Swine flu: a quick overview--and new New York and Kansas cases

Sorry for the radio silence--I've been working on grants and manuscripts like a fiend, and so have tried to limit as many distractions as possible (which, unfortunately, includes blogging). However, the swine flu news is right up my alley, so I do just want to say a few words about it, and point you to some excellent stories already up elsewhere.

First, in case you've not been paying attention to the news in the last few days, there have been 8 reported cases of swine influenza infections in humans (6 in California and 2 in Texas, with additional suspected cases) and reports from Mexico suggesting as many as 1000 ill and 68 dead from influenza in the past month or so. Of the Mexican cases, a dozen thus far have been confirmed to be the same strain as the US swine flu strain from California/Texas.

What does all this mean? Much more after the jump.

It's been awhile since I posted on anything flu-related here. Though cases of H5N1 continue to be uncovered on a regular basis, the media furor has died down a bit, and the government and local health agencies have been working behind the scenes to prepare for the possibility of an influenza pandemic. Long time readers will recall a post from awhile back, when influenza virologist Robert Webster gave a talk at the University. He emphasized:

...that, while H5N1 is the "bird flu" that's receiving the lion's share of media (and scientific!) attention right now, other serotypes of avian influenza have circulated recently, including H7N7 and H9N2. During the H7N7 outbreak in the Netherlands, 30 million chickens were destroyed, and there were over 300 human cases of conjunctivitis. There also was evidence of human to human spread, and one death from the outbreak. Additionally, there was serological evidence of H7N7 infection in pigs, which have long been a concern as a potential "mixing vessel" between avian and human-type influenza viruses. The take-home message: H5N1 ain't all that has the potential to become a nasty pandemic strain, and we need to keep our eyes peeled.

Keep our eyes peeled indeed. This swine strain, serotype H1N1 (the "classic" swine flu serotype) is apparently a triple reassortant, carrying genes from human, swine, and avian influenza viruses. A few things make this outbreak concerning.

One, we see occasional swine influenza infections in humans on a somewhat regular basis. There was an outbreak associated with a fair in Ohio a few years back, and research by my colleague Greg Gray here at the university has showed that mild or asymptomatic infections of swine workers with swine influenza viruses are more common than we realize (David Brown of the Washington Post has a nice summary of that background here). However, those infected in California and Texas have no known contact with pigs--suggesting they acquired this virus from a human source.

Two, while the cases in the US have been mild and no deaths have occurred that we're aware of, it seems in Mexico that young people are dying from this--a group that is typically not hard-hit by seasonal influenza viruses. Readers familiar with influenza and know the history of the 1918 influenza pandemic will recall that the "young and healthy" were disproportionally struck by that virus as well--so this knowledge is currently disconcerting and worrisome, but there are so many gaps in our information as far as what's really going on in Mexico that it's difficult to make heads or tails out of this data right now.

Third, is this really a new virus? So few influenza isolates are actually analyzed each year (in proportion to the number of people infected) that we aren't sure yet whether this is something brand-new, or something that has been circulating at a low level for awhile, but just hadn't been picked up. After all, H1N1 is a common serotype, so additional molecular testing is needed to determine that it's "swine flu" versus "human" H1N1.

Fourth, and going along with that third point--how widespread is this? We have confirmed cases from Mexico, California, and Texas, which suggest it could be spreading in the southern parts of North America--but a breaking news report says that cases have also been confirmed in Kansas and New York, but it doesn't say whether they've been definitively matched to the strains from the SW US and Mexico. The NY Times reports that some students at the NY school had recently traveled to Mexico and could have potentially brought the infection back from that trip, if it's confirmed.

In summary, this is a fast-developing story, and it will take much more investigation and field work to determine the true extent of the virus's spread in the population; to figure out where it originated (one blog suggests a Mexican hog confinement according to some local Mexican papers, but that is conjecture at this point); how it jumped to humans; and how efficiently it's transmitted. Whether this burns out or spreads worldwide, it certainly shows once again the importance of surveillance and monitoring of influenza strains, and demonstrates that improving our infrastructure due to concerns about H5N1 will benefit us whether that serotype, or another emergent strain, ends up being the next global influenza threat.

