Swine flu: more on the genetics of the virus

A reader (hat tip, sandy) has pointed me to a very interesting interview with CDC's chief virologist, Ruben Donis, in Science Magazine's blog, ScienceInsider. In it he provides further information on the confusing reports about the species origin of the current swine flu, originally said to be of swine, human and bird origin but later claimed to be only swine. It may be that both are true, depending on how you look at it.

According to Donis, who has been sequencing the isolates, the virus is all recent swine but bears the marks of human and avian ancestry in some genes. Different genes have different close relatives. Influenza genes make 11 proteins but are packaged into eight discrete segments. The HA, NA and matrix proteins are the ones seen most readily by the immune system, but there can be an immune response to the protein products of any of the genes. Donis said in his analyses the HA gene (the H-part of H1N1) is equidistant on the family tree of swine flu viruses from those that circulate in the US and Asia/Europe, hanging out on a "lonely branch" all by itself. In other words, it doesn't have any evidence close swine relatives. The NA and matrix genes have close relatives, all swine. So where are the human and bird genes?

Starting in 1918, when it was thought we gave pigs our influenza viruses from the pandemic, all swine viruses in the US were H1N1 viruses. Suddenly, in 1998 that switched to H3N2 and caused large outbreaks of swine flu in the midwest. Why did this happen all of a sudden? H3N2 refers to subtypes of HA and NA on the surface of the viral particle. There are proteins inside the virus, too, and inside there were differences. The PB1 gene, like the H3 and N2, were human. The PA and PB2 genes (involved in viral replication machinery) were bird origin. The remaining genes were typical pig viruses seen in North America. So this was a triple reassortant (swine, human, bird). At the moment we don't know where or when or how this happened ten years ago, but the new combination was considerably more fit than the H1N1 and soon crowded it out. In effect, the pigs had a "pandemic" (more accurately, a North American panzootic) with H3N2. So is this a pig virus or a human-pig-bird virus or what?

Q: How does it tie to the current outbreak?

R.D.: Where does all this talk about avian and human genes come from? I was describing a fully swine virus. For [the] last 10 years, this has been a fully swine virus. Can you tell I have an accent? I’m a U.S. citizen but I have the roots in Argentina. It’s like me. I’ve been in the U.S. since 1980. I’m a U.S. citizen but I have an accent. (Jon Cohen interview with Ruben Donis, ScienceInsider)

The novel members of the curren swine flu constellation seem to be the swine origin NA and matrix proteins with an Asian-like lineage. How did they get here? Donis points out that North American viruses were actually exported to Asia when many countries imported US swine flu. Asian and European swine viruses have already mixed a fair amount so they are referred to as the Eurasian lineage. So that might explain how the North American swine segments (with the human and avian parts since 1998) got to Asia. How did they get back here? The return trip was not necessarily made via a pig. It could have been a person. We don't know. But Donis doesn't think the mixing happened in Mexico, but the phylogenetically isolated HA gene isn't very informative as to where.

What about the Veracruz pig farm (Smithfield Farms)?

Q: What do you think about the pig farm in Veracruz?

R.D.: I don’t know the details. They said they had a huge operation and the workers were not getting sick; that’s what the company claims. The only suspicious thing in that story is this is the largest farm in Mexico. The fact that the index case also is from the area makes it interesting.

Q: Do large farms have more swine flu?

R.D.: Not really. Even folks who have 50 pigs have to buy feed and supply from vendors that go from farm to farm, and they don’t wash their boots or whatever. Usually the virus is transmitted very effectively.

How concerned is CDC's chief virologist?

Q: What do you think of this outbreak?

R.D.: This is the first one I’ve seen firsthand as a virologist. The avian influenza outbreak is not comparable because this is unfolding so quickly. This reminds me of SARS. With avian there’s very little transmission. And even with SARS, transmission was far less.

Q: Does this one scare you?

R.D.: I saw figures that do scare you. We’ve received 300 samples from Mexico, and these cover the span of February, March, and April. And you look at flu A, traditionally it’s A/H1 or A/H3 or it's B up until the end of March. There are two or three cases up to [the] last days of March that are swine. Then in April they skyrocket. So all the cases in the D.F. areas [Mexico City], where most samples came from, it really transmits very efficiently.

Q: What is the date of first sample?

R.D.: I think it’s the end of March, the first positive specimen.

Q: Did Mexico react quickly enough?

R.D.: They didn’t know. They probably thought it was regular flu.

This is a very interesting interview and ScienceInsider seems to have some good sources. Recommended.

