Swine Flu and You

Regular readers know that I like to touch back to the published research when we talk about a topic. Obviously swine flu is brand new, and it would be pretty darn fast to get good research out on the subject. Luckily there is at least one very recent article that is very relevant.

The CDC releases a weekly morbidity and mortality report online, they can be found here. For some reason the researchblogging.org citation isn’t quite working, so the article we’re discussing is found here, and an update to it found here.

So what do the articles say? Sadly they don’t say a lot. The initial article is a pair of case studies in southern California, the update includes 6 more cases – four from California and two from Texas, and mentions the outbreak in Mexico. In the two initial cases in the report, the same virus appears to have been isolated – it is an H1N1 strain of influenza. The CDC has further described this as a swine flu virus. The new cases in the update were still in the process of typing as of the publication if this article, but preliminarily it looks like the same virus.

In all cases, the patients have not been exposed to pigs. It looks more like the disease spread from person to person. As I said previously, you don’t get swine flu from eating pork. You get it from being exposed to a person with swine flu. If you work closely with pigs, it’s entirely possible you could get swine flu from a sick, life pig.

The viruses they found were resistant to amantadine and rimantadine – two common antiviral medications. However the viruses were sensitive to zanamavir and oseltamivir – better known as Relenza, and Tamiflu respectively. This is great news. The US has pretty large stockpiles of zanamavir and oseltamivir, and the government is already deploying these for use. So if this does end up being a pretty large breakout, or even a pandemic, we are in good shape treatment-wise.

That’s about all that’s covered in the article, I’d like to use that as a jumping off point for some relevant education on influenza in general, and this outbreak in particular. It’ll be in multiple parts, but today we’ll just discuss some basics – including why public health officials are so trigger happy about influenza outbreaks.

We talked about H1N1 earlier, what does that mean? Well there are two types of influenza: influenza A and influenza B. We won’t be discussing influenza B today, the virus we’re worrying about with this outbreak is a subtype of influenza A virus. Influenza A viruses are divided up into subtypes based on two surface proteins – hemagglutinin, and neuraminidase. These proteins are numbered, and different subtypes can infect sets of different species. The species that most commonly infect people are H1N1, and H3N2. The much feared Avian flu is a variety of H5N1.

Now that doesn’t mean that one H1N1 is the same as every other H1N1. Influenza can be further broken down into different strains. The influenza vaccine this year contains a H1N1 strain, but not the same strain that is in this outbreak.

This is where it gets complicated. The influenza virus evolves over time, to evade our immune systems. It can do this in two big ways. One is called antigenic drift, and the other is called antigenic shift.

Antigenic drift is what we normally think of when we think of evolution. Over time, as the virus reproduces, mutations occur and as they occur, those proteins – hemagglutinin and neuraminidase – change too. Eventually, the right mutations occur and the proteins are different enough to look “new” to our immune system, to not be the same virus to our immune system. The thing is, since they just mutated from a virus we’re familiar with, they’re still somewhat familiar to us, not completely different.

Antigenic shift is far scarier. Each gene in influenza’s genome is in it’s own separate chunk of DNA. If two or more different influenza viruses infect the same cell, their DNA chunks can mix together, and the virus can pops out can be completely new. For example it could have some primarily human infecting DNA, and some primarily pig infecting DNA. A virus like that could be completely new to our immune system, and that can be scary.

The balance of evidence says that this swine flu outbreak results from an antigenic shift event. That’s why people are freaking out. That’s one of the reasons that the CDC was pretty quick to declare this a public health emergency. We don’t know yet if this is or even if it could be a pandemic, but we’re prepping in case it is.

It’s worth noting that as far as we can tell so far, the American cases are very different from the Mexican cases. The American cases appear to be relatively self limited –people don’t seem to be getting so sick that they die. Many of the Mexican cases appear to be resulting in hospitalizations and death. This is despite the fact that they seem to be the same virus, genetically we are seeing different things. We do not why that is. If I see credible information on the reason, I’ll be sure to post it here in followup.

So, is this swine flu outbreak the new 1918 flu? Or is it a mere hiccup, not even worth worrying about in the grand scheme of things? The unsatisfying real answer is that it’s too early to tell. It would be like watching a college basketball game, and after 5 minutes saying “aha, this is the next Magic vs Bird in NCAA finals!” 

In the mean time, do your part: wash your hands, and if you or your child is sick, take the day off. If you’d like more posts like this, or like my initial swine flu post, check back here, I’ll be trying to post at least once a day.