Other sites to keep an eye on:

Effect Measure


Daily Kos (Dem from CT)

Flu Wiki

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Welcome back, Tara, no matter how briefly. And thanks for giving us another informed, common sense view of the situation.

Hi Tara, I agree with the above comment and appreciate the analysis!

By TorontoPDF (not verified) on 25 Apr 2009 #permalink

Ditto! I was hoping you'd blog soon on the swine flu cases. Your analyses are usually clear and concise.

There have been a few avian flu cases here in China recently, but no where near the swine flu numbers seen in Mexico. The avian cases have typically involved farm families who keep a lot of (free range) chickens, and transmission to the general population has so far been negligble. At least, that's what the local media say.


Given the similarity in the age groups, don't you think this is due to cytokine storm and if so, doesn't that indicate that this is a particularly virulent form of influenza?


is it typical for multiple flu strains to be infecting populations at the same time? Does anyone know in 1918 if other flus were killed off by the H1N1 at the time?

Here in Minneapolis St. Paul, my kid's pediatrician reported on Wednesday (before we heard of this) that they are seeing two clusters of respiratory illness that they think are both some flu, though one has the oddity of gastroenteritis with it. Anecdotally, parents are reporting their children are getting sick and taking weeks to get well, with bounceback fever. None of these docs have been typing the virus in any of this--they aren't even encouraging their patients to come in. how will we know if this is related or not? How do you get effective morbidity/mortality/infection rates if you don't count those who aren't totally compromised by the illness?

A few quick comments...

As I understand it, the natural hosts of flu are principally migratory birds, e.g., ducks and geese. Geese often carry as many as twelve different strains of flu at any given time. As migratory birds are natural hosts, flu and migratory birds are typically co-adapted, meaning that infections are typically asymptomatic or at least of low virulence.

Like HIV, flu is a single strand RNA virus. HIV has ten chromosomes whereas flue has eight. (I remember this particular fact since migration may take place in any one of the eight noble directions -- e.g., the Tao.) However, being a retrovirus that employs reverse transcription, HIV is missense. Flu transcribes normally and is therefore sense (+). Both are (I believe) roughly the same size. After HIV, flu is the fastest mutating virus known to infect humans.

However, flu mutates primarily by means of recombination. As such, migratory birds act as mixing vessels in which new strains evolve. One of the greatest barriers to flu jumping species to humans lies in our lower body temperature -- particularly in the lungs -- as "bird flus" are typically adapted to the higher body temperature of birds.

However, some animals act essentially as half-way stations between birds and humans. Pigs are well known for this. They will act as mixing vessels in which recombination can take place between bird and human strains of the flu virus.

Just noticed...

Apparently this strain is virulent in young adults with healthy immune systems. In this respect similar to the 1918. Shades of a cytokine storm in which a strong immune system overreacts to the virus and turns against itself -- where the strength of the immune system works against it. Good thing flu season is almost over.

Good thing flu season is almost over.

Not in New Zealand.

By Heraclides (not verified) on 26 Apr 2009 #permalink

Is there a good way for public health system to determine the answer to your point #3? My family had a whopper of a flu about 2 months ago, and I am reading many anecdotes about doctors commenting on seeing many instances of flu with diarrhea, which is apparently abnormal for them. So, to your point, this thing could have already run most of it's course, but we are only now aware that this strain exists and looking for it.
Then again, I would think that there are tests being performed of people with flu symptoms all over the world now, and we are only seeing confirmed cases where people who visited Mexico recently.

Timothy Chase,
"Like HIV, flu is a single strand RNA virus. HIV has ten chromosomes whereas flue has eight. (I remember this particular fact since migration may take place in any one of the eight noble directions -- e.g., the Tao.) However, being a retrovirus that employs reverse transcription, HIV is missense. Flu transcribes normally and is therefore sense (+). Both are (I believe) roughly the same size. After HIV, flu is the fastest mutating virus known to infect humans."