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Wanted to draw attention to this wonderful interview with CDC virologist Ruben Donis, chief of the molecular virology and vaccines branch at the U.S. Centers for Disease Control and Prevention, from ScienceInsider. It's echoes nicely some of the themes I and others have been trying to hit in this…
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Can you often include the fact that thousands of humans die every year from flu. Yes, Swine Flu seems to be different, but we should also do hygienic practices daily.

Hand washing, staying home when sick, encouraging sick workmates to go home, etc.

By ThirtyFiveUp (not verified) on 30 Apr 2009 #permalink


Thank you very much.

By Bioethics Enth… (not verified) on 30 Apr 2009 #permalink

Lisa , the GP (In case you are still interested ):

This is what the Mexican Authorities are saying to the public now:

Yesterday a press briefing was scheduled to take place at 6:00 p.m. it actually took place at 9:00 p.m. The usual update of numbers was announced. A totally different number from the previously given, 99 confirmed cases of H1N1 (still alive) and 8 deaths confirmed by H1N1. They clarified that this was the numbers they would work with from now on. ONLY the confirmed cases.

Then they announced the cease of all ânon essential activitiesâ in the public sector, as well as the mercantile sector. They assured the continuing of activities in banks, and markets, trash collection, public transportation etc. (May 1st and May 5th were already a Holiday)

Previously that morning Mexicoâs Cityâs Mare had announced the cease of activities in restaurants and food stands in the City and was severely criticized.

At 11:00 p.m. The President addressed the Nation and tried to calm down the public. Saying we would pull through, that everything needed to be done was being done, that the level 5 alert raised by WHO didnât meant the situation in Mexico was any worse, and that more supplies were coming including more face masks and medicine. (Sounded to me like a pep talk). The President hadnât make any appearance since the initial outbreak on Thursday.

This morning (8:00) the Mare updated the local number of deaths just one more. Very brief report in comparison to the previous ones.

Just a few minutes ago 12:30 p.m. the Secretary of Communications informed about the measures being taken on airports (thermal cameras, information stands, heath check points).

By Bioethics Enth… (not verified) on 30 Apr 2009 #permalink

Hand washing, staying home when sick, encouraging sick workmates to go home, etc.

Not going to happen when staying home when sick comes out of a single, 10 day a year paid time off pool. Last month, my cube farm had at least 8 obviously sick people -- all showing up for their 9 to 5. If I can stand, I'm going in.

Great and informative blog Revere(s). One of the things I can't really fathom is what is happening in Mexico. Shutting down the government and so much commercial activity seems like a really, really, severe reaction to something that has killed 8(?) - 160(?) people and doesn't seem to be swamping hospitals. I haven't seen any reports that hospitals are bursting with swine flu victims (much less morgues).

So what gives? Why this really strong reaction? Seems like the economic dislocations by these measures will be more of a public health problem than the swine flu. Out of work people will be more prone to get sick and lack health care.

Am I reading this all wrong? Is it way to early to understand what is happening? But if it is too early to guess what is happening, why is the Mexican government guessing in a way that is prompting such major disruptions?

I found this a little disconcerting.

My daughter, who was on a field trip with 40 or so youngsters two days ago, developed a fever (101) w/vomiting and diarrhea. I told her to call Kaiser (we live in Ca and are surrounded by just a few H1N1 cases, yet still surrounded on all sides) and the nurse rebuffed her concerns by telling her she just "had the stomach flu" and "not to worry".

Granted, she probably does have the stomach flu, but somehow, given the changeable situation, this seems a bit off putting.

Your views?

Several tourist destinations are closed,in MX I read that Tamiflu was OTC in Mexico, is this correct? I am not sure if that would mean anything as expensive as it is.

@ Eric: Honestly, at some point this week I think the Mexican authorities realized they had neither the resources or medicine to adequately combat this flu case by case. The numbers of suspected cases and deaths included likely hundreds of common flu cases, and this new variety was presenting a growing danger.

The fastest thing they could do to stamp it out then was to shut down the public mingling. Honestly, keeping the number low by stamping out social interaction is good when compared to the possibility of overrun hospitals and tens of thousands of dead with a medical system incapable of caring for even a fraction of the total possible victim number.

We have had a lot of stomach flu in my area, even brought in by out of state people coming for a one day seminar, it seems to be everywhere, my girlfriend was pretty sick but I have not heard of any fever, even in a 4 year old that has had it for several days now,

One thing that is worrying me is that here in the UK no-one seems to be taking much notice. Even the media seems to have calmed down a touch after the alarming headlines at the beginning of the week. I am keeping an eye on developments, but most people I speak to seem to think the threat is overblown: "it's only mild flu"; "it's only the media with a juicy story"; "it's a convenient story to take the heat off the financial crisis".