Centers for Disease Control and Prevention (CDC). (2009). Swine Influenza A (H1N1) infection in two children–Southern California, March-April 2009. MMWR Morb Mortal Wkly Rep., 58 (15), 400-402 DOI: 19390508

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13 Comments on “Swine Flu and You”

  1. Here’s the health advisory from the CDC:


    Note that they’re not even recommending stopping travel to affected areas.

  2. DDW Says:

    Nice post. I am adding a link with a good diagram of antigenic shift. I find a visual representation is much easier to understand, especially when the reader lacks a biochemistry background.

  3. The CDC is recommending a “travel precaution”, NOT recommending not travelling to mexico, but recommending taking appropriate prophylactic measures if you do.

    I think the issue right now is making sure everyone does the simple things to avoid spreading any infectious issues we may have – hand washing, covering your mouth, taking the day off if you’re sick. If things get worse, we can address that, but right now, the “emergency” is so that we can approach the problem head on, instead of playing catch up.

    Great diagram, DDW, those who didn’t love my explanation, I highly recommend reading his link, it’s very intuitive.

    • When we train new sales reps, who will be going into hospitals, clinics and such, we make it a critical point that they constantly wash their hands. My mother used to scream at me if I didn’t wash my hands. Good advice (sans the screaming).

  4. Tsu Dho Nimh Says:

    Many of the Mexican cases appear to be resulting in hospitalizations and death.

    Mexico, as far as I can tell from reading their press releases, is or was only tracking hospitalized cases. The USA and other countries are counting all virologically confirmed cases. That would definitely skew the apparent severity of the illness.

    They have also commented that the deaths were among people who had been severely ill for several days before they came to the clinic, and recommended that people come in if they had signs of the flu.

    After the resulting stampede on Saturday: 5900 clinic visits, 5600 ordinary respiratory illnesses, 300 or so “suspicious” cases getting followup, and 25 hospitalized.

    • I’ve seen mixed reviews – the problem seems to be that mexico isn’t necessarily diagnosing this properly, it’s not clear how many people are actually dieing of the flu itself and how many are having secondary issues, and how many didn’t actually have swine flu to begin with.

  5. MXH Says:

    However the viruses were sensitive to zanamavir and oseltamivir – better known as Relenza, and Tamiflu respectively. This is great news. The US has pretty large stockpiles of zanamavir and oseltamivir, and the government is already deploying these for use. So if this does end up being a pretty large breakout, or even a pandemic, we are in good shape treatment-wise.

    I hope that people don’t go crazy and start taking these antivirals for every runny nose they get, like they did a few years ago with the bird flu (H5N1). The last thing we need is a drug resistant flu pandemic.

  6. Tsu Dho Nimh Says:


    “que según cifras oficiales ha afectado a 1,384 personas, de las cuales 929 han sido dadas de alta, 374 permanecen hospitalizadas y 81 han muerto” … has affected 1384 persons, of which 929 are registered/enrolled (I have no clue what that means in this context), 374 remain hospitalized, and 81 have died.

    And they continue by saying that in three days they will have definitive testing measures – part of the problem is that they did not have whatever it takes to definitely identify this virus.

    • My understanding is that their labs weren’t capable of identifying the virus, but that they had tried to fly up samples to Winnipeg. The whole thing sounded like the situation is not well in hand.

  7. HoleyMind Says:

    I know there is not a vaccine for this yet, but that got me thinking of things I’ve heard before about flu vaccines. I have no idea how they pick what strains to put in the vaccines any given year, but I do know it’s only for a couple or so. I think I’ve heard or read, however, that the vaccines help (or may help) against other strains.. so the shot will still do you good even if they picked wrong. So I’m wondering: Is that true about flu vaccines? If so, does it apply in this case? I’m wondering if one who had the flu vaccine this past season would fare better than one who didn’t. but even if both answers are yes, I realize that maybe it’s been too long and that vaccination itself no longer applies, is no longer effective. That would just figure.

    • When making vaccines they make their best guess as to what strains will be present. Different strains have some overlap, thats more complicated, and it depends on just how different their proteins are from one another.
      Thats what makes these reassorted strains (the ones that have undergone antigenic shift) so dangerous, they won’t be at all similar to strains you’ve seen.

      It’s not a time thing, your vaccinated immunity is more or less still good from year to year.

      It’s evolution in action. The strain you see next year isn’t the strain you saw this year. And the reassorted strains aren’t like anything you’ve ever seen before!

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