Just two minor corrections on HIV; it was two copies of its chromosome per particle, not ten and it is positive sense not negative. Influenza on the other hand is, I believe, negative sense, not positive. I'm not a huge influenza buff so Tara or anyone else, please correct me if I'm wrong.

By Poodle Stomper (not verified) on 26 Apr 2009 #permalink

As I read about the swine flu, I am concerned about ways that the disease can be spread that may not be considered due to modern technoloty.

What is the expected time period when the disease remains viable on a dry surface?

Are the anticeptic wipes we get in packets are sufficient to eliminate it.

It seems to me that library books, especially through the interlibrary loan service would be an efficient way of transmitting the virus. Sick people often read as they are dealing with hours in bed. This would put both library employees and patrons in danger. If the length of time a book was contagious could be know, perhaps books could be 'quarentined' during this period.

Also, a possibly more dangerous are rental videos and DVDs for the same reason as library books. Here my question would be if anticeptic wipes will eliminate the problem. It would be impossible to use this method on all the pages of an infected book, but it could be a simple preventative.

It seems like now is the time to consider precautions like this

Barbara Hardy

By BarbaraLea (not verified) on 26 Apr 2009 #permalink

Does anyone know what the incubation period is for this
type of flu ?
How it jumped from birds to swine then humans ?
Are we really dealing with the flu virus or something
that has mutated into a super virus ?
This is Spring. Flu survives best in the cold.
Mexico seems like such an unlikely place to start let alone
spread a flu virus.

We need to take heed of the cautionary measures the CDC lets out, especially now that The Obama Virus has broken out in Ohio. The CDC should have a description of the symptoms we should look out for on their website. Google it if necessary. Also, I found this related item on some other site, maybe of interest: "It's another H1N1 strain of Influenza A, the same general strain that caused the 1918 pandemic." If that's even relationally true, then The O Bug is just beginning to rear its many heads. The expression, "An ounce of prevention....", that's definitely still true. Unlike China and Africa, our communications is traditionally not controlled, but under the new administration the amount of proven cases will likely be constrained by government sources, making the aptly named Obama Virus, or Obama Bug, all that formidable. Someone here mentioned library books as a transmission medium. Another important transmission medium are the bars, handles, surfaces and seats on public buses, subways, trains and restrooms, and in taxi cabs, and public door handles and surfaces.

By Lavertinger (not verified) on 26 Apr 2009 #permalink

There's a cluster of flu in the last week in PA that I'm aware of (I had it). In my case, I was positive for Type A on the Quidel QuickVue test. This flu was much nastier than past flu's that I've had, and the GI symptoms were very unpleasant.

I called the Quidel IR contact on Friday to ask what result the swine flu from Mexico would give if run through their QuickVue flu test and as of April 24th their R&D group hadn't been able to obtain samples to test. So he didn't know.

This statement "After all, H1N1 is a common serotype, so additional molecular testing is needed to determine that it's "swine flu" versus "human" H1N1" is in conflict with CDC posts such as this: "Since March 2009, a number of confirmed human cases of a new strain of swine influenza A (H1N1) virus infection in the U.S. and internationally have been identified. An investigation into these cases is ongoing. For more information see Human Swine Flu Investigation."

Based on my recent and past experience with government officials, I don't necessarily trust the CDC statements to be completely accurate, however.

MarketBlogic, I don't see how those are in conflict. Think of it as zooming in on a specific influenza strain. The largest group is just "influenza", which includes influenza types A, B, and C. Most of what we're concerned about when it comes to human disease is influenza A. These are further broken down into serotypes based on the H and N proteins (so you'll see things like H1N1 or H5N1), but even these are further broken down into different strains within those serotypes (hence different types of "human" H1N1 versus "swine" H1N1, etc.) Does that make any more sense?

Is it possible that this new strain - a combination of swine flu and bird flu - occurred naturally?

The thing about library books is that paper is quite dry and tends to soak up moisture in the air. Airborne infections don't like being dried out this way and if your book has previously soaked up flu carrying droplets, you'd need to lick the pages to pick up the infection. Don't.
Libraries know their books don't like moisture and control their air well. They are probly among the safest places to be in a flu outbreak.

And laverninger, Grow the fuck up.

This flu scares me what if it mutates to something worse, so bad that it'll take months and months to cure it? WoW already in ohio close to indiana where i live and the schools are not well kept believe me. I hope none of my family doesnt catch it. And i believe there is a way to get rid of it people should try colloidal silver it is known to kill almost every virus and keep your immune system very good! Lately people are saying that colloidal silver can work in one day. For people who get this virus i think you should try this stuff.

I'd stay away from colloidal silver and stick to something that won't cause argyria and turn me into a smurf. Do you have any credible sources supporting that this will kill the influenza virus in vivo? I realize a lot of quack "natural medicine" makers promote this but I'd like to see some real studies supporting it. Are there any?

By Poodle Stomper (not verified) on 26 Apr 2009 #permalink

The colloidal silver thing has only ever been a trap for fools. They fall for it and turn blue. Then we all point and laugh.

Hi Tara,

I've been doing some researching on the possible CAFO link for TrackerNews.net and found enough that suggests a major vulnerability, if not a direct link. fyi: http://tinyurl.com/czk9yf

Also, right now there are bunch of links on TN re vaccine & drug research (including an article on how to detect fake tamiflu...).



Hoo boy ... colloidal silver, loony conspiracy theories, loonier conspiracy theories, an article that praises David Kirby ... the cranks really come out for flu pandemics, don't they?

When i heard "swine flu", i predicted that Tara would have something interesting to say about it. Does that make me psychic?

Uhm, i don't think so.

Barbara asked, "What is the expected time period when the disease remains viable on a dry surface?"

Unless the surface is grossly contaminated with respiratory mucus, not very long. IF the surface is contaminated with extremely large quantities of virus (higher than people normally shed) you can recover some active virus for up to three days.

IF you add large quantities of respiratory mucus AND large quantities of virus, up to 17 days. But that's "gross contamination" in both meanings of the word.

They way you get infected by virus that is on a surface is that you handle the object and then touch your eyes, eat or somehow get the virus from hand to a mucus membrane. Frequent handwashing is all it takes to disrupt this route of infection.

By Tsu Dho Nimh (not verified) on 27 Apr 2009 #permalink

The U.S. is lying about the so called swin flue, for political reasons (as always, they need someone to blame) in order to save face. â50 people have contacted the swin flu and not one has dead in the U.S.?â In Mexico, 100 people have died? The U.S. has more or less about 35,000 cases of the flu deaths per year, way more than Mexico. Those people in Mexico have dead for a smart flu Bomb that kills only Mexicans and spares Americans? The people who are dying from the flu in the U.S., the Medical establishment for Embarrassment and blame, In order to save face and promote the lies will simply say âit was some other flu. Is this some type of intelligent test? "MAN ARE AMERECANS STUPID" do you think youâre kidding the world? Youâre not. Mexico knows exactly what you doing; they have a long History of Americas stupidity and crap. I donât care if itâs the lizard flu the American who died or dead

Does anyone know what the cause of morbidity is in the new swine flu outbreak? For some reason there is no information on the actual cause of deaths! This is crucial information for all medical personnel.

Hi -

Tara - interesting info. Question - if the H1N1 is airborne carried by moisture would removing (or 'filtering') moisture to a smaller particulate size 'stop' the virus from moving along? Does the H1N1 enjoy or dislike an acid-like surface??

Your thoughts are appreciated.



Oh hey now all the snake oil sales people are coming out with more colloidal silver BS. More crap to peddle to the masses, I suppose.

By Poodle Stomper (not verified) on 30 Apr 2009 #permalink

I have been checking on this swine flu tracking website http://www.swine-flu-tracker.com/ on and off for the last couple of days now and its kinda scary seeing how it this strain of flu is spreading.

In fact, it is known that human and avian influenza viruses from time to time to deliver the hogs and pigs can be used for "mixing vessels for these viruses, which means that viruses can exchange genetic material and leads to the production of a new virus hybrid. This led to think that maybe a pandemic virus may arise as a result of the restructuring of the pigs.