I'm worried no-one is taking it seriously, and if TS does HTF then it will be too late and panic will ensue. The health authorities are advising people to cover their mouths when they cough and to wash their hands, but even at that I don't see many taking notice.

Should we be worried or is it better that people aren't panicking?

Hi Steven R.

Thanks for the response.

So, will this shut down of Mexico just delay the onset mass infection? It'll be hard to keep 100 million people from going about their business for more than a few days. Are you expecting their hospitals (and ours, and everyone's) to be overwhelmed in the next few weeks once people start going about normal business again? That doesn't sound good.

So, I'm now feeling much less optimistic about this. It may not be nearly as bad as Bird Flu, but even a "mild" pandemic seems really, really bad. I can see the rationale around Phase 5.


Let me offer some insight into Mexican government and its citizens.

We donât trust the government at all. If they say âblackâ we immediately think to ourselves âwhiteâ. And we do this with GOOD reason, because for the last hundred years weâve been lied to and cheated by our own government. We thought that things would change with President Fox, we were even hopeful with his administration. (very much like American people with President Obama) Instead it turned out to be the same. President Calderon is from the same political party as Fox, therefore we are skeptical at best.

So if the government initially said ânot to panicâ what the general public immediately did was just THAT

By Bioethics Enth… (not verified) on 30 Apr 2009 #permalink

Is it possible this could have been going around Texas for more than a few weeks? Is there a test to see if someone has already had it and recovered? They are mostly testing people who went to Mexico for spring break and their friends. What if this has been going around for months in the north Texas area and was thought to be regular flu? I had a flu shot, but in February, I felt like I had a light case of the flu with some vomiting as well. I would love to think I have already had it and recovered. Is this just wishful thinking?

Thanks for posting this interview, revere. As you noted, per the interview, the HA gene is equidistant on the family tree of swine flu viruses from those that circulate in the US and Asia/Europe, on a "lonely branch" all by itself without close relatives, and that it has "been evolving somewhere and we didn't know about it." Is the latter explanation the only possible explanation, or is it even conceivable that this virus could have been manufactured? Yeah, potential tinfoil-hat territory, I know, but the following exchange is what makes me, as a layperson, wonder:

Q: How about pathogenesis? Can you tease that out in vitro?

R.D.: One traditional approach is to take advantage of viral modules that allow you to assemble different teams, to make reassortants that take a virus say from North America that doesn't transmit, and you swap one gene from the virus that does transmit. If the hypothesis is that hemagglutinin is responsible, you put in the background of the genes from the old virus. You need an animal model, usually the ferret.

So if it's possible for the good doctor (Donis) to do this sort of thing, in order to test an hypothesis, isn't it equally possible for a bad doctor (read: terrorist) to do it too, and then release it into the environment?

tenpenny: yes. But if you're looking for prime suspects, mother nature's M.O. is an infinitely better match.

tenpenny: This is painstaking and difficult work to do and beyond the ability of most labs. Moreover it wouldn't tell how to make the virus into a pathogen. Donis was responding to the question of what makes the flu virus virulent and so far we still don't know that. This is basic science, not practical and applied science. Terrorists wouldn't use a weapon like this as it doesn't further any aims. They are as likely to get sick as anyone and if they aren't blamed they get nothing out of it. All economies in the world will suffer. Terrorists use guns and bombs which we conveniently make available to them. Nature, however, is an amazingly efficient bioterrorist. She does it all the time. One of my medical school professors used to say, "When you hear hoofbeats, don't immediately think of zebras."

This was just posted on Fox News. It seems to say the US may have immunity due to the flu vaccinations taken for years. Any thoughts?

Q: Dr. Manny: The reason that this flu pandemic seems to be less deadly than what we saw in Mexico is perhaps that the American population has some passive immunity to some portion of this new virus â and that indeed â one of the unintended benefits of the regular flu vaccine we have been administering over decades is that itâs created some protection â even from this latest virus that has popped up. Is there any truth to this?

A: Dr. Gross: In the flu vaccine â for more than the past 30 years â weâve had an H1N1 strain in the standard flu vaccine that everyone gets⦠at least since 1976 when we had the last swine flu scare. So the theory goes that if youâve had a vaccine that has a N1 in it... when you encounter a slightly different H1 (which is what the swine flu is) that you will be protected from severe illness and death, but not from getting a cold or a bad cold from that flu strain.

The other thing is we havenât seen reports of a lot of older people getting H1N1 influenza A⦠so they must certainly be immune. An educated guess here would be that these older people may not be coming down with this new strain because most of them â particularly if they got the standard vaccine â would have some degree of immunity.

So the big question to ask here is: Did most of the people in the U.S. that had pretty mild cases of swine flu â did they get vaccinated with the regular influenza shot in the past couple years?

And the same goes for the victims in Mexico.

Did the people who fell ill or die get the standard flu vaccine?

These are very good indicators about the effectiveness of our standard influenza vaccine. And of course this all points to the importance of getting immunized every year.

Thanks, revere. Points well taken. How good, in general, in surveillance in pigs? Is it surprising that this virus apparently has been circulating and evolving undetected in pigs prior to this outbreak in humans? I would have thought, perhaps naively, that animal surveillance offers at least a semi-reliable, early-warning system for potential human pandemics. Hasn't that been one premise behind avian surveillance for some years now? So, have we been blindsided here with this previously unknown, undetected porcine strain? Or should we have never expected animal surveillance to be that good in the first place?

LC (or anyone who can answer): I once heard someone say a flu shot gives less effective or shorter immunity than actually getting the flu. It made me wonder if it was better to just get sick. (most years!) The quoted interview makes it sound as if the immunity from a shot is long-lasting. Can you say if that's so?

Another question (which weakens my 'just get sick' thought) is, what if you never get the flu? Can you still develop immunity from it being around?


(Revere, I love the hoofbeats/zebra saying.)

Hi Revere,

While I regard the whole terrorist scenario very, very unlikely, I would caution against assigning that kind of "rational" thinking to terrorists. In arguing against the remote possibility of bio-terrorism, I'd stick to evidence closer to the genetics / technical issues associated with Swine flu, and not on the motivations of people (which are often strange and unpredictable).

I'm an anthropologist, and from my perspective, there are many, many kinds of rationality out there. There are weirder things possible than some group developing a world-view where engineering a super-virus (that will be self-destructive, unpredictable, etc.) IS rational.

Fortunately, most terrorists are usually have limited imaginations, and are much, much more likely to have much more local ambitions than sickening all of humanity. In other words, if I had to worry about this stuff and allocate resources for public health, I'd regard risks of antibiotic-resistant TB far worse than terrorist doomsday cults.

That said, there is some interesting (high-quality) thinking that we're really bad at rationally preparing for remote but existential risks (asteroids, particle accelerator disasters, doomsday-cults, etc.). Check out Nick Bostrom at Oxford for reasoned discussion of far-out risks. Understanding how to deal with risk, especially for really rare but really bad events, is still in its infancy.

I'm sorry if I diverted attention to from the main focus on this site. More to the point. Why have we not seen analyses of sequences direct from Mexico, especially from cases where people have died?

What's the hold-up? Or is this happening now and hasn't hit the news yet?

I have a question. Would you suggest putting people on Airborne to help prevent swine flu? I wouldn't however my mother came home today with an OrlandoHealth Swine Flu Alert notice to physicians stating that if patients meet certain criteria that they should be placed on Airborne. She is a nurse at a doctor's office and questioned the alert when they received it.

Virus survival on surfaces

CBS news in Southern California is broadcasting & replaying an interview with a school official on the closing of a high school and cancellation of its upcoming prom in June. Mike Ridgeway of Pollard High School in Corona has stated that he is not disinfecting any surfaces in the school because he understands that viruses only live for 2 hours on surfaces.

I seem to remember some time back, Revere, that you discussed our knowledge (or lack thereof) of how long viruses survive on surfaces. There were many variables to consider, but I seem to remember it was thought that they could live much longer than 2 hours.

There would not be much incentive to disinfect surfaces with the money and time involved if you only had to wait 2 hours.

How long do these nasty viruses hang around?

Though I take it from time to time just because it picks me up a little bit when I'm down with a cold, there is no proof that Airborne does anything. In fact, they paid millions to the FTC over false advertising.

I agree that the purposeful release of a manufactured virus seems extremely unlikely. But what about an accidental release from a viral lab? Is that somewhat less unlikely? Has it ever happened? How many viral labs are there in Mexico?

Mexico's latest update: 260 infected 12 deaths both confirmed.

Apparently new laboratories are being set up and staff being trained therefore more speedy updates.

By Bioethics Enth… (not verified) on 30 Apr 2009 #permalink


We do not have "viral labs" here in Mexico, nor can we sequence any genome.

By Bioethics Enth… (not verified) on 30 Apr 2009 #permalink

"But what about an accidental release from a viral lab? Is that somewhat less unlikely?"

Last year the UK foot-and-mouth disease was released from an animal lab and Britian initially claimed it was impossible a nearby afflicted farm could be traced to a lab accident. Faulty ventilation system.
1970s USSR released weaponized anthrax accidentally and wiped out a town.
The lab at Winnipeg is secure. I don't think they do any mental health screening. But then again they do for NASA astronauts and presidents and you still have one crapping herself across the country in a car and the other callously initiating mid-1980s Atlantic exercises that have USSR preparing to retaliate for a feared impending USA first nuclear strike. I'd say the danger here is there are only hundreds or so Level 4 biolab workers now and these genetic manipulation technologies will be available to anyone with money assuming existing research safeguards.
Probably a network of biosensors solves this along with Orwellian Rapid Response quarantine procedures but the is almost complete agreement among those with cash and careers in this crisis to junk the WHO Rapid Response contingency rather than improve it.

By Phillip Huggan (not verified) on 30 Apr 2009 #permalink

Sorry if this has been asked before, but how easily could H1N1 and H5N1 recombine? And how fast?

If and when the swine flu takes hold in Asia where bird flu is already established, is it inevitable that a hybrid version appears that combines the worst elements of both?

Seems this should be the real fear, but I see no one talking about it.


I wondered the same thing and found this.


"To investigate the transmission of influenza viruses via hands and environmental surfaces, the survival of laboratory-grown influenza A and influenza B viruses on various surfaces was studied. Both influenza A and B viruses survived for 24-48 hr on hard, nonporous surfaces such as stainless steel and plastic but survived for less than 8-12 hr on cloth, paper, and tissues. Measurable quantities of influenza A virus were transferred from stainless steel surfaces to hands for 24 hr and from tissues to hands for up to 15 min. Virus survived on hands for up to 5 min after transfer from the environmental surfaces. These observations suggest that the transmission of virus from donors who are shedding large amounts could occur for 2-8 hr via stainless steel surfaces and for a few minutes via paper tissues. Thus, under conditions of heavy environmental contamination, the transmission of influenza virus via fomites may be possible."


"But what about an accidental release from a viral lab?"

In UK, 2007 had Foot and Mouth Disease which was caused by the virus leakage from a government lab accidently.

Thanks Pat.

It seems from this study one could deduce that the staff at the school who are moving chairs & tables to sweep up the classrooms are most at risk of picking up any virus and that if the school is closed for 4 days or more, the students will not be at risk from surfaces when they return.

The public hearing the broadcast, however, may erroneously believe hard surfaces contaminated by people shedding virus to be safer than they really are.
A little bleach around the house with a sick family member would be useful.

I was reading an article in the L.A. Times this morning that stated that quote "this strain is less severe then even the average flu". This was a front page article, and it seemed, at least to me, to be a particularly calming piece of news to hear. From what I could discern, this distinction came from an analysis of the virus's genome, which took place very recently. However, upon arriving home, I checked around the web, and no news of this sort--namely, stating that the H1N1 is not as much cause for concern as previously thought--could be found. Is this "less severe" story an exaggeration at the overly calm end of the spectrum, or is this virus really not as bad as initially expected? I'm a tad confused, I was hoping someone could offer some advice.

By Patrick N. (not verified) on 30 Apr 2009 #permalink

Interesting addition to the discussion on how long the virus can survive on hard (non human) surfaces. Here in Denver, the news is reporting that we have two confirmed cases. One was a woman who went on a Mexican cruise, the other was a baggage handler at Denver Int'l Airport. He is a 40 something male and was/is hospitalized. Now assuming that he contracted the virus via his baggage handling duties and not direct contact with another infected human (which we have no confirmation of), is this a noteworthy development? From what I've read on this blog, one would think that the viral load from handling baggage that has been sitting in the cargo hold from Mexico for several hours would be little to none.

In any case, I'm extrapolating many assumptions from very little information. Here's the story:


The reason hospitals are giving the brush off to people calling worrying about this flu, is that they don't want people who don't have it, but are panicky, to come to the hospital, where maybe there really *are* cases, and become infected.

If you get sick, assess the severity of your illness.

Is this something you would call the doctor for in the absence of this pandemic news? If so, call the doc. If not, don't call the doc.

Same basic principle applies to whether to call/go to a hospital. If you wouldn't go in the absence of pandemic, don't go in the presence of one.

The main difference with the pandemic going on, then, is that you should be much more fastidious about not infecting other people with whatever it is you, or your household, has. In other words, stay home.

Since this virus now appears to be of low pathogenicity (weak) for most people, the best strategy if you have a mild case is to hunker down and deal with it on your own, so that medical facilities are left open to deal with the cases that become too severe or complicated for home-based management.

I suspect--I hope--that public health offices will set up 'flu hotlines' or websites that can be used to help people with milder illness identify if what they have really is the flu, as that would allow better counting of the mild cases in the community.

And, as I said before, if you aren't sick, the easiest place to get sick is to go where the sick people are--doctors' offices and hospitals. It would suck to go to the doctor with merely a mild flu virus, and come home with a bacteria picked up there that would put you in the hospital 3 days later for bacterial pneumonia.

Since the evidence so far suggests a mild virus, each individual sufferer should not worry too much. This wave of the pandemic is reduced to a simple exercise in managing demand on hospitals; if a lot of people are sick in the community, even if only a tiny fraction need medical care, in absolute numbers this could turn out to be too many for the local hospital to handle.

So the public health officials are rightfully freaking out wondering where they're going to get the extra beds and staff for that tiny fraction, because that is their responsibility. But as individuals, we don't need to freak because the odds of any one of us getting sick enough to need the hospital look like they're going to be pretty low.

By Lisa the GP (not verified) on 30 Apr 2009 #permalink

> Donis said in his analyses the HA gene
> (the H-part of H1N1) is equidistant on the
> family tree of swine flu viruses from
> those that circulate in the US and Asia/Europe,

huh ? I'm puzzled about this statement.
HA is clearly classical swine going back to 1918,
nothing Eurasian in it.
Maybe he was looking at protein sequences, not nucleotides ?


Working at an Intâl airportâthe possibilities for infection seem endlessâso many surfaces, so many people from so many places. If he works there, he probably eats there, uses the restroom, handles money, etc. If he washes his hands he may still touch the door handle or door, touch tables, chairs, or counters in eateries, get sneezed upon, etc. , as well as handle baggage. It would be a real challenge to avoid a novel virus coming through.

In the 70s, I once worked in animation in closed space with a group of people all day. One of my colleagues became ill one day with fever, body aches, headache, exhaustion, muscle aches, pain behind the eyes, etc. Luckily her dad was a doctor and he figured out that she had contracted dengue feverâa virus transmitted by a certain type a mosquito not found in Hollywood, California. As it turned out, she had met some friends at the airport who were returning from Asia and must have been bitten by a mosquito that had hitched a ride to L.A.X. None of us then had even heard of dengue fever, so we kidded her about having jungle rot. It shows you can catch some unusual diseases in an Intâl airport.

Pat: "Sorry if this has been asked before, but how easily could H1N1 and H5N1 recombine? And how fast?"

I asked about this in the first few days of this event and revere discounted it as unlikely, though I can't remember why specidifically.

There are some "tin-foil hat" loose ends floating around that still bother me. Has anyone yet reported an explanation as to how Baxter in Austria shipped that very same feared combination (a sample containing both H1N1 + H5N1) to an associated Czech lab for vaccine maunfacture? Seems that extremely unlikely and commensurately suspicious event got burried somewhere. Do I remember someone on this blog later mentioning that the same sample was shipped to 18 other Baxter labs...or did I dream that?

Finally, in the Rubin Davis interview, Tenpenny alludes to his response to the question of purposeful bioterrorism, that the ferret is the animal model that would be used to test such a sample. If I remember correctly, the Czech lab discovered this incredibly unlikely mixture it had been sent, when all of its ferrets died after being dosed with it.

Anybody hear anything more about the Baxter SNAFU??

I understand this novel H1N1 virus is missing a protein therefore it is not suspected to be as virulent or lethal as one might originally think. Does anyone have any info on this?

Paul, you can't remember why because you're stupid or because you think Revere's answer was vague and you don't know how to communicate this?
The 18 samples were a dangerous virus that was thought to be safe virus and shipped accidentally. Nothing to do with combining two spearate strains. Look forward to answering this again tomorrow.

By Phillip Huggan (not verified) on 30 Apr 2009 #permalink

"Is this something you would call the doctor for in the absence of this pandemic news? If so, call the doc. If not, don't call the doc.

Same basic principle applies to whether to call/go to a hospital. If you wouldn't go in the absence of pandemic, don't go in the presence of one." Lisa

The response, here, is not one derived from reflection, Lisa. People give in to their fears, and their emotions, first, Lisa; especially when they are confronted with something that is entirely unfamiliar. That is why we are cursed with Republicans.

Regaring accidental lab releases, some of you out there may recall an intentional but non-malicious "release" that occurred a couple of years ago when an H2N2 influenza virus (1977 "Russian flu") was sent to several clinical laboratories throughout the USA as part of a routine proficiency testing through the College of American Pathologists. After it was sent out, the potential risk to the public born prior to 1977 was identified as a concern and a scramble ensued (on the public health dept front) to seek out and ensure the proper destruction of each viral sample and subsequent health status of laboratorians potentially at risk (the risk was deemed low). So, this sort of thing has happened before. Thankfully no documented cases of H2N2 arose from this, which could have been trouble since the virus had not been circulating in the United States for 30 years.

Can anyone clarify: If someone suspects they are infected, how important is it to get prescribed antivirals? Do we know how many people would get a more serious illness if they don't get early treatment? Seems this is important to know in order to decide if/when to seek treatment. Since tamiflu works only if prescribed in first two days, won't people be less likely to wait and treat at home if that means it will be too late for tamiflu to work?

Phillip, I don't know what I said to so offend you - please tell me so I'll try not to repeat the offense again. I believe, in comparison to most of this audience, that I am relatively stupid, but still meant no offense. I also would in no way intend to impugn revere's intelligence nor willingness to explain anything to anyone, nor his ability to do so. I don't believe I asked this question before, but I may not remember that I did.

I guess I also missed the resolution to the Baxter event. You're saying it was accidental; I must have missed that. Thanks for answering my question, it's reassuring to know that.

"Phillip, I don't know what I said to so offend you"

I forgot.

By Phillip Huggan (not verified) on 01 May 2009 #permalink

"Can anyone clarify: If someone suspects they are infected, how important is it to get prescribed antivirals?"

A Canadian newscast says if you get the anti-virals within 1-2 days after some event (I think after infection but it could've been after showing symptoms) the subsequent flu symptoms are less extreme. If you have any risk factor for pneumonia, people who have died are dying from (atypical) pneumonia, it is probably very important to get those antivirals ealry if possible. Maybe whatever traditional flu risk factors that don't usually apply to 20-40 year olds and do apply to 1-4 year olds and elderly, also apply to 20-40 year olds this time around (for example, living in 3rd world and/or at altitude).

By Phillip Huggan (not verified) on 01 May 2009 #permalink

"Q: Did Mexico react quickly enough?

R.D.: They didn't know. They probably thought it was regular flu."

Remarkably interesting, Revere. I was somewhat unhappy with Mexico, when I first became aware of this situation (several days before the story broke in the MSM), but, after reconsidering the details, it was obvious that Mexico was not at fault, here. They could not have known what they were dealing with.

It's in the process of "seeding" a population, as I see it; it would be difficult to find a more heterogeneous population than exists in North America. It is very quickly becoming global, which is to its advantage, of course; and now, to me at least, it appears that a battle may be brewing. In 1918, H1N1 seeded a significant segment of the world's general population in its first relatively benign wave. This one appears to be doing the same thing. It has waited (no intent, here, of course) until the ubiquitous seasonal flu strains have all but expired, and then it has begun to express itself (no rivals to contend with). Donis has noted how infectious it is, and how rapidly it is moving. It will likely be firmly established, before the advent of the next cycle of typical seasonal influenza, in the Northern Hemisphere. That will confer an inherent, considerable advantage upon it, with respect to its rivals. The 1918 H1N1 took full advantage of this opportunity by expressing before its seasonal rivals generally tend to express. It also set out to kill them off, with a vengeance, by disabling or killing vast numbers of their potential seasonal hosts (it already had a vast host population; if it killed off every other person on the planet, it would not matter in the least). The first H1N1, that we are fully conversant with, took this approach; neither H2N2, nor H3N2, employed this same "strategy." Why (it was obviously a very successful strategy, at the time; H1N1 dominated the planet from 1918, until it was displaced by H2N2 in 1957)?

H1N1 may be back to reclaim the title. My guess, right now, is that we will likely see how it goes, in the coming fall. Watching what it has done, so far, I would have to say that my money is riding on H1N1, at this point. The virulence thing seems to be entirely up in the air, though. Maybe this one will use a different approach than that employed by its 1918 relative (or, perhaps this "family" just has an affinity for this stuff; maybe it's simply genetically deranged; sort of like the family in "The Texas Chainsaw Massacre")?

That Fox article dates the first US case as March 30th. Edgar Hernandez, down in Mexico, started showing symptoms on April 2nd. I would have a hard time believing given the time frame and the distance involved that one caught it from the virus the other had. Both are probably several generations from patient zero.

So that really opens up when/where the patient zero is. It could be Mexico or California or even (less likely) somewhere else.

While it can quite well be argued that the Mexican government has handled the current outbreak with a greater level of transparency (at least since April 23rd) and the Mexican media with a greater level of probing than would have been the case a few years ago, examples of the old-style on both sides are still to be found (blatant lies and omissions from certain, fortunately rare, goverment officials, obvious questions not asked by the media).

Recently an UNAM professor, touted as one of the most prominent virologists in the country, travelled to El Perote, Veracruz and held a press conference in which he expounded on how there was no evidence to support the claim that the virus originated in Granjas Carroll. To someone who has experienced some of the uglier quirks of politics and also of academia in this country (Mexico) such a display reeks of using academic "prestige" to claim the grass is purple if that's what will help one's influential buddies. In this press conference no mention was made of what scientific tests might help corroborate the innocence of the farms; it was simply stated that there "do not exist scientific bases to prove that the operation of the pork farms... produced the outbreaks of respiratory illnesses and influenza, as has been speculated" (see http://www.el-universal.com.mx/notas/595237.html for example, in spanish). It would seem a lot more useful - if the farms really are innocent - for the scientist to describe a process by which at least certain doubts could be eliminated.

I am an academic, but not in a field related to health, and so I would like to ask for help/sugestions on the following:
Are there tests which could be performed on the population of La Gloria to see

1) if they have antibodies to this flu and
2) if they were recently administered Oseltamivir or Zanamivir?

There are a couple of peculiar features to this story which motivate these questions: the parents of the famous boy Edgar were apparently first told by their doctor, after test results came in, that he had NOT had swine flu, then suddenly the governor showed up at their house with presents for the boy and told the family that the boy HAD in fact had swine flu; the boy and most of the town were given "antibiotics" at the time of the sweeping illnesses there and houses were "fumigated" by the authorities; it is further claimed that among all the sick in La Gloria (30% of town population), Edgar was the ONLY one to have had swine flu. Perhaps this is true, but could it not easily be verified?

By mexobserver (not verified) on 01 May 2009 #permalink

mexobserver: I'm going off my memory of a couple days ago but I remember reading that they swabbed 29 or 39 people and Edgar was the only positive in that sample. So there are a lot of unknown cases.

Peggy: I don't know about the US but in Canada they _aren't_ giving out anti-virals unless you're severely hospitalized (no one yet), already had pneumonia, or in isolation. You can't walk into emergency and get them because you have flu symptoms.

The La Gloria/Granjas Carroll/Smithfield story is still evolving. It seems to me unlikely that Edgar was the zero case. The flu swabs had been taken in response to political protests against the pig farms, specifically the smelly waste, and because two children had died, in February and I believe early March. It was not until after a couple of people died of pneumonia in April in faraway states in Mexico, San Luis Potosi and Northern Baja California, that the La Gloria samples were sent off to Winnipeg. Edgar's was the only one A/H1N1. Now the CDC is saying the California cases were earlier. The pig farmers and Mexican health authorities have been taking samples from the pigs and sending to the national university. The pig farmers are naturally concerned about losses among the pigs, and regularly vaccinate and take precautions. So far, the Mexican health authorities have not been able to confirm that the pig farms had anything to do with the outbreak, and in fact there was a flu outbreak in La Gloria, but it was seasonal flu, only one A/H1N1. I think the term "swine flu" or "la gripa porcina" might have been misleading. Part of the problems in making decisions under uncertainty as here is being able to resist preconceptions, such as political bias against CAFOs. There surely is need for more transparency here, especially when Egypt is slaughtering 300,000 pigs and China refuses to buy pork from Mexico.

By Joe Shuren (not verified) on 02 May 2009 #permalink

Wow, Phillip, you're a stunning jackass (By the way, I did mean to be offensive just then). Are you this rude to people in real life or is it just when you're on the blogosphere, where acting like such a bully has no real consequences?

Joe Shuren - tests were not done on the majority of the over 500 sick in La Gloria (or 1200 depending on source). In fact, people in the town are now protesting calling for the bodies of 2 or 3 children (I don't have exact figure) who died in the March pneumonia outbreak to be exhumed and analyzed. Initial municipal health authorities concluded at the time that flies breeding in pig wastes were the disease vector. This was later swept under the rug. The fly theory may not be true at all, but is certainly worth investigating along with other explanations. And I agree the key is that this must be done in a transparent manner - without fear of concluding something that may adversely affect CAFO's, nor unjustifiably making negative claims about their practises. There is quite enough money and power protecting CAFO's already and I think one cannot fairly label people's distrust of such operations as "prejudice". In fact the vast majority of meat-eaters in the world know little about CAFO's and consume their meat without a second thought.

By mexobserver (not verified) on 03 May 2009 #permalink

My Mom had the 1918 flu as a girl. Do I and my sister have a passive immunity to the H1N1 flu? we are in our 70's.


By Ann Williams (not verified) on 06 Oct 2009 #permalink

Ann: Nothing from your mom, but folks our age seem to have less risk for this virus than for seasonal flu. We aren't sure why.