when a pandemic does strike.

How should you prepare?

The website is the federal government’s one-stop source for pandemic flu-related information, and it offers useful advice on how to prepare.  The following checklist comes from that site and will help you to make a good start toward doing what you can to keep your family safe:

 1. To plan for a pandemic:

¨ Store a two week supply of water and food. During a pandemic, if you cannot get to a store, or if stores are out of supplies, it will be important for you to have extra supplies on hand. This can be useful in other types of emergencies, such as power outages and disasters.

¨ Periodically check your regular prescription drugs to ensure a continuous supply in your home.

¨ Have nonprescription drugs and other health supplies on hand, including pain re­lievers, stomach remedies, cough and cold medicines, fluids with electrolytes, and vitamins.

¨ Talk with family members and loved ones about how they would be cared for if they got sick, or what will be needed to care for them in your home.

¨ Volunteer with local groups to prepare and assist with emergency response.

¨ Get involved in your community as it works to prepare for an influenza pandemic.

2. To limit the spread of germs and prevent infection:

¨ Teach your children to wash hands frequently with soap and water, and model the correct behavior.

¨ Teach your children to cover coughs and sneezes with tissues, and be sure to model that behavior.

¨ Teach your children to stay away from others as much as possible if they are sick. Stay home from work and school if sick.

3. Items to have on hand for an extended stay at home:

Examples of food and non-perishables

¨ Ready-to-eat canned meats, fish, fruits, vegetables, beans, and soups

¨ Protein or fruit bars

¨ Dry cereal or granola

¨ Peanut butter or nuts

¨ Dried Fruit

¨ Crackers

¨ Canned juices

¨ Bottled water

¨ Canned or jarred baby food and formula

¨ Pet food

¨ Other nonperishable foods

Examples of medical, health, and emergency supplies

¨ Prescribed medical supplies such as glucose and blood-pressure monitoring equipment

¨ Soap and water, or alcohol-based (60-95%) hand wash

¨ Medicines for fever, such as acetaminophen or ibuprofen

¨ Thermometer

¨ Anti-diarrheal medication

¨ Vitamins

¨ Fluids with electrolytes

¨ Cleansing agent/soap

¨ Flashlight

¨ Batteries

¨ Portable radio

¨ Manual can opener

¨ Garbage bags

¨ Tissues, toilet paper, disposable diapers

How can you help?

If you are interested in helping your community prepare for and respond to a possible flu pandemic, consider volunteering through your local Medical Reserve Corps unit.  You don’t need to be a medical professional to join; you just have to be willing to help. You can find out more about the Medical Reserve Corps and how to contact your local unit at

You can also volunteer through the American Red Cross (, your local Community Emergency Response Team (CERT) ( or any of the national, state or local Voluntary Agencies Active in Disaster (VOADs) found here:

Take home message

There’s no need to panic.  Right now, we don’t know whether this new swine flu virus will become a pandemic or just fizzle out.  It’s just too early to tell.  But either way, now is a good time to review your plans for keeping your family safe during a flu pandemic.  Make sure you have two weeks worth of non-perishable food and water at home.  Make sure you have a continuous supply of any medications you rely on.  Keep up to date with the latest information and advice at, and consider volunteering to help your community in the event of a public health emergency.  Because even if this isn’t the next flu pandemic, eventually there will be one.  Being prepared before it strikes could make all the difference for you and your